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[
{
"created": "2024-02-13T16:42:06.592156Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "4.13",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "reviewed gene: SLC26A1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None",
"entity_name": "SLC26A1",
"entity_type": "gene"
},
{
"created": "2024-02-13T16:40:28.744785Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "4.13",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "Classified gene: SLC26A1 as Red List (low evidence)",
"entity_name": "SLC26A1",
"entity_type": "gene"
},
{
"created": "2024-02-13T16:40:28.729558Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "4.13",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "Gene: slc26a1 has been classified as Red List (Low Evidence).",
"entity_name": "SLC26A1",
"entity_type": "gene"
},
{
"created": "2024-02-13T16:32:48.152965Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "4.12",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "Publications for gene: SLC26A1 were set to 27210743; 20160351; 30383413; 27125215; 24250268",
"entity_name": "SLC26A1",
"entity_type": "gene"
},
{
"created": "2023-08-10T14:25:46.781301Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "4.9",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "commented on gene: SLC12A1",
"entity_name": "SLC12A1",
"entity_type": "gene"
},
{
"created": "2023-08-10T14:14:19.986543Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "4.9",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "Tag monogenic-polygenic tag was added to gene: SLC12A1.",
"entity_name": "SLC12A1",
"entity_type": "gene"
},
{
"created": "2023-08-10T14:13:04.989420Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "4.9",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "Phenotypes for gene: SLC12A1 were changed from Type 1 Bartter syndrome: infantile onset, pregnancy noted for polyhydramnios; Hyperprostagladinuria; Hypokalaemia and metabolic alkalosis +/- nephrocalcinosis; Antenatal Bartter Syndrome; Bartter syndrome, type 1, 601678 to Bartter syndrome, type 1, OMIM:601678; Bartter disease type 1, MONDO:0100344",
"entity_name": "SLC12A1",
"entity_type": "gene"
},
{
"created": "2023-08-10T14:10:51.323944Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "4.8",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "Publications for gene: SLC12A1 were set to PMID: 21631963; 21189980; 20219833; 19513753; 19096086; 18830715; 17998760; 16807401",
"entity_name": "SLC12A1",
"entity_type": "gene"
},
{
"created": "2023-08-10T12:23:50.639813Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "4.7",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "Phenotypes for gene: CLCNKA were changed from Bartter syndrome, type 4b, digenic, 613090 to Bartter syndrome, type 4b, digenic, OMIM:613090; Bartter disease type 4B, MONDO:0000909",
"entity_name": "CLCNKA",
"entity_type": "gene"
},
{
"created": "2023-08-10T12:20:40.170549Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "4.6",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "changed review comment from: Comment on mode of inheritance: Digenic CLCNKA & CLCNKB variants are associated with Bartter syndrome, type 4b, digenic (OMIM:613090)(PMID: 15044642;18310267). The current GMS rare disease bioinformatic pipeline does not allow for interpretation of digenic events.; to: Comment on mode of inheritance: Digenic CLCNKA & CLCNKB variants are associated with Bartter syndrome, type 4b, digenic (OMIM:613090)(PMID: 15044642;18310267;32488762). The current GMS rare disease bioinformatic pipeline does not allow for interpretation of digenic events.",
"entity_name": "CLCNKA",
"entity_type": "gene"
},
{
"created": "2023-08-10T12:15:46.763523Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "4.6",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "Publications for gene: CLCNKA were set to 15044642; 18310267",
"entity_name": "CLCNKA",
"entity_type": "gene"
},
{
"created": "2023-08-10T12:08:42.082941Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "4.5",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "Added comment: Comment on mode of inheritance: Digenic CLCNKA & CLCNKB variants are associated with Bartter syndrome, type 4b, digenic (OMIM:613090)(PMID: 15044642;18310267). The current GMS rare disease bioinformatic pipeline does not allow for interpretation of digenic events.",
"entity_name": "CLCNKA",
"entity_type": "gene"
},
{
"created": "2023-08-10T12:08:42.030889Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "4.5",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "Mode of inheritance for gene: CLCNKA was changed from BIALLELIC, autosomal or pseudoautosomal to Other",
"entity_name": "CLCNKA",
"entity_type": "gene"
},
{
"created": "2023-08-10T12:07:52.180744Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "4.4",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "Publications for gene: CLCNKA were set to ",
"entity_name": "CLCNKA",
"entity_type": "gene"
},
{
"created": "2023-08-10T12:02:39.997196Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "4.3",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "Tag polygenic tag was added to gene: CLCNKA.",
"entity_name": "CLCNKA",
"entity_type": "gene"
},
{
"created": "2023-08-10T09:34:40.725891Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "4.3",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "Added comment: Comment on mode of inheritance: The mode of inheritance for CLCNKB should be BIALLELIC, autosomal or pseudoautosomal. Although digenic CLCNKB & CLCNKA variants are associated with Bartter syndrome, type 4b, digenic (OMIM:613090), this phenotype is not relevant to this panel and the current GMS rare disease bioinformatic pipeline does not allow for interpretation of digenic events.",
"entity_name": "CLCNKB",
"entity_type": "gene"
},
{
"created": "2023-08-10T09:34:40.707578Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "4.3",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "Mode of inheritance for gene: CLCNKB was changed from BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal",
"entity_name": "CLCNKB",
"entity_type": "gene"
},
{
"created": "2023-08-10T09:30:48.922419Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "4.2",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "Tag monogenic-polygenic tag was added to gene: CLCNKB.\nTag Q3_23_MOI tag was added to gene: CLCNKB.",
"entity_name": "CLCNKB",
"entity_type": "gene"
},
{
"created": "2023-08-10T09:15:39.887841Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "4.2",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "reviewed gene: CLCNKB: Rating: GREEN; Mode of pathogenicity: None; Publications: 120550, 9326936, 15717167; Phenotypes: Bartter syndrome, type 3, OMIM:607364, Bartter disease type 3, MONDO:0011822; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal",
"entity_name": "CLCNKB",
"entity_type": "gene"
},
{
"created": "2023-08-08T16:40:38.172558Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "4.2",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "Phenotypes for gene: CLCNKB were changed from Bartter syndrome, type 3, 607364; Type 3 Bartter syndrome; Bartter syndrome, type 4b, digenic, 613090; BARTTER SYNDROME TYPE 4B to Bartter syndrome, type 3, OMIM:607364; Bartter disease type 3, MONDO:0011822; Bartter syndrome, type 4b, digenic, OMIM:613090; Bartter disease type 4B, MONDO:0000909",
"entity_name": "CLCNKB",
"entity_type": "gene"
},
{
"created": "2023-07-20T08:18:22.030795Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "4.1",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "reviewed gene: SLC26A1: Rating: RED; Mode of pathogenicity: None; Publications: 36719378; Phenotypes: hyperoxaluria; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal",
"entity_name": "SLC26A1",
"entity_type": "gene"
},
{
"created": "2023-03-22T15:48:50.796171Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "4.1",
"user_name": "Achchuthan Shanmugasundram",
"item_type": "panel",
"text": "Panel version 4.0 has been signed off on 2023-03-22",
"entity_name": null,
"entity_type": null
},
{
"created": "2023-03-22T15:47:45.854895Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "4.0",
"user_name": "Achchuthan Shanmugasundram",
"item_type": "panel",
"text": "promoted panel to version 4.0",
"entity_name": null,
"entity_type": null
},
{
"created": "2023-03-01T21:42:40.940109Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "3.7",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Tag Q1_23_promote_green tag was added to gene: WDR72.\nTag Q1_23_NHS_review tag was added to gene: WDR72.",
"entity_name": "WDR72",
"entity_type": "gene"
},
{
"created": "2023-03-01T21:42:04.976814Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "3.7",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Phenotypes for gene: WDR72 were changed from distal renal tubular acidosis; amelogenesis imperfecta to distal renal tubular acidosis, MONDO:0015827; Amelogenesis imperfecta, type IIA3, OMIM:613211; amelogenesis imperfecta hypomaturation type 2A3, MONDO:0013181",
"entity_name": "WDR72",
"entity_type": "gene"
},
{
"created": "2023-03-01T20:14:04.456022Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "3.6",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Publications for gene: WDR72 were set to PMID: 30028003; 30779877; 31959358; 33033857",
"entity_name": "WDR72",
"entity_type": "gene"
},
{
"created": "2023-03-01T20:13:51.696358Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "3.5",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Classified gene: WDR72 as Amber List (moderate evidence)",
"entity_name": "WDR72",
"entity_type": "gene"
},
{
"created": "2023-03-01T20:13:51.693831Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "3.5",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Added comment: Comment on list classification: Promoting this gene to amber with a recommendation of green rating following GMS review. There are 5 cases with nephrocalcinosis reported and biallelic variants in this gene.",
"entity_name": "WDR72",
"entity_type": "gene"
},
{
"created": "2023-03-01T20:13:51.677472Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "3.5",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Gene: wdr72 has been classified as Amber List (Moderate Evidence).",
"entity_name": "WDR72",
"entity_type": "gene"
},
{
"created": "2023-03-01T20:12:58.522131Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "3.4",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: WDR72",
"entity_name": "WDR72",
"entity_type": "gene"
},
{
"created": "2023-02-08T13:52:29.238776Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "3.4",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Tag new-gene-name tag was added to gene: SLC9A3R1.",
"entity_name": "SLC9A3R1",
"entity_type": "gene"
},
{
"created": "2023-02-08T13:52:14.850583Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "3.4",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: SLC9A3R1: Added new-gene-name tag, new approved HGNC gene symbol for SLC9A3R1 (HGNC:11075) is NHERF1.",
"entity_name": "SLC9A3R1",
"entity_type": "gene"
},
{
"created": "2023-01-30T14:29:02.908742Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "3.4",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "Tag Q3_22_rating was removed from gene: RRAGD.\nTag Q3_22_MOI was removed from gene: RRAGD.\nTag Q3_22_NHS_review was removed from gene: RRAGD.",
"entity_name": "RRAGD",
"entity_type": "gene"
},
{
"created": "2023-01-30T14:27:51.209558Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "3.4",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "Tag Q3_21_MOI was removed from gene: ATP6V0A4.\nTag watchlist_moi was removed from gene: ATP6V0A4.",
"entity_name": "ATP6V0A4",
"entity_type": "gene"
},
{
"created": "2023-01-30T14:26:27.054105Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "3.4",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "Tag Q3_22_MOI was removed from gene: SLC34A3.\nTag Q3_22_NHS_review was removed from gene: SLC34A3.",
"entity_name": "SLC34A3",
"entity_type": "gene"
},
{
"created": "2023-01-30T14:21:54.805968Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "3.4",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "commented on gene: SLC34A3",
"entity_name": "SLC34A3",
"entity_type": "gene"
},
{
"created": "2023-01-30T14:21:54.785534Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "3.4",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "reviewed gene: RRAGD: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: ",
"entity_name": "RRAGD",
"entity_type": "gene"
},
{
"created": "2023-01-30T14:21:54.767464Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "3.4",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "commented on gene: ATP6V0A4",
"entity_name": "ATP6V0A4",
"entity_type": "gene"
},
{
"created": "2023-01-30T13:51:56.915241Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "3.3",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "Source NHS GMS was added to SLC34A3.\nMode of inheritance for gene SLC34A3 was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal",
"entity_name": "SLC34A3",
"entity_type": "gene"
},
{
"created": "2023-01-30T13:51:56.778945Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "3.3",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "Source Expert Review Green was added to RRAGD.\nSource NHS GMS was added to RRAGD.\nRating Changed from Amber List (moderate evidence) to Green List (high evidence)",
"entity_name": "RRAGD",
"entity_type": "gene"
},
{
"created": "2023-01-30T13:51:56.622569Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "3.3",
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "Source NHS GMS was added to ATP6V0A4.\nMode of inheritance for gene ATP6V0A4 was changed from BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal",
"entity_name": "ATP6V0A4",
"entity_type": "gene"
},
{
"created": "2022-12-20T12:28:47.596361Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "3.2",
"user_name": "Arina Puzriakova",
"item_type": "entity",
"text": "gene: SLC26A6 was added\ngene: SLC26A6 was added to Nephrocalcinosis or nephrolithiasis. Sources: Literature\nwatchlist tags were added to gene: SLC26A6.\nMode of inheritance for gene: SLC26A6 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown\nPublications for gene: SLC26A6 were set to 35115415\nPhenotypes for gene: SLC26A6 were set to Enteric hyperoxaluria and nephrolithiasis\nAdded comment: Cornière et al. 2022 (PMID: 35115415) identified a single family with a heterozygous missense VUS (c.1519C>T/p.R507W) in the SLC26A6 gene. However, the variant was found in 5 out of 280 674 alleles reported in gnomAD (Europeans and South Asians). In vitro studies showed that the variant affects both SLC26A6 transport activity and membrane surface expression, in turn reducing Cl− dependant oxalate transport. Cotransfection studies indicated a dominant-negative effect on WT. Slc26a6 null mice similarly displayed hyperoxalemia and hyperoxaluria which were caused by defective intestinal back-secretion of dietary oxalate (PMID: 21170874; 32660969)\r\n\r\nSLC26A6 is currently not associated with any human phenotype in OMIM or G2P. \nSources: Literature",
"entity_name": "SLC26A6",
"entity_type": "gene"
},
{
"created": "2022-11-30T15:15:51.162674Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "3.1",
"user_name": "Achchuthan Shanmugasundram",
"item_type": "panel",
"text": "Panel version 3.0 has been signed off on 2022-11-30",
"entity_name": null,
"entity_type": null
},
{
"created": "2022-11-30T15:15:03.622311Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "3.0",
"user_name": "Achchuthan Shanmugasundram",
"item_type": "panel",
"text": "promoted panel to version 3.0",
"entity_name": null,
"entity_type": null
},
{
"created": "2022-11-21T17:57:12.120996Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.40",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "gene: WDR72 was added\ngene: WDR72 was added to Nephrocalcinosis or nephrolithiasis. Sources: Expert list\nMode of inheritance for gene: WDR72 was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: WDR72 were set to PMID: 30028003; 30779877; 31959358; 33033857\nPhenotypes for gene: WDR72 were set to distal renal tubular acidosis; amelogenesis imperfecta\nPenetrance for gene: WDR72 were set to Complete\nReview for gene: WDR72 was set to GREEN\nAdded comment: Sources: Expert list",
"entity_name": "WDR72",
"entity_type": "gene"
},
{
"created": "2022-09-28T18:04:49.428270Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.40",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Mode of inheritance for gene: RRAGD was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted",
"entity_name": "RRAGD",
"entity_type": "gene"
},
{
"created": "2022-09-28T18:00:57.123295Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.39",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Classified gene: RRAGD as Amber List (moderate evidence)",
"entity_name": "RRAGD",
"entity_type": "gene"
},
{
"created": "2022-09-28T18:00:57.120336Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.39",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Added comment: Comment on list classification: Promoting this gene from grey to amber but with a recommendation of green rating following GMS review.",
"entity_name": "RRAGD",
"entity_type": "gene"
},
{
"created": "2022-09-28T18:00:57.104080Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.39",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Gene: rragd has been classified as Amber List (Moderate Evidence).",
"entity_name": "RRAGD",
"entity_type": "gene"
},
{
"created": "2022-09-28T18:00:27.393475Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.38",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Tag Q3_22_rating tag was added to gene: RRAGD.\nTag Q3_22_MOI tag was added to gene: RRAGD.\nTag Q3_22_NHS_review tag was added to gene: RRAGD.",
"entity_name": "RRAGD",
"entity_type": "gene"
},
{
"created": "2022-09-28T17:59:50.606429Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.38",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Phenotypes for gene: RRAGD were changed from hypomagnesaemia, nephrocalcinosis, salt wasting, cardiomyopathy to hypomagnesaemia; nephrocalcinosis; salt wasting; cardiomyopathy; tubular renal disease-cardiomyopathy syndrome, MONDO:0019130",
"entity_name": "RRAGD",
"entity_type": "gene"
},
{
"created": "2022-09-28T17:58:32.697677Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.37",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Mode of inheritance for gene: RRAGD was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown",
"entity_name": "RRAGD",
"entity_type": "gene"
},
{
"created": "2022-09-28T17:58:16.116889Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.36",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: RRAGD",
"entity_name": "RRAGD",
"entity_type": "gene"
},
{
"created": "2022-09-26T16:15:34.296203Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.36",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "gene: RRAGD was added\ngene: RRAGD was added to Nephrocalcinosis or nephrolithiasis. Sources: Other\nMode of inheritance for gene: RRAGD was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted\nPublications for gene: RRAGD were set to 34607910\nPhenotypes for gene: RRAGD were set to hypomagnesaemia, nephrocalcinosis, salt wasting, cardiomyopathy\nPenetrance for gene: RRAGD were set to Complete\nMode of pathogenicity for gene: RRAGD was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments\nReview for gene: RRAGD was set to GREEN\nAdded comment: so far only a single paper, but with 9 patients/families \nSources: Other",
"entity_name": "RRAGD",
"entity_type": "gene"
},
{
"created": "2022-08-02T23:15:04.244371Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.36",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Tag Q3_22_MOI tag was added to gene: SLC34A3.\nTag Q3_22_NHS_review tag was added to gene: SLC34A3.",
"entity_name": "SLC34A3",
"entity_type": "gene"
},
{
"created": "2022-08-02T23:14:30.801168Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.36",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Phenotypes for gene: SLC34A3 were changed from Hypophosphatemic rickets with hypercalciuria, 241530; HHRH; recent publication added nephrolithiasis. to Hypophosphatemic rickets with hypercalciuria, OMIM:241530; HHRH; hereditary hypophosphatemic rickets with hypercalciuria, MONDO:0009431",
"entity_name": "SLC34A3",
"entity_type": "gene"
},
{
"created": "2022-08-02T23:12:44.364546Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.35",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Publications for gene: SLC34A3 were set to 25296721; 26543054; 24924704; 24700880",
"entity_name": "SLC34A3",
"entity_type": "gene"
},
{
"created": "2022-08-02T23:12:22.809624Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.34",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Publications for gene: SLC34A3 were set to PMID: 25296721; 26543054; 24924704; 24700880",
"entity_name": "SLC34A3",
"entity_type": "gene"
},
{
"created": "2022-08-02T23:12:12.339481Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.33",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Added comment: Comment on mode of inheritance: Leaving MOI as Biallelic for now but with recommendation for change to BOTH mono and bi-allelic at the next GMS review.",
"entity_name": "SLC34A3",
"entity_type": "gene"
},
{
"created": "2022-08-02T23:12:12.319839Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.33",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Mode of inheritance for gene: SLC34A3 was changed from BIALLELIC, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal",
"entity_name": "SLC34A3",
"entity_type": "gene"
},
{
"created": "2022-07-21T11:05:20.676716Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.32",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "reviewed gene: SLC34A3: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 16358214, 27939817, 24700880, 17968493; Phenotypes: hypercalciuria, nephrocalcinosis, nephrolithiasis, hypophosphataemia; Mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal",
"entity_name": "SLC34A3",
"entity_type": "gene"
},
{
"created": "2022-03-07T23:21:24.823224Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.32",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Tag Q3_21_rating was removed from gene: MOCOS.\nTag Q3_21_NHS_review was removed from gene: MOCOS.",
"entity_name": "MOCOS",
"entity_type": "gene"
},
{
"created": "2022-03-07T23:21:03.284800Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.32",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: MOCOS: The rating of this gene has been updated following NHS Genomic Medicine Service approval.",
"entity_name": "MOCOS",
"entity_type": "gene"
},
{
"created": "2022-03-07T23:20:40.994472Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.31",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Source Expert Review Green was added to MOCOS.\nRating Changed from Amber List (moderate evidence) to Green List (high evidence)",
"entity_name": "MOCOS",
"entity_type": "gene"
},
{
"created": "2022-03-07T23:12:20.454125Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.30",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Phenotypes for gene: HNF4A were changed from Fanconi renotubular syndrome 4, with maturity-onset diabetes of the young, 616026 to Fanconi renotubular syndrome 4, with maturity-onset diabetes of the young, OMIM:616026",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2022-03-07T23:11:57.617789Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.29",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Tag for-review was removed from gene: HNF4A.",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2022-03-07T23:11:27.192479Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.29",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Phenotypes for gene: VPS33B were changed from Arthrogryposis, renal dysfunction, and cholestasis 1, 208085 to Arthrogryposis, renal dysfunction, and cholestasis 1, OMIM:208085",
"entity_name": "VPS33B",
"entity_type": "gene"
},
{
"created": "2022-03-07T23:11:09.122277Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.28",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Tag for-review was removed from gene: VPS33B.",
"entity_name": "VPS33B",
"entity_type": "gene"
},
{
"created": "2022-03-07T23:10:38.480648Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.28",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Phenotypes for gene: VIPAS39 were changed from Arthrogryposis, renal dysfunction, and cholestasis 2, 613404 to Arthrogryposis, renal dysfunction, and cholestasis 2, OMIM:613404",
"entity_name": "VIPAS39",
"entity_type": "gene"
},
{
"created": "2022-03-07T23:10:19.639692Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.27",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Tag for-review was removed from gene: VIPAS39.",
"entity_name": "VIPAS39",
"entity_type": "gene"
},
{
"created": "2022-03-07T23:09:52.954269Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.27",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: VIPAS39",
"entity_name": "VIPAS39",
"entity_type": "gene"
},
{
"created": "2022-03-07T23:09:52.918293Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.27",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: VPS33B",
"entity_name": "VPS33B",
"entity_type": "gene"
},
{
"created": "2022-03-07T23:09:52.892323Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.27",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: HNF4A: The rating of this gene has been updated following NHS Genomic Medicine Service approval. The reviewers note that nephrocalcinosis is a feature of Fanconi renotubular syndrome.",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2022-03-07T23:09:35.158508Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.26",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Source Expert Review Green was added to VIPAS39.\nRating Changed from Amber List (moderate evidence) to Green List (high evidence)",
"entity_name": "VIPAS39",
"entity_type": "gene"
},
{
"created": "2022-03-07T23:09:35.043064Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.26",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Source Expert Review Green was added to VPS33B.\nRating Changed from Amber List (moderate evidence) to Green List (high evidence)",
"entity_name": "VPS33B",
"entity_type": "gene"
},
{
"created": "2022-03-07T23:09:34.928895Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.26",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Source Expert Review Green was added to HNF4A.\nRating Changed from Amber List (moderate evidence) to Green List (high evidence)",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2021-11-22T12:08:11.057510Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.25",
"user_name": "Arina Puzriakova",
"item_type": "entity",
"text": "Phenotypes for gene: HPRT1 were changed from Lesch-Nyhan syndrome, 300322 to Hyperuricemia, HRPT-related, OMIM:300323; Lesch-Nyhan syndrome, OMIM:300322",
"entity_name": "HPRT1",
"entity_type": "gene"
},
{
"created": "2021-08-19T13:18:21.594124Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.24",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Tag Q3_21_NHS_review tag was added to gene: MOCOS.",
"entity_name": "MOCOS",
"entity_type": "gene"
},
{
"created": "2021-08-19T11:33:58.592346Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.24",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Classified gene: MOCOS as Amber List (moderate evidence)",
"entity_name": "MOCOS",
"entity_type": "gene"
},
{
"created": "2021-08-19T11:33:58.588820Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.24",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Added comment: Comment on list classification: Promoting from grey to amber, with a recommendation for green rating following GMS review. 2 cases where urolithiasis is part of the Xanthinuria type 2 phenotype. Additional evidence from animal models.",
"entity_name": "MOCOS",
"entity_type": "gene"
},
{
"created": "2021-08-19T11:33:58.567672Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.24",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Gene: mocos has been classified as Amber List (Moderate Evidence).",
"entity_name": "MOCOS",
"entity_type": "gene"
},
{
"created": "2021-08-19T11:22:18.234494Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.23",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Phenotypes for gene: MOCOS were changed from Xanthinuria type II (MIM603592) to Xanthinuria, type II, OMIM:603592",
"entity_name": "MOCOS",
"entity_type": "gene"
},
{
"created": "2021-08-19T11:22:05.586138Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.22",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Publications for gene: MOCOS were set to PMID: 11302742; 17368066; 14624414; 25967871; 34356852; 32073534; 30758870; 27919260",
"entity_name": "MOCOS",
"entity_type": "gene"
},
{
"created": "2021-08-19T11:21:52.009256Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.21",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Tag Q3_21_rating tag was added to gene: MOCOS.",
"entity_name": "MOCOS",
"entity_type": "gene"
},
{
"created": "2021-08-19T11:21:10.918598Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.21",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "reviewed gene: MOCOS: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Xanthinuria, type II, OMIM:603592; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal",
"entity_name": "MOCOS",
"entity_type": "gene"
},
{
"created": "2021-08-11T11:32:11.422747Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.21",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "gene: MOCOS was added\ngene: MOCOS was added to Nephrocalcinosis or nephrolithiasis. Sources: Literature\nMode of inheritance for gene: MOCOS was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: MOCOS were set to PMID: 11302742; 17368066; 14624414; 25967871; 34356852; 32073534; 30758870; 27919260\nPhenotypes for gene: MOCOS were set to Xanthinuria type II (MIM603592)\nPenetrance for gene: MOCOS were set to Incomplete\nReview for gene: MOCOS was set to GREEN\nAdded comment: This gene had not been previously included in this panel, but there is good evidence from several publications that recessive loss-of-function variants in MOCOS are associated with Xanthinuria type 2. There is also a good pathophysiologic basis: MOCOS encodes a necessary co-factor for the 2 enzymes that degrade Xanthine, XDH and AOX1.\r\nMoreover, there are spontaneous animal models, with MOCOS variants identified in a goat (PMID 30758870) and Tyrolean grey cattle (PMID 27919260). \nSources: Literature",
"entity_name": "MOCOS",
"entity_type": "gene"
},
{
"created": "2021-07-16T15:15:51.198401Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.21",
"user_name": "Arina Puzriakova",
"item_type": "entity",
"text": "Publications for gene: ATP6V0A4 were set to ",
"entity_name": "ATP6V0A4",
"entity_type": "gene"
},
{
"created": "2021-07-16T14:52:36.974236Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.20",
"user_name": "Arina Puzriakova",
"item_type": "entity",
"text": "Tag Q3_21_MOI tag was added to gene: ATP6V0A4.\nTag watchlist_moi tag was added to gene: ATP6V0A4.",
"entity_name": "ATP6V0A4",
"entity_type": "gene"
},
{
"created": "2021-07-16T14:50:44.709354Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.20",
"user_name": "Arina Puzriakova",
"item_type": "entity",
"text": "Added comment: Comment on mode of inheritance: Literature search showed that a single Japanese individual was reported in 2016 (PMID: 27274828) with a supposedly pathogenic heterozygous variant p.S544L. Hypokalemia, nephrocalcinosis and alkaluria suggesting distal renal tubular acidosis (dRTA) were detected, but metabolic acidosis was not evident. In 2020, a second Han Chinese family with five dRTA patients was reported (PMID: 32123165) who harboured the same p.S544L heterozygous variant. Some patients in this family were more severely affected than the previous case, displaying more severe complete dRTA with hypokalemia, osteoporosis, and kidney stones. Note this family also harboured 3 other homozygous variants in the ATP6V0A4 gene but these were ruled out, presumably due to MAF. \r\n\r\nApart from these two reports’ alternations in ATP6V0A4 have been found to be inherited recessively (heterozygous parent carriers are unaffected), and multiple such cases have been described in literature (references added to publications list). \r\n\r\nAt this moment there is only enough evidence to support an Amber rating for the monoallelic form - single heterozygous variant identified in 2 families from a similar ethnic background which does not suffice the inclusion criteria.\r\n\r\nMOI should be changed from 'BOTH mono- and biallelic' to 'BIALLELIC' only at the next GMS panel review (tagged) until additional evidence emerges supporting heterozygous variants as disease-causing.",
"entity_name": "ATP6V0A4",
"entity_type": "gene"
},
{
"created": "2021-07-16T14:50:44.688863Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.20",
"user_name": "Arina Puzriakova",
"item_type": "entity",
"text": "Mode of inheritance for gene: ATP6V0A4 was changed from BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal",
"entity_name": "ATP6V0A4",
"entity_type": "gene"
},
{
"created": "2021-07-15T11:06:39.124198Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.19",
"user_name": "Arina Puzriakova",
"item_type": "entity",
"text": "Phenotypes for gene: ATP6V0A4 were changed from distal renal tubular acidosis; Compensated or uncomensated dRTA and/or recurrent stone formation, usually with hypocitraturia. +/- deafness; Renal tubular acidosis, distal, autosomal recessive to Distal renal tubular acidosis 3, with or without sensorineural hearing loss, OMIM:602722",
"entity_name": "ATP6V0A4",
"entity_type": "gene"
},
{
"created": "2021-05-04T16:59:49.146589Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.18",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Phenotypes for gene: OCRL were changed from Lowe syndrome, 309000; Dent disease 2, 300555; As for CLCN5 (Nephrocalcinosis with low molecular weight proteinuria and pregressive CKD) but may include intellectual disability and other features of Lowe syndrome to Lowe syndrome, OMIM:309000; Dent disease 2, OMIM:300555; As for CLCN5 (Nephrocalcinosis with low molecular weight proteinuria and pregressive CKD) but may include intellectual disability and other features of Lowe syndrome",
"entity_name": "OCRL",
"entity_type": "gene"
},
{
"created": "2021-05-04T16:59:11.654275Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.17",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Publications for gene: OCRL were set to ",
"entity_name": "OCRL",
"entity_type": "gene"
},
{
"created": "2021-05-04T16:58:53.605887Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.16",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "reviewed gene: OCRL: Rating: ; Mode of pathogenicity: None; Publications: 33517444; Phenotypes: ; Mode of inheritance: None",
"entity_name": "OCRL",
"entity_type": "gene"
},
{
"created": "2020-10-20T15:33:23.358046Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.16",
"user_name": "Arina Puzriakova",
"item_type": "entity",
"text": "Classified gene: VIPAS39 as Amber List (moderate evidence)",
"entity_name": "VIPAS39",
"entity_type": "gene"
},
{
"created": "2020-10-20T15:33:23.355005Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.16",
"user_name": "Arina Puzriakova",
"item_type": "entity",
"text": "Added comment: Comment on list classification: Changed rating from Green to Amber so that Green genes on this panel reflect the NHS signed-off version. This will be reviewed at the next GMS panel update (added 'for-review' tag).",
"entity_name": "VIPAS39",
"entity_type": "gene"
},
{
"created": "2020-10-20T15:33:23.328611Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.16",
"user_name": "Arina Puzriakova",
"item_type": "entity",
"text": "Gene: vipas39 has been classified as Amber List (Moderate Evidence).",
"entity_name": "VIPAS39",
"entity_type": "gene"
},
{
"created": "2020-10-20T15:33:12.072706Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.15",
"user_name": "Arina Puzriakova",
"item_type": "entity",
"text": "Tag for-review tag was added to gene: VIPAS39.",
"entity_name": "VIPAS39",
"entity_type": "gene"
},
{
"created": "2020-10-20T15:32:45.743518Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.15",
"user_name": "Arina Puzriakova",
"item_type": "entity",
"text": "Classified gene: VPS33B as Amber List (moderate evidence)",
"entity_name": "VPS33B",
"entity_type": "gene"
},
{
"created": "2020-10-20T15:32:45.740333Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.15",
"user_name": "Arina Puzriakova",
"item_type": "entity",
"text": "Added comment: Comment on list classification: Changed rating from Green to Amber so that Green genes on this panel reflect the NHS signed-off version. This will be reviewed at the next GMS panel update (added 'for-review' tag).",
"entity_name": "VPS33B",
"entity_type": "gene"
},
{
"created": "2020-10-20T15:32:45.714022Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.15",
"user_name": "Arina Puzriakova",
"item_type": "entity",
"text": "Gene: vps33b has been classified as Amber List (Moderate Evidence).",
"entity_name": "VPS33B",
"entity_type": "gene"
},
{
"created": "2020-10-20T15:32:35.681247Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.14",
"user_name": "Arina Puzriakova",
"item_type": "entity",
"text": "Tag for-review tag was added to gene: VPS33B.",
"entity_name": "VPS33B",
"entity_type": "gene"
},
{
"created": "2020-10-19T14:26:20.054607Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.14",
"user_name": "Arina Puzriakova",
"item_type": "entity",
"text": "Classified gene: HNF4A as Amber List (moderate evidence)",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2020-10-19T14:26:20.048887Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.14",
"user_name": "Arina Puzriakova",
"item_type": "entity",
"text": "Added comment: Comment on list classification: Changed rating to Amber so that Green genes on this panel reflect the NHS signed-off version. This will be reviewed at the next GMS panel update.",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2020-10-19T14:26:19.953566Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.14",
"user_name": "Arina Puzriakova",
"item_type": "entity",
"text": "Gene: hnf4a has been classified as Amber List (Moderate Evidence).",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2020-06-24T11:50:51.264260Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.13",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Tag for-review tag was added to gene: HNF4A.",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2020-04-21T16:01:55.034122Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.13",
"user_name": "Rebecca Foulger",
"item_type": "entity",
"text": "Classified gene: VPS33B as Green List (high evidence)",
"entity_name": "VPS33B",
"entity_type": "gene"
},
{
"created": "2020-04-21T16:01:55.026744Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.13",
"user_name": "Rebecca Foulger",
"item_type": "entity",
"text": "Gene: vps33b has been classified as Green List (High Evidence).",
"entity_name": "VPS33B",
"entity_type": "gene"
},
{
"created": "2020-04-21T16:01:44.086748Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.12",
"user_name": "Rebecca Foulger",
"item_type": "entity",
"text": "gene: VPS33B was added\ngene: VPS33B was added to Nephrocalcinosis or nephrolithiasis. Sources: Literature\nMode of inheritance for gene: VPS33B was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: VPS33B were set to 15052268; 22753090\nPhenotypes for gene: VPS33B were set to Arthrogryposis, renal dysfunction, and cholestasis 1, 208085\nAdded comment: Added to panel as Green gene as advised by Helen Brittain, Genomics England Clinical Team. This rating should be reviewed by GLHs at the date of next GMS panel update. ARC phenotype (MIM:208085) is appropriate for the panel, and sufficient cases to support causation (see also the other ARC gene, VIPAS39). \nSources: Literature",
"entity_name": "VPS33B",
"entity_type": "gene"
},
{
"created": "2020-04-21T15:50:17.808663Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.11",
"user_name": "Rebecca Foulger",
"item_type": "entity",
"text": "Classified gene: VIPAS39 as Green List (high evidence)",
"entity_name": "VIPAS39",
"entity_type": "gene"
},
{
"created": "2020-04-21T15:50:17.797090Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.11",
"user_name": "Rebecca Foulger",
"item_type": "entity",
"text": "Gene: vipas39 has been classified as Green List (High Evidence).",
"entity_name": "VIPAS39",
"entity_type": "gene"
},
{
"created": "2020-04-21T15:50:06.846181Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.10",
"user_name": "Rebecca Foulger",
"item_type": "entity",
"text": "commented on gene: VIPAS39: PMID:20190753 (Cullinane et al., 2010) identify biallelic (homozygous or compound het) variants in 7 probands from consanguineous families with ARC (MIM:613404) from various ethnic backgrounds (Turkish, Croation, Israeli Arab, Italian). Variants include Q179X, T250ArgfsX279, R220X, Q291X, M1R. The paper does not further discuss the kidney phenotype.",
"entity_name": "VIPAS39",
"entity_type": "gene"
},
{
"created": "2020-04-21T15:49:46.558060Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.10",
"user_name": "Rebecca Foulger",
"item_type": "entity",
"text": "gene: VIPAS39 was added\ngene: VIPAS39 was added to Nephrocalcinosis or nephrolithiasis. Sources: Literature\nMode of inheritance for gene: VIPAS39 was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: VIPAS39 were set to 20190753\nPhenotypes for gene: VIPAS39 were set to Arthrogryposis, renal dysfunction, and cholestasis 2, 613404\nAdded comment: Added to panel as Green following advice from Helen Brittain, Genomics England Clinical Team. Nephrocalcinosis is a feature of the phenotype. Other syndromes are on this panel (Lesch-Nyhan and Lowe syndrome) as Green, and therefore rated Green to match. This rating should be reviewed by GLHs at the date of next GMS panel update. \nSources: Literature",
"entity_name": "VIPAS39",
"entity_type": "gene"
},
{
"created": "2020-03-25T17:47:21.871518Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.9",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Publications for gene: SLC26A1 were set to 27210743; 20160351; 30383413; 27125215",
"entity_name": "SLC26A1",
"entity_type": "gene"
},
{
"created": "2020-03-25T17:46:35.009398Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.8",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Publications for gene: SLC26A1 were set to 27210743; 27210743; 20160351; 30383413; 27125215",
"entity_name": "SLC26A1",
"entity_type": "gene"
},
{
"created": "2020-03-25T17:46:20.958670Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.7",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Publications for gene: SLC26A1 were set to 27210743; 27210743; 20160351",
"entity_name": "SLC26A1",
"entity_type": "gene"
},
{
"created": "2020-03-25T17:45:41.746704Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.6",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Classified gene: SLC26A1 as Amber List (moderate evidence)",
"entity_name": "SLC26A1",
"entity_type": "gene"
},
{
"created": "2020-03-25T17:45:41.743092Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.6",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Added comment: Comment on list classification: Changing rating from grey to amber. Although there are several reported cases there is also evidence that the reported variants are not causative.",
"entity_name": "SLC26A1",
"entity_type": "gene"
},
{
"created": "2020-03-25T17:45:41.724177Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.6",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Gene: slc26a1 has been classified as Amber List (Moderate Evidence).",
"entity_name": "SLC26A1",
"entity_type": "gene"
},
{
"created": "2020-03-25T17:45:31.916327Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.5",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Classified gene: SLC26A1 as Amber List (moderate evidence)",
"entity_name": "SLC26A1",
"entity_type": "gene"
},
{
"created": "2020-03-25T17:45:31.912812Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.5",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Added comment: Comment on list classification: Changing rating from grey to amber. Although there are several reported cases there is also evidence that the reported variants are not causative.",
"entity_name": "SLC26A1",
"entity_type": "gene"
},
{
"created": "2020-03-25T17:45:31.893527Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.5",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Gene: slc26a1 has been classified as Amber List (Moderate Evidence).",
"entity_name": "SLC26A1",
"entity_type": "gene"
},
{
"created": "2020-03-25T17:39:58.312644Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.4",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "changed review comment from: Provisionally associated with ?Nephrolithiasis, calcium oxalate #167030 (AR) in OMIM. \r\n\r\nPMID: 30383413 - Whittamore et al 2019 - were unable to were unable to reproduce the hyperoxaluria, hyperoxalemia, and urolithiasis of the original SAT-1-KO mouse model. \r\n\r\nPMID: 27125215 - Wu et al 2016 - report that Human SLC26A1-mediated anion exchange differs from that of its rodent orthologs. Also using Xenopus oocytes they find that the C41W, A56T (also reported by Gee et al) variants found in a Mexican child with recessive proximal tubular Fanconi Syndrome and the Q566R and M132T variants from Dawson et al 2013 did not alter the functional properties tested of SLC26A1 and so the proposal that these are pathogenic variants for Renal Fanconi Syndrome disease or nephrolithiasis is NOT supported. \r\n\r\nPMID: 27210743 - Gee et al 2016 - report 2 unrelated individuals. Case 1 - individual of Macedonian descent (A3054-21) who is from non-consanguineous parents and clinically presented with acute renal failure due to bilateral obstructive calculi, nephrocalcinosis, and bilateral ureteropelvic junction obstruction. Two compound heterozygous missense mutations (c.554C>T, p.Thr185Met and c.1073C>T, p.Ser358Leu) in SLC26A1 are reported. They have minor allele freq below 0.0006 in dbSNP. Case 2 - European-American boy (B641-12) who had nephrolithiasis and was born to consanguineous parents. A homozygous missense mutation (c.166G>A, p.Ala56Thr) in SLC26A1 was found. Its minor allele frequency is 0.0002 in dbSNP. \r\n\r\nPMID: 24250268 - Dawson et al 2013 - screened the SLC26A1 gene in a cohort of 13 individuals with recurrent calcium oxalate urolithiasis. Found one individual was heterozygous R372H; 4 individuals were heterozygous Q556R; one patient was homozygous Q556R; and one patient with severe nephrocalcinosis (requiring nephrectomy) was homozygous Q556R and heterozygous M132T. The Q556R variant is found at a high allele frequency (0.3484 in NCBI). \r\n\r\nPMID: 20160351 - Dawson et al 2010 - Sat1-/- mice (SLC26A1) exhibited hyperoxaluria with hyperoxalemia, nephrocalcinosis, and calcium oxalate stones in their renal tubules and bladder.\r\n\r\nSummary:\r\nAlthough there are 3+ cases (2 biallelic in Gee et al, 3 monalleleic and 2 biallelic in Dawson et al 2013), plus a mouse model (Dawson et all 2010), the high minor allele frequency of the Q556R variant and the lack of altered function in protein with the A56T and M132T variants (Wu et al), and the lack of reproducibility of the mouse model phenotype cast doubt on the causative role of these variants. Therefore this gene should be rated amber until more evidence for their role in nephrocalcinosis can be established.; to: Provisionally associated with ?Nephrolithiasis, calcium oxalate #167030 (AR) in OMIM. \r\n\r\nPMID: 30383413 - Whittamore et al 2019 - were unable to reproduce the hyperoxaluria, hyperoxalemia, and urolithiasis of the original SAT-1-KO mouse model. \r\n\r\nPMID: 27125215 - Wu et al 2016 - report that Human SLC26A1-mediated anion exchange differs from that of its rodent orthologs. Also using Xenopus oocytes they find that the C41W, A56T (also reported by Gee et al) variants found in a Mexican child with recessive proximal tubular Fanconi Syndrome and the Q566R and M132T variants from Dawson et al 2013 did not alter the functional properties tested of SLC26A1 and so the proposal that these are pathogenic variants for Renal Fanconi Syndrome disease or nephrolithiasis is NOT supported. \r\n\r\nPMID: 27210743 - Gee et al 2016 - report 2 unrelated individuals. Case 1 - individual of Macedonian descent (A3054-21) who is from non-consanguineous parents and clinically presented with acute renal failure due to bilateral obstructive calculi, nephrocalcinosis, and bilateral ureteropelvic junction obstruction. Two compound heterozygous missense mutations (c.554C>T, p.Thr185Met and c.1073C>T, p.Ser358Leu) in SLC26A1 are reported. They have minor allele freq below 0.0006 in dbSNP. Case 2 - European-American boy (B641-12) who had nephrolithiasis and was born to consanguineous parents. A homozygous missense mutation (c.166G>A, p.Ala56Thr) in SLC26A1 was found. Its minor allele frequency is 0.0002 in dbSNP. \r\n\r\nPMID: 24250268 - Dawson et al 2013 - screened the SLC26A1 gene in a cohort of 13 individuals with recurrent calcium oxalate urolithiasis. Found one individual was heterozygous R372H; 4 individuals were heterozygous Q556R; one patient was homozygous Q556R; and one patient with severe nephrocalcinosis (requiring nephrectomy) was homozygous Q556R and heterozygous M132T. The Q556R variant is found at a high allele frequency (0.3484 in NCBI). \r\n\r\nPMID: 20160351 - Dawson et al 2010 - Sat1-/- mice (SLC26A1) exhibited hyperoxaluria with hyperoxalemia, nephrocalcinosis, and calcium oxalate stones in their renal tubules and bladder.\r\n\r\nSummary:\r\nAlthough there are 3+ cases (2 biallelic in Gee et al, 3 monalleleic and 2 biallelic in Dawson et al 2013), plus a mouse model (Dawson et all 2010), the high minor allele frequency of the Q556R variant and the lack of altered function in protein with the A56T and M132T variants (Wu et al), and the lack of reproducibility of the mouse model phenotype cast doubt on the causative role of these variants. Therefore this gene should be rated amber until more evidence for their role in nephrocalcinosis can be established.",
"entity_name": "SLC26A1",
"entity_type": "gene"
},
{
"created": "2020-03-25T17:39:43.318743Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.4",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "changed review comment from: Provisionally associated with ?Nephrolithiasis, calcium oxalate #167030 (AR) in OMIM. \r\n\r\nPMID: 27125215 - Wu et al 2016 - report that Human SLC26A1-mediated anion exchange differs from that of its rodent orthologs. Also using Xenopus oocytes they find that the C41W, A56T (also reported by Gee et al) variants found in a Mexican child with recessive proximal tubular Fanconi Syndrome and the Q566R and M132T variants from Dawson et al 2013 did not alter the functional properties tested of SLC26A1 and so the proposal that these are pathogenic variants for Renal Fanconi Syndrome disease or nephrolithiasis is NOT supported. \r\n\r\nPMID: 27210743 - Gee et al 2016 - report 2 unrelated individuals. Case 1 - individual of Macedonian descent (A3054-21) who is from non-consanguineous parents and clinically presented with acute renal failure due to bilateral obstructive calculi, nephrocalcinosis, and bilateral ureteropelvic junction obstruction. Two compound heterozygous missense mutations (c.554C>T, p.Thr185Met and c.1073C>T, p.Ser358Leu) in SLC26A1 are reported. They have minor allele freq below 0.0006 in dbSNP. Case 2 - European-American boy (B641-12) who had nephrolithiasis and was born to consanguineous parents. A homozygous missense mutation (c.166G>A, p.Ala56Thr) in SLC26A1 was found. Its minor allele frequency is 0.0002 in dbSNP. \r\n\r\nPMID: 24250268 - Dawson et al 2013 - screened the SLC26A1 gene in a cohort of 13 individuals with recurrent calcium oxalate urolithiasis. Found one individual was heterozygous R372H; 4 individuals were heterozygous Q556R; one patient was homozygous Q556R; and one patient with severe nephrocalcinosis (requiring nephrectomy) was homozygous Q556R and heterozygous M132T. The Q556R variant is found at a high allele frequency (0.3484 in NCBI). \r\n\r\nPMID: 20160351 - Dawson et al 2010 - Sat1-/- mice (SLC26A1) exhibited hyperoxaluria with hyperoxalemia, nephrocalcinosis, and calcium oxalate stones in their renal tubules and bladder.\r\n\r\nSummary:\r\nAlthough there are 3+ cases (2 biallelic in Gee et al, 3 monalleleic and 2 biallelic in Dawson et al 2013), plus a mouse model (Dawson et all 2010), the minor allele frequency of the Q556R variant and the lack of altered function for when protein with the A56T and M132T variants are expressed (Wu et al) cast doubt on the causative role of these variants. Therefore this gene should be rated amber until more evidence for their role in nephrocalcinosis can be established.; to: Provisionally associated with ?Nephrolithiasis, calcium oxalate #167030 (AR) in OMIM. \r\n\r\nPMID: 30383413 - Whittamore et al 2019 - were unable to were unable to reproduce the hyperoxaluria, hyperoxalemia, and urolithiasis of the original SAT-1-KO mouse model. \r\n\r\nPMID: 27125215 - Wu et al 2016 - report that Human SLC26A1-mediated anion exchange differs from that of its rodent orthologs. Also using Xenopus oocytes they find that the C41W, A56T (also reported by Gee et al) variants found in a Mexican child with recessive proximal tubular Fanconi Syndrome and the Q566R and M132T variants from Dawson et al 2013 did not alter the functional properties tested of SLC26A1 and so the proposal that these are pathogenic variants for Renal Fanconi Syndrome disease or nephrolithiasis is NOT supported. \r\n\r\nPMID: 27210743 - Gee et al 2016 - report 2 unrelated individuals. Case 1 - individual of Macedonian descent (A3054-21) who is from non-consanguineous parents and clinically presented with acute renal failure due to bilateral obstructive calculi, nephrocalcinosis, and bilateral ureteropelvic junction obstruction. Two compound heterozygous missense mutations (c.554C>T, p.Thr185Met and c.1073C>T, p.Ser358Leu) in SLC26A1 are reported. They have minor allele freq below 0.0006 in dbSNP. Case 2 - European-American boy (B641-12) who had nephrolithiasis and was born to consanguineous parents. A homozygous missense mutation (c.166G>A, p.Ala56Thr) in SLC26A1 was found. Its minor allele frequency is 0.0002 in dbSNP. \r\n\r\nPMID: 24250268 - Dawson et al 2013 - screened the SLC26A1 gene in a cohort of 13 individuals with recurrent calcium oxalate urolithiasis. Found one individual was heterozygous R372H; 4 individuals were heterozygous Q556R; one patient was homozygous Q556R; and one patient with severe nephrocalcinosis (requiring nephrectomy) was homozygous Q556R and heterozygous M132T. The Q556R variant is found at a high allele frequency (0.3484 in NCBI). \r\n\r\nPMID: 20160351 - Dawson et al 2010 - Sat1-/- mice (SLC26A1) exhibited hyperoxaluria with hyperoxalemia, nephrocalcinosis, and calcium oxalate stones in their renal tubules and bladder.\r\n\r\nSummary:\r\nAlthough there are 3+ cases (2 biallelic in Gee et al, 3 monalleleic and 2 biallelic in Dawson et al 2013), plus a mouse model (Dawson et all 2010), the high minor allele frequency of the Q556R variant and the lack of altered function in protein with the A56T and M132T variants (Wu et al), and the lack of reproducibility of the mouse model phenotype cast doubt on the causative role of these variants. Therefore this gene should be rated amber until more evidence for their role in nephrocalcinosis can be established.",
"entity_name": "SLC26A1",
"entity_type": "gene"
},
{
"created": "2020-03-25T17:20:29.661457Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.4",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: SLC26A1",
"entity_name": "SLC26A1",
"entity_type": "gene"
},
{
"created": "2020-03-24T15:00:39.429166Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.4",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Classified gene: HNF4A as Green List (high evidence)",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2020-03-24T15:00:39.425454Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.4",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Added comment: Comment on list classification: Although only one variant reported in all cases, there are now 7 cases in which the R76W/R63W (depending on reference transcript used) variant has been found in patients with Fanconi renotubular syndrome and nephrocalcinosis is a feature. Fly model also supports a pathogenic role for this variant.",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2020-03-24T15:00:39.407550Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.4",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Gene: hnf4a has been classified as Green List (High Evidence).",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2020-03-24T14:53:13.907329Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.3",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "changed review comment from: Note the same codon is reported as R76W and R63W in different paper depending on whether NM_000457 or NM_175914 is used as the reference transcript. \r\n\r\nAdditional papers including those cited by Zornitza Stark:\r\n\r\nPMID: 31875549 - Marchesin et al 2019 - Fly model which shows that the R85W variant in Drosophila nephrocytes works in a dominant-negative and cytotoxic effect. Expression of dHNF4 harboring the FRTS mutation affects the catabolism of lipid droplets in nephrocytes by interfering with mitochondrial function. They also showed that the FRTS mutation caused nuclear depletion and cytosolic aggregation of a wild-type dHNF4 reporter protein. The cytosolic aggregates have a cytotoxic affect. By contrast, the expression of another known close mutation in the DNA-binding domain, R89W (that leads to MODY1 but not to FRTS; Hamilton et al., 2014), did not cause any dominant-negative or cytotoxic effects.\r\n\r\nPMID: 30005691 - Liu et al 2018 1 case of a 10-year-old girl of Chinese Han ethnicity who presented with renal Fanconi syndrome, infantile hyperinsulinemic hypoglycemia, and transient cholestasis. In addition, she presented with bilateral severe hearing loss. Renal ultrasonography showed nephrocalcinosis. Gene analysis showed a heterozygous p.R63W mutation in the HNF4A gene that is responsible for Fanconi syndrome and hyperinsulinemic hypoglycemia. (NOTE: no transcript identifier given but they refer to this as the same variant as R76W). \r\n\r\nPMID: 28693455 - Walsh et al 2917 - 1 case of mother and son with heterozygous c.187C > T; p.Arg63Trp in HNF4A and Renal Fanconi syndrome. Mother is reported to have mild nephrocalcinosis \r\n\r\nPMID: 22802087 - Stanescu et al 2012 - 1 case that presented as a newborn with diazoxide-responsive hyperinsulinism and later developed renal Fanconi syndrome, hypophosphatemic rickets, and hepatic glycogenosis. Sequencing of HNF4A (MODY1) revealed a missense, de novo mutation (p.Arg76Trp, c.226C→T), (NM_000457) which is a known disease-causing MODY1 mutation in HNF4A. Nephrocalcinosis not specifically mentioned. \r\n\r\nNo nephrocalcinosis reported:\r\nPMID: 28458902 - Clemente et al 2017 - 1 patient with congenital hyperinsulinaemic hypoglycaemia, rickets with craniotabes, wrist widening, genu varum and motor impairment. non-gap metabolic acidosis with acidified urine suggestive of proximal tubular acidosis, glycosuria with generalised aminoaciduria and tubular type proteinuria. Says this patient did NOT have the same ‘atypical’ Fanconi syndrome with hypercalciuria with relative hypocalcaemia, hypermagnesaemia, nephrocalcinosis and renal impairment as the patients reported by Hamilton et al 2014. A de novo variant p.Arg63Trp, c.187C > T (reference sequence: NM_175914.4) was found. \r\n\r\nPMID: 27245055 - Improda et al 2016 - 2 infants with the p.R63W mutation HNF4A with macrosomia and atypical Fanconi syndrome, in addition to hyperinsulinaemic hypoglycaemia. No nephrocalcinosis reported but this may be due to young age. \r\n; to: Note the same codon is reported as R76W and R63W in different paper depending on whether NM_000457 or NM_175914 is used as the reference transcript. \r\n\r\nAdditional papers including those cited by Zornitza Stark:\r\n\r\nPMID: 31875549 - Marchesin et al 2019 - Fly model which shows that the R85W variant in Drosophila nephrocytes works in a dominant-negative and cytotoxic effect. Expression of dHNF4 harboring the FRTS mutation affects the catabolism of lipid droplets in nephrocytes by interfering with mitochondrial function. They also showed that the FRTS mutation caused nuclear depletion and cytosolic aggregation of a wild-type dHNF4 reporter protein. The cytosolic aggregates have a cytotoxic affect. By contrast, the expression of another known close mutation in the DNA-binding domain, R89W (that leads to MODY1 but not to FRTS; Hamilton et al., 2014), did not cause any dominant-negative or cytotoxic effects.\r\n\r\nPMID: 31949432 - Anyiam et al 2019 - described patient with Renal Fanconi syndrome and R63W mutation through 3rd pregnancy. She had a history of progressive renal insufficiency, persistent proteinuria, nephrocalcinosis, and recurrent nephrolithiasis. \r\n\r\nPMID: 30005691 - Liu et al 2018 1 case of a 10-year-old girl of Chinese Han ethnicity who presented with renal Fanconi syndrome, infantile hyperinsulinemic hypoglycemia, and transient cholestasis. In addition, she presented with bilateral severe hearing loss. Renal ultrasonography showed nephrocalcinosis. Gene analysis showed a heterozygous p.R63W mutation in the HNF4A gene that is responsible for Fanconi syndrome and hyperinsulinemic hypoglycemia. (NOTE: no transcript identifier given but they refer to this as the same variant as R76W). \r\n\r\nPMID: 28693455 - Walsh et al 2917 - 1 case of mother and son with heterozygous c.187C > T; p.Arg63Trp in HNF4A and Renal Fanconi syndrome. Mother is reported to have mild nephrocalcinosis \r\n\r\nPMID: 22802087 - Stanescu et al 2012 - 1 case that presented as a newborn with diazoxide-responsive hyperinsulinism and later developed renal Fanconi syndrome, hypophosphatemic rickets, and hepatic glycogenosis. Sequencing of HNF4A (MODY1) revealed a missense, de novo mutation (p.Arg76Trp, c.226C→T), (NM_000457) which is a known disease-causing MODY1 mutation in HNF4A. Nephrocalcinosis not specifically mentioned. \r\n\r\nNo nephrocalcinosis reported:\r\nPMID: 28458902 - Clemente et al 2017 - 1 patient with congenital hyperinsulinaemic hypoglycaemia, rickets with craniotabes, wrist widening, genu varum and motor impairment. non-gap metabolic acidosis with acidified urine suggestive of proximal tubular acidosis, glycosuria with generalised aminoaciduria and tubular type proteinuria. Says this patient did NOT have the same ‘atypical’ Fanconi syndrome with hypercalciuria with relative hypocalcaemia, hypermagnesaemia, nephrocalcinosis and renal impairment as the patients reported by Hamilton et al 2014. A de novo variant p.Arg63Trp, c.187C > T (reference sequence: NM_175914.4) was found. \r\n\r\nPMID: 27245055 - Improda et al 2016 - 2 infants with the p.R63W mutation HNF4A with macrosomia and atypical Fanconi syndrome, in addition to hyperinsulinaemic hypoglycaemia. No nephrocalcinosis reported but this may be due to young age. \r\n",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2020-03-24T14:47:53.309988Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.3",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "changed review comment from: Summary\r\n3 publications (Hamilton et al 2014, Lui et al 2018, Walsh et al 2017) report 6 cases of patients with R76W/R63W variants in which nephrocalcinosis is a feature. Fly model (Marchesin et al 2019) shows that the equivalent variant in Drosophila nephrocytes works in a dominant-negative and cytotoxic effect.; to: Summary\r\n4 publications (Hamilton et al 2014, Lui et al 2018, Walsh et al 2017, Anyiam et al 2019) report 7 cases of patients with R76W/R63W variants in which nephrocalcinosis is a feature. Fly model (Marchesin et al 2019) shows that the equivalent variant in Drosophila nephrocytes works in a dominant-negative and cytotoxic effect.",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2020-03-24T14:37:27.049471Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.3",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: HNF4A: Summary\r\n3 publications (Hamilton et al 2014, Lui et al 2018, Walsh et al 2017) report 6 cases of patients with R76W/R63W variants in which nephrocalcinosis is a feature. Fly model (Marchesin et al 2019) shows that the equivalent variant in Drosophila nephrocytes works in a dominant-negative and cytotoxic effect.",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2020-03-24T14:33:45.937946Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.3",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "changed review comment from: Note the same codon is reported as R76W and R63W in different paper depending on whether NM_000457 or NM_175914 is used as the reference transcript. \r\n\r\nAdditional papers cited by Zornitza Stark:\r\n\r\nPMID: 31875549 - Marchesin et al 2019 - Fly model which shows that the R85W variant in Drosophila nephrocytes works in a dominant-negative and cytotoxic effect. Expression of dHNF4 harboring the FRTS mutation affects the catabolism of lipid droplets in nephrocytes by interfering with mitochondrial function. They also showed that the FRTS mutation caused nuclear depletion and cytosolic aggregation of a wild-type dHNF4 reporter protein. The cytosolic aggregates have a cytotoxic affect. By contrast, the expression of another known close mutation in the DNA-binding domain, R89W (that leads to MODY1 but not to FRTS; Hamilton et al., 2014), did not cause any dominant-negative or cytotoxic effects.\r\n\r\nPMID: 30005691 - Liu et al 2018 1 case of a 10-year-old girl of Chinese Han ethnicity who presented with renal Fanconi syndrome, infantile hyperinsulinemic hypoglycemia, and transient cholestasis. In addition, she presented with bilateral severe hearing loss. Renal ultrasonography showed nephrocalcinosis. Gene analysis showed a heterozygous p.R63W mutation in the HNF4A gene that is responsible for Fanconi syndrome and hyperinsulinemic hypoglycemia. (NOTE: This seems to be the same codon as the R76W variant as the paper refers to it as such). \r\n\r\n\r\nPMID: 22802087 - Stanescu et al 2012 - 1 case that presented as a newborn with diazoxide-responsive hyperinsulinism and later developed renal Fanconi syndrome, hypophosphatemic rickets, and hepatic glycogenosis. Sequencing of HNF4A (MODY1) revealed a missense, de novo mutation (p.Arg76Trp, c.226C→T), (NM_000457) which is a known disease-causing MODY1 mutation in HNF4A. Nephrocalcinosis not specifically mentioned. \r\n\r\nNo nephrocalcinosis reported:\r\nPMID: 28458902 - Clemente et al 2017 - 1 patient with congenital hyperinsulinaemic hypoglycaemia, rickets with craniotabes, wrist widening, genu varum and motor impairment. non-gap metabolic acidosis with acidified urine suggestive of proximal tubular acidosis, glycosuria with generalised aminoaciduria and tubular type proteinuria. Says this patient did NOT have the same ‘atypical’ Fanconi syndrome with hypercalciuria with relative hypocalcaemia, hypermagnesaemia, nephrocalcinosis and renal impairment as the patients reported by Hamilton et al 2014. A de novo variant p.Arg63Trp, c.187C > T (reference sequence: NM_175914.4) was found. \r\n; to: Note the same codon is reported as R76W and R63W in different paper depending on whether NM_000457 or NM_175914 is used as the reference transcript. \r\n\r\nAdditional papers including those cited by Zornitza Stark:\r\n\r\nPMID: 31875549 - Marchesin et al 2019 - Fly model which shows that the R85W variant in Drosophila nephrocytes works in a dominant-negative and cytotoxic effect. Expression of dHNF4 harboring the FRTS mutation affects the catabolism of lipid droplets in nephrocytes by interfering with mitochondrial function. They also showed that the FRTS mutation caused nuclear depletion and cytosolic aggregation of a wild-type dHNF4 reporter protein. The cytosolic aggregates have a cytotoxic affect. By contrast, the expression of another known close mutation in the DNA-binding domain, R89W (that leads to MODY1 but not to FRTS; Hamilton et al., 2014), did not cause any dominant-negative or cytotoxic effects.\r\n\r\nPMID: 30005691 - Liu et al 2018 1 case of a 10-year-old girl of Chinese Han ethnicity who presented with renal Fanconi syndrome, infantile hyperinsulinemic hypoglycemia, and transient cholestasis. In addition, she presented with bilateral severe hearing loss. Renal ultrasonography showed nephrocalcinosis. Gene analysis showed a heterozygous p.R63W mutation in the HNF4A gene that is responsible for Fanconi syndrome and hyperinsulinemic hypoglycemia. (NOTE: no transcript identifier given but they refer to this as the same variant as R76W). \r\n\r\nPMID: 28693455 - Walsh et al 2917 - 1 case of mother and son with heterozygous c.187C > T; p.Arg63Trp in HNF4A and Renal Fanconi syndrome. Mother is reported to have mild nephrocalcinosis \r\n\r\nPMID: 22802087 - Stanescu et al 2012 - 1 case that presented as a newborn with diazoxide-responsive hyperinsulinism and later developed renal Fanconi syndrome, hypophosphatemic rickets, and hepatic glycogenosis. Sequencing of HNF4A (MODY1) revealed a missense, de novo mutation (p.Arg76Trp, c.226C→T), (NM_000457) which is a known disease-causing MODY1 mutation in HNF4A. Nephrocalcinosis not specifically mentioned. \r\n\r\nNo nephrocalcinosis reported:\r\nPMID: 28458902 - Clemente et al 2017 - 1 patient with congenital hyperinsulinaemic hypoglycaemia, rickets with craniotabes, wrist widening, genu varum and motor impairment. non-gap metabolic acidosis with acidified urine suggestive of proximal tubular acidosis, glycosuria with generalised aminoaciduria and tubular type proteinuria. Says this patient did NOT have the same ‘atypical’ Fanconi syndrome with hypercalciuria with relative hypocalcaemia, hypermagnesaemia, nephrocalcinosis and renal impairment as the patients reported by Hamilton et al 2014. A de novo variant p.Arg63Trp, c.187C > T (reference sequence: NM_175914.4) was found. \r\n\r\nPMID: 27245055 - Improda et al 2016 - 2 infants with the p.R63W mutation HNF4A with macrosomia and atypical Fanconi syndrome, in addition to hyperinsulinaemic hypoglycaemia. No nephrocalcinosis reported but this may be due to young age. \r\n",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2020-03-24T14:13:57.082910Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.3",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "changed review comment from: Additional papers cited by Zornitza Stark:\r\n\r\nPMID: 31875549 - Marchesin et al 2019 - Fly model which shows that the R85W variant in Drosophila nephrocytes works in a dominant-negative and cytotoxic effect. Expression of dHNF4 harboring the FRTS mutation affects the catabolism of lipid droplets in nephrocytes by interfering with mitochondrial function. They also showed that the FRTS mutation caused nuclear depletion and cytosolic aggregation of a wild-type dHNF4 reporter protein. The cytosolic aggregates have a cytotoxic affect. By contrast, the expression of another known close mutation in the DNA-binding domain, R89W (that leads to MODY1 but not to FRTS; Hamilton et al., 2014), did not cause any dominant-negative or cytotoxic effects.\r\n\r\nPMID: 30005691 - Liu et al 2018 1 case of a 10-year-old girl of Chinese Han ethnicity who presented with renal Fanconi syndrome, infantile hyperinsulinemic hypoglycemia, and transient cholestasis. In addition, she presented with bilateral severe hearing loss. Gene analysis showed a heterozygous p.R63W mutation in the HNF4A gene that is responsible for Fanconi syndrome and hyperinsulinemic hypoglycemia. \r\n\r\nPMID: 22802087 - Stanescu et al 2012 - 1 case that presented as a newborn with diazoxide-responsive hyperinsulinism and later developed renal Fanconi syndrome, hypophosphatemic rickets, and hepatic glycogenosis. Sequencing of HNF4A (MODY1) revealed a missense, de novo mutation (p.Arg76Trp, c.226C→T) which is a known disease-causing MODY1 mutation in HNF4A. \r\n\r\nPMID: 28458902 - to be finished\r\n; to: Note the same codon is reported as R76W and R63W in different paper depending on whether NM_000457 or NM_175914 is used as the reference transcript. \r\n\r\nAdditional papers cited by Zornitza Stark:\r\n\r\nPMID: 31875549 - Marchesin et al 2019 - Fly model which shows that the R85W variant in Drosophila nephrocytes works in a dominant-negative and cytotoxic effect. Expression of dHNF4 harboring the FRTS mutation affects the catabolism of lipid droplets in nephrocytes by interfering with mitochondrial function. They also showed that the FRTS mutation caused nuclear depletion and cytosolic aggregation of a wild-type dHNF4 reporter protein. The cytosolic aggregates have a cytotoxic affect. By contrast, the expression of another known close mutation in the DNA-binding domain, R89W (that leads to MODY1 but not to FRTS; Hamilton et al., 2014), did not cause any dominant-negative or cytotoxic effects.\r\n\r\nPMID: 30005691 - Liu et al 2018 1 case of a 10-year-old girl of Chinese Han ethnicity who presented with renal Fanconi syndrome, infantile hyperinsulinemic hypoglycemia, and transient cholestasis. In addition, she presented with bilateral severe hearing loss. Renal ultrasonography showed nephrocalcinosis. Gene analysis showed a heterozygous p.R63W mutation in the HNF4A gene that is responsible for Fanconi syndrome and hyperinsulinemic hypoglycemia. (NOTE: This seems to be the same codon as the R76W variant as the paper refers to it as such). \r\n\r\n\r\nPMID: 22802087 - Stanescu et al 2012 - 1 case that presented as a newborn with diazoxide-responsive hyperinsulinism and later developed renal Fanconi syndrome, hypophosphatemic rickets, and hepatic glycogenosis. Sequencing of HNF4A (MODY1) revealed a missense, de novo mutation (p.Arg76Trp, c.226C→T), (NM_000457) which is a known disease-causing MODY1 mutation in HNF4A. Nephrocalcinosis not specifically mentioned. \r\n\r\nNo nephrocalcinosis reported:\r\nPMID: 28458902 - Clemente et al 2017 - 1 patient with congenital hyperinsulinaemic hypoglycaemia, rickets with craniotabes, wrist widening, genu varum and motor impairment. non-gap metabolic acidosis with acidified urine suggestive of proximal tubular acidosis, glycosuria with generalised aminoaciduria and tubular type proteinuria. Says this patient did NOT have the same ‘atypical’ Fanconi syndrome with hypercalciuria with relative hypocalcaemia, hypermagnesaemia, nephrocalcinosis and renal impairment as the patients reported by Hamilton et al 2014. A de novo variant p.Arg63Trp, c.187C > T (reference sequence: NM_175914.4) was found. \r\n",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2020-03-23T18:14:16.585425Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.3",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "changed review comment from: Additional papers cited by Zornitza Stark:\r\n\r\nPMID: 31875549 - Marchesin et al 2019 - Fly model. Used Drosophila nephrocytes as a model for proximal tubules to study the function of HNF4A and the impact of the FRTS-associated R85W mutation. Expression of dHNF4 harboring the FRTS mutation affects the catabolism of lipid droplets in nephrocytes by interfering with mitochondrial function. They also showed that the FRTS mutation promotes the nuclear export of a wild-type reporter protein, thereby reducing transcriptional output in a dominant-negative manner and promoting the formation of cytotoxic dHNF4 aggregates in the cytosol.\r\nReview to be continued. \r\n\r\nPMID: 22802087\r\nPMID: 30005691\r\nPMID: 28458902; to: Additional papers cited by Zornitza Stark:\r\n\r\nPMID: 31875549 - Marchesin et al 2019 - Fly model which shows that the R85W variant in Drosophila nephrocytes works in a dominant-negative and cytotoxic effect. Expression of dHNF4 harboring the FRTS mutation affects the catabolism of lipid droplets in nephrocytes by interfering with mitochondrial function. They also showed that the FRTS mutation caused nuclear depletion and cytosolic aggregation of a wild-type dHNF4 reporter protein. The cytosolic aggregates have a cytotoxic affect. By contrast, the expression of another known close mutation in the DNA-binding domain, R89W (that leads to MODY1 but not to FRTS; Hamilton et al., 2014), did not cause any dominant-negative or cytotoxic effects.\r\n\r\nPMID: 30005691 - Liu et al 2018 1 case of a 10-year-old girl of Chinese Han ethnicity who presented with renal Fanconi syndrome, infantile hyperinsulinemic hypoglycemia, and transient cholestasis. In addition, she presented with bilateral severe hearing loss. Gene analysis showed a heterozygous p.R63W mutation in the HNF4A gene that is responsible for Fanconi syndrome and hyperinsulinemic hypoglycemia. \r\n\r\nPMID: 22802087 - Stanescu et al 2012 - 1 case that presented as a newborn with diazoxide-responsive hyperinsulinism and later developed renal Fanconi syndrome, hypophosphatemic rickets, and hepatic glycogenosis. Sequencing of HNF4A (MODY1) revealed a missense, de novo mutation (p.Arg76Trp, c.226C→T) which is a known disease-causing MODY1 mutation in HNF4A. \r\n\r\nPMID: 28458902 - to be finished\r\n",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2020-03-23T13:35:45.413729Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.3",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: HNF4A: Additional papers cited by Zornitza Stark:\r\n\r\nPMID: 31875549 - Marchesin et al 2019 - Fly model. Used Drosophila nephrocytes as a model for proximal tubules to study the function of HNF4A and the impact of the FRTS-associated R85W mutation. Expression of dHNF4 harboring the FRTS mutation affects the catabolism of lipid droplets in nephrocytes by interfering with mitochondrial function. They also showed that the FRTS mutation promotes the nuclear export of a wild-type reporter protein, thereby reducing transcriptional output in a dominant-negative manner and promoting the formation of cytotoxic dHNF4 aggregates in the cytosol.\r\nReview to be continued. \r\n\r\nPMID: 22802087\r\nPMID: 30005691\r\nPMID: 28458902",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2020-02-13T11:38:12.575970Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.3",
"user_name": "Eleanor Williams",
"item_type": "panel",
"text": "Panel version has been signed off",
"entity_name": null,
"entity_type": null
},
{
"created": "2020-02-13T11:37:43.110914Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.2",
"user_name": "Eleanor Williams",
"item_type": "panel",
"text": "Panel types changed to Rare Disease 100K; GMS Rare Disease Virtual; GMS Rare Disease; GMS signed-off",
"entity_name": null,
"entity_type": null
},
{
"created": "2020-01-16T05:13:31.047002Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.0",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "gene: SLC26A1 was added\ngene: SLC26A1 was added to Nephrocalcinosis or nephrolithiasis. Sources: Expert list\nMode of inheritance for gene: SLC26A1 was set to BIALLELIC, autosomal or pseudoautosomal\nPublications for gene: SLC26A1 were set to 27210743; 27210743; 20160351\nPhenotypes for gene: SLC26A1 were set to Nephrolithiasis, calcium oxalate, MIM#167030\nReview for gene: SLC26A1 was set to GREEN\ngene: SLC26A1 was marked as current diagnostic\nAdded comment: Three unrelated families and a mouse model. \nSources: Expert list",
"entity_name": "SLC26A1",
"entity_type": "gene"
},
{
"created": "2020-01-16T05:07:39.723934Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.0",
"user_name": "Zornitza Stark",
"item_type": "entity",
"text": "reviewed gene: HNF4A: Rating: GREEN; Mode of pathogenicity: None; Publications: 31875549, 24285859, 22802087, 30005691, 28458902; Phenotypes: Fanconi renotubular syndrome 4, with maturity-onset diabetes of the young, OMIM #616026; Mode of inheritance: None; Current diagnostic: yes",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2019-12-04T14:45:48.520341Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "2.0",
"user_name": "Eleanor Williams",
"item_type": "panel",
"text": "promoted panel to version 2.0",
"entity_name": null,
"entity_type": null
},
{
"created": "2019-12-04T14:44:58.152768Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.52",
"user_name": "Eleanor Williams",
"item_type": "panel",
"text": "Panel types changed to Rare Disease 100K; GMS Rare Disease; GMS signed-off",
"entity_name": null,
"entity_type": null
},
{
"created": "2019-11-14T09:20:38.690662Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.51",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Classified gene: SLC9A3R1 as Amber List (moderate evidence)",
"entity_name": "SLC9A3R1",
"entity_type": "gene"
},
{
"created": "2019-11-14T09:20:38.687582Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.51",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Added comment: Comment on list classification: Changing the rating of this gene to Amber in light of the expert review that highlights that the proposed pathogenic variants are found at higher than expected frequency in the general population.",
"entity_name": "SLC9A3R1",
"entity_type": "gene"
},
{
"created": "2019-11-14T09:20:38.669113Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.51",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Gene: slc9a3r1 has been classified as Amber List (Moderate Evidence).",
"entity_name": "SLC9A3R1",
"entity_type": "gene"
},
{
"created": "2019-11-13T16:58:38.401002Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.50",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "changed review comment from: In the original publication (PMID: 18784102 - Karim et al 2008), Karim et al examine 159 patients with either nephrolithiasis or bone demineralisation. They find variants in SLC9A3R1 in 4 patients from 3 families. These 3 variants are now listed in gnomAD with a combined frequency of just over 2%. Thus, the frequency of these variants in the patient cohort is essentially the same as in the general population. \r\nSeveral publications subsequently report variants in this gene in cohorts with nephrolithiasis/calcinosis, but again essentially with either the same or even lower frequency as in the normal population:\r\n1) Daga et al (Kidney Int. 2018 Jan;93(1):204-213. doi: 10.1016/j.kint.2017.06.025): 1 out of 51 families\r\n2) Braun et al (Clin J Am Soc Nephrol. 2016 Apr 7;11(4):664-72. doi: 10.2215/CJN.07540715): 1 out of 143\r\n3) Halbritter et al (J Am Soc Nephrol. 2015 Mar; 26(3): 543–551doi: 10.1681/ASN.2014040388): 2 out of 268\r\n\r\nThus, there are several lines of evidence arguing against SLC9A3R1 being a disease causing gene:\r\n1) the frequency of variants in SLC9A3R in itself higher than expected for a dominant disease gene (3% combined frequency of missense and pLoF in gnomAD)\r\n2) there are 231 missende variants in this gene listed in gnomAD versus 211.7 expected, based on gene length (Z=-0.48), thus the gene is not constrained against missense variants\r\n3) the frequency of variants in patients with nephrolithiasis/calcinosis is essentially the same as in the general population\r\n\r\nThe clinical relevance of any variants identified in SLC9A3R1 is thus questionable.; to: In the original publication (PMID: 18784102 - Karim et al 2008), Karim et al examine 159 patients with either nephrolithiasis or bone demineralisation. They find variants in SLC9A3R1 in 4 patients from 3 families. These 3 variants are now listed in gnomAD with a combined frequency of just over 2%. Thus, the frequency of these variants in the patient cohort is essentially the same as in the general population. \r\nSeveral publications subsequently report variants in this gene in cohorts with nephrolithiasis/calcinosis, but again essentially with either the same or even lower frequency as in the normal population:\r\n1) Daga et al (Kidney Int. 2018 Jan;93(1):204-213. doi: 10.1016/j.kint.2017.06.025): 1 out of 51 families\r\n2) Braun et al (Clin J Am Soc Nephrol. 2016 Apr 7;11(4):664-72. doi: 10.2215/CJN.07540715): 1 out of 143\r\n3) Halbritter et al (J Am Soc Nephrol. 2015 Mar; 26(3): 543–551doi: 10.1681/ASN.2014040388): 2 out of 268\r\n\r\nThus, there are several lines of evidence arguing against SLC9A3R1 being a disease causing gene:\r\n1) the frequency of variants in SLC9A3R in itself is higher than expected for a dominant disease gene (3% combined frequency of missense and pLoF in gnomAD)\r\n2) there are 231 missense variants in this gene listed in gnomAD versus 211.7 expected, based on gene length (Z=-0.48), thus the gene is not constrained against missense variants\r\n3) the frequency of variants in patients with nephrolithiasis/calcinosis is essentially the same as in the general population\r\n\r\nThe clinical relevance of any variants identified in SLC9A3R1 is thus questionable.",
"entity_name": "SLC9A3R1",
"entity_type": "gene"
},
{
"created": "2019-11-13T16:57:37.993779Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.50",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "changed review comment from: In the original publication (PMID: 18784102 - Karim et al 2008), Karim et al examine 159 patients with either nephrolithiasis or bone demineralisation. they find variants in SLC9A3R1 in 4 patients from 3 families. These variants are now listed in gnomAD with a combined frequency of just over 2%. Thus, the frequency of these variants in the patient cohort is essentially the same as in the general population. \r\nSeveral publications subsequently report variants in this gene in cohorts with nephrolithiasis/calcinosis, but again essentially with either the same or even lower frequency as in the normal population:\r\n1) Daga et al (Kidney Int. 2018 Jan;93(1):204-213. doi: 10.1016/j.kint.2017.06.025): 1 out of 51 families\r\n2) Braun et al (Clin J Am Soc Nephrol. 2016 Apr 7;11(4):664-72. doi: 10.2215/CJN.07540715): 1 out of 143\r\n3) Halbritter et al (J Am Soc Nephrol. 2015 Mar; 26(3): 543–551doi: 10.1681/ASN.2014040388): 2 out of 268\r\n\r\nThus, not only is the frequency of variants in SLC9A3R in itself higher than expected for a dominant disease gene, but the frequency of variants in patients with nephrolithiasis/calcinosis is essentially the same as in the general population and the likelihood that they disease causing is thus very unlikely.; to: In the original publication (PMID: 18784102 - Karim et al 2008), Karim et al examine 159 patients with either nephrolithiasis or bone demineralisation. They find variants in SLC9A3R1 in 4 patients from 3 families. These 3 variants are now listed in gnomAD with a combined frequency of just over 2%. Thus, the frequency of these variants in the patient cohort is essentially the same as in the general population. \r\nSeveral publications subsequently report variants in this gene in cohorts with nephrolithiasis/calcinosis, but again essentially with either the same or even lower frequency as in the normal population:\r\n1) Daga et al (Kidney Int. 2018 Jan;93(1):204-213. doi: 10.1016/j.kint.2017.06.025): 1 out of 51 families\r\n2) Braun et al (Clin J Am Soc Nephrol. 2016 Apr 7;11(4):664-72. doi: 10.2215/CJN.07540715): 1 out of 143\r\n3) Halbritter et al (J Am Soc Nephrol. 2015 Mar; 26(3): 543–551doi: 10.1681/ASN.2014040388): 2 out of 268\r\n\r\nThus, there are several lines of evidence arguing against SLC9A3R1 being a disease causing gene:\r\n1) the frequency of variants in SLC9A3R in itself higher than expected for a dominant disease gene (3% combined frequency of missense and pLoF in gnomAD)\r\n2) there are 231 missende variants in this gene listed in gnomAD versus 211.7 expected, based on gene length (Z=-0.48), thus the gene is not constrained against missense variants\r\n3) the frequency of variants in patients with nephrolithiasis/calcinosis is essentially the same as in the general population\r\n\r\nThe clinical relevance of any variants identified in SLC9A3R1 is thus questionable.",
"entity_name": "SLC9A3R1",
"entity_type": "gene"
},
{
"created": "2019-11-13T16:42:44.759650Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.50",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "commented on gene: SLC9A3R1",
"entity_name": "SLC9A3R1",
"entity_type": "gene"
},
{
"created": "2019-11-13T11:13:40.330488Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.50",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "changed review comment from: Associated with Nephrolithiasis/osteoporosis, hypophosphatemic, 2 #612287 (AD) in OMIM. A previous name for SLC9A3R1 is NHERF1. \r\n\r\nEvidence for association comes from PMID: 18784102 - Karim et al 2008 - sequencing of the coding region of NHERF1 in 92 patients who presented with either renal stones or bone demineralization, together with normal serum PTH concentrations and who had no evidence of any usual causes of these disorders (e.g., hyperparathyroidism, hyperthyroidism, or an increased FGF-23 plasma concentration). These were group 1 patients. They identified three distinct missense mutations in the NHERF1 gene in four unrelated patients from group 1 (328C->G, L110V; 458G->A, R153Q; 673G->A, E225K). \r\n\r\nThey also studied patients who did not have renal stones or bone demineralization (group 2) who were referred to the clinical investigation department for renal assessment before undergoing a potentially nephrotoxic treatment for psoriasis. One patient in group 2 had an NHERF1 mutation (L110V). This patient had a low TmP/GFR value.; to: Associated with Nephrolithiasis/osteoporosis, hypophosphatemic, 2 #612287 (AD) in OMIM. A previous name for SLC9A3R1 is NHERF1. \r\n\r\nEvidence for association comes from PMID: 18784102 - Karim et al 2008 - sequencing of the coding region of NHERF1 in 92 patients who presented with either renal stones or bone demineralization, together with normal serum PTH concentrations and who had no evidence of any usual causes of these disorders (e.g., hyperparathyroidism, hyperthyroidism, or an increased FGF-23 plasma concentration). These were group 1 patients. They identified three distinct missense mutations in the NHERF1 gene in four unrelated patients from group 1 (328C->G, L110V; 458G->A, R153Q; 673G->A, E225K). \r\n\r\nThey also studied patients who did not have renal stones or bone demineralization (group 2) who were referred to the clinical investigation department for renal assessment before undergoing a potentially nephrotoxic treatment for psoriasis. One patient in group 2 had an NHERF1 mutation (L110V). This patient had a low TmP/GFR value.\r\n\r\n\r\nPMID: 28893421 - Daga et al 2018 - performed WES in 65 individuals from 51 families with nephrolithiasis and/or a finding of nephrocalcinosis on renal ultrasound, who manifested before the age of 25 years. They found 1 individual with a heterozygous pathogenic variant in SLC9A3R1 (c.673G>A, p.E225K). ",
"entity_name": "SLC9A3R1",
"entity_type": "gene"
},
{
"created": "2019-11-13T11:04:43.773900Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.50",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: SLC9A3R1",
"entity_name": "SLC9A3R1",
"entity_type": "gene"
},
{
"created": "2019-11-07T23:21:43.512615Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.50",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "changed review comment from: Comment on list classification: Demoting this gene from green to red. A PubMed search didn't find publications listing nephrocalicinosis/nephrolithiasis in association with this gene. Hypermagnesuria no hypomagnesemia is included on the eligibility statement for this disease.; to: Comment on list classification: Demoting this gene from green to red. A PubMed search didn't find publications listing nephrocalicinosis/nephrolithiasis in association with this gene. Hypermagnesuria not hypomagnesemia is included on the eligibility statement for this disease.",
"entity_name": "TRPM6",
"entity_type": "gene"
},
{
"created": "2019-11-07T23:19:54.261191Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.50",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Phenotypes for gene: HNF4A were changed from to Fanconi renotubular syndrome 4, with maturity-onset diabetes of the young, 616026",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2019-11-07T23:19:31.908936Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.49",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Publications for gene: HNF4A were set to ",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2019-11-07T23:15:29.476119Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.48",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Phenotypes for gene: SLC4A1 were changed from distal renal tubular acidosis to distal renal tubular acidosis; Renal tubular acidosis, distal, AD, 179800; Renal tubular acidosis, distal, AR 611590",
"entity_name": "SLC4A1",
"entity_type": "gene"
},
{
"created": "2019-11-06T17:11:13.606893Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.47",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Added comment: Comment on mode of inheritance: In OMIM Autosomal recessive for Bartter syndrome, type 3\t607364 and Digenic recessive for Bartter syndrome, type 4b, digenic 613090.",
"entity_name": "CLCNKB",
"entity_type": "gene"
},
{
"created": "2019-11-06T17:11:13.577192Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.47",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Mode of inheritance for gene: CLCNKB was changed from BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal",
"entity_name": "CLCNKB",
"entity_type": "gene"
},
{
"created": "2019-11-06T17:05:03.835861Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.46",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Added comment: Comment on mode of pathogenicity: Expert review states that Hypocalcemia can be caused by a mutation that inappropriately activates the receptor",
"entity_name": "CASR",
"entity_type": "gene"
},
{
"created": "2019-11-06T17:05:03.803784Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.46",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Mode of pathogenicity for gene: CASR was changed from to Other",
"entity_name": "CASR",
"entity_type": "gene"
},
{
"created": "2019-11-06T17:02:04.074244Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.45",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Added comment: Comment on mode of inheritance: AR in OMIM and Biallelic in Gene2Phenotype for\tBartter syndrome, type 4a",
"entity_name": "BSND",
"entity_type": "gene"
},
{
"created": "2019-11-06T17:02:04.054539Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.45",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Mode of inheritance for gene: BSND was changed from BIALLELIC, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal",
"entity_name": "BSND",
"entity_type": "gene"
},
{
"created": "2019-11-06T16:58:59.117281Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.44",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Phenotypes for gene: ATP6V1B1 were changed from distal renal tubular acidosis to distal renal tubular acidosis; Renal tubular acidosis with deafness 267300",
"entity_name": "ATP6V1B1",
"entity_type": "gene"
},
{
"created": "2019-11-06T16:58:05.214639Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.43",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: ATP6V0A4",
"entity_name": "ATP6V0A4",
"entity_type": "gene"
},
{
"created": "2019-11-06T16:28:10.008048Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.43",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Classified gene: PHEX as Green List (high evidence)",
"entity_name": "PHEX",
"entity_type": "gene"
},
{
"created": "2019-11-06T16:28:10.005082Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.43",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Added comment: Comment on list classification: In light of expert review and consultation with the Genomics England clinical team it was decided to promote this gene from red to green. >3 cases reported with variants in this gene in patients with nephrocalicinosis.",
"entity_name": "PHEX",
"entity_type": "gene"
},
{
"created": "2019-11-06T16:28:09.987406Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.43",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Gene: phex has been classified as Green List (High Evidence).",
"entity_name": "PHEX",
"entity_type": "gene"
},
{
"created": "2019-11-06T16:26:08.308233Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.42",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "changed review comment from: Comment on mode of inheritance: Following XLD mode of inhertiance in OMIM, so changing to X-Linked: hemizyous mutation in males, monoallelic in females.; to: Comment on mode of inheritance: Following XLD mode of inhertiance in OMIM, so changing to X-Linked: hemizyous mutation in males, monoallelic in females. Monoallelic variants causing disease in females are reported e.g. PMID: 10439971 Filisetti et al 1999",
"entity_name": "PHEX",
"entity_type": "gene"
},
{
"created": "2019-11-06T16:11:21.023633Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.42",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Publications for gene: PHEX were set to ",
"entity_name": "PHEX",
"entity_type": "gene"
},
{
"created": "2019-11-06T16:10:55.341955Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.41",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Phenotypes for gene: PHEX were changed from to Hypophosphatemic rickets, X-linked dominant 307800",
"entity_name": "PHEX",
"entity_type": "gene"
},
{
"created": "2019-11-06T16:09:28.184413Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.40",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Classified gene: FAM20A as Green List (high evidence)",
"entity_name": "FAM20A",
"entity_type": "gene"
},
{
"created": "2019-11-06T16:09:28.179455Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.40",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Added comment: Comment on list classification: Upgrading from red to green. 3 independent cases where nephrocalcinosis is reported plus mouse knockout data showing a renal phenotype.",
"entity_name": "FAM20A",
"entity_type": "gene"
},
{
"created": "2019-11-06T16:09:28.154232Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.40",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Gene: fam20a has been classified as Green List (High Evidence).",
"entity_name": "FAM20A",
"entity_type": "gene"
},
{
"created": "2019-11-06T16:07:14.050437Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.39",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Classified gene: TRPM6 as Red List (low evidence)",
"entity_name": "TRPM6",
"entity_type": "gene"
},
{
"created": "2019-11-06T16:07:14.045195Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.39",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Added comment: Comment on list classification: Demoting this gene from green to red. A PubMed search didn't find publications listing nephrocalicinosis/nephrolithiasis in association with this gene. Hypermagnesuria no hypomagnesemia is included on the eligibility statement for this disease.",
"entity_name": "TRPM6",
"entity_type": "gene"
},
{
"created": "2019-11-06T16:07:14.017241Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.39",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Gene: trpm6 has been classified as Red List (Low Evidence).",
"entity_name": "TRPM6",
"entity_type": "gene"
},
{
"created": "2019-10-30T15:37:36.620461Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.38",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Added comment: Comment on mode of inheritance: Following XLD mode of inhertiance in OMIM, so changing to X-Linked: hemizyous mutation in males, monoallelic in females.",
"entity_name": "PHEX",
"entity_type": "gene"
},
{
"created": "2019-10-30T15:37:36.601867Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.38",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Mode of inheritance for gene: PHEX was changed from X-LINKED: hemizygous mutation in males, biallelic mutations in females to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)",
"entity_name": "PHEX",
"entity_type": "gene"
},
{
"created": "2019-10-30T15:29:19.527549Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.37",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Phenotypes for gene: SLC7A9 were changed from Cystinuria to Cystinuria 220100",
"entity_name": "SLC7A9",
"entity_type": "gene"
},
{
"created": "2019-10-30T15:19:49.859562Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.36",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Phenotypes for gene: SLC3A1 were changed from Cystinuria to Cystinuria 220100",
"entity_name": "SLC3A1",
"entity_type": "gene"
},
{
"created": "2019-10-30T15:17:27.728157Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.35",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "changed review comment from: Comment on mode of inheritance: The evidence for biallelic inheritance is stronger so setting to this for now.; to: Comment on mode of inheritance: The evidence for biallelic inheritance is stronger so setting to this for now. AR in OMIM. ",
"entity_name": "SLC22A12",
"entity_type": "gene"
},
{
"created": "2019-10-30T15:13:50.666184Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.35",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "changed review comment from: Comment on Mode of Inheritance - PMID: 25907713 reports that female carriers can have mild symptoms of Dent disease so Xlinked (monoalllelic in females) may be more appropriate. However, in OMIM the mode of inheritance for Hypophosphatemic rickets, Nephrolithiasis, type I and Proteinuria, low molecular weight, with hypercalciuric nephrocalcinosis) is XLR so keeping as Xlinked (biallelic in females) just now.; to: Comment on Mode of Inheritance - PMID: 25907713 reports that female carriers can have mild symptoms of Dent disease so Xlinked (monoalllelic in females) may be more appropriate. However, in OMIM the mode of inheritance for Dents disease, Hypophosphatemic rickets, Nephrolithiasis, type I and Proteinuria, low molecular weight, with hypercalciuric nephrocalcinosis is XLR so keeping as Xlinked (biallelic in females) just now.",
"entity_name": "CLCN5",
"entity_type": "gene"
},
{
"created": "2019-10-30T15:03:36.440839Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.35",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Phenotypes for gene: SLC2A9 were changed from to Hypouricemia, renal, 2, 612076",
"entity_name": "SLC2A9",
"entity_type": "gene"
},
{
"created": "2019-10-30T15:03:19.013393Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.34",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Publications for gene: SLC2A9 were set to ",
"entity_name": "SLC2A9",
"entity_type": "gene"
},
{
"created": "2019-10-30T15:02:22.017022Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.33",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Classified gene: SLC2A9 as Green List (high evidence)",
"entity_name": "SLC2A9",
"entity_type": "gene"
},
{
"created": "2019-10-30T15:02:22.013832Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.33",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Added comment: Comment on list classification: Changing rating from red to green. 3 unrelated cases with Hypouricemia, renal, with Nephrolithiasis in some family members.",
"entity_name": "SLC2A9",
"entity_type": "gene"
},
{
"created": "2019-10-30T15:02:21.997272Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.33",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Gene: slc2a9 has been classified as Green List (High Evidence).",
"entity_name": "SLC2A9",
"entity_type": "gene"
},
{
"created": "2019-10-30T14:59:18.587071Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.32",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Added comment: Comment on mode of inheritance: Both monoallelic and biallelic for Hypouricemia, renal. However, the reported cases with nephrolithiasis are homozygous.",
"entity_name": "SLC2A9",
"entity_type": "gene"
},
{
"created": "2019-10-30T14:59:18.566378Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.32",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Mode of inheritance for gene: SLC2A9 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal",
"entity_name": "SLC2A9",
"entity_type": "gene"
},
{
"created": "2019-10-30T14:57:08.900415Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.31",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "changed review comment from: Associated with Hypouricemia, renal, 2\t#612076\t(AD, AR) in OMIM. \r\n\r\nPMID: 19926891 - Dinour et al 2010 - studied two unrelated consanguineous families who had severe hereditary hypouricemia and did not have a URAT1 defect. Both families had homozygous SLC2A9 mutations: A missense mutation (L75R) in six affected members of one family and a 36-kb deletion, resulting in a truncated protein, in the other. Nephrolithiasis was seen in some members of both families. \r\n\r\nPMID: 21256783 - Stiburkova et al 2011 - proband and her brother from a Czech family with renal hypouricemia have a one nucleotide homozygote insertion in exon 3 in the SLC2A9 gene resulting in a truncated protein (p.Ile118HisfsX27). The brother showed urolithiasis. \r\n\r\nPMID: 19026395 - Matsuo et al 2008 - report two loss-of-function heterozygous mutations in GLUT9 (SLC2A9)(R380W and R198C) in renal hypouricemic patients who have no URAT1 mutations but it is not reported whether they have Nephrocalcinosis/nephrolithiasis.\r\n\r\nPMID: 21810765 - 2 cases renal hypouricemia and variants in SLC2A9 - no nephrolithiasis reported\r\nPMID: 29486147 - 2 cases with renal hypouricemia and variants in SLC2A9 - no nephrolithiasis reported\r\nPMID: 27116386 - 1 case with renal hypouricemia and variant in SLC2A9 - no nephrolithiasis reported\r\nPMID: 24940677 - 1 case with renal hypouricaemia and variant in SLC2A9 - no mention of nepthrolithiasis\r\n\r\nSummary, clear association of variants in SLC2A9 with renal hypouricaemia . 3 cases reported with nepthrolithiasis/urothilthiasis but many more cases where it is not mentioned. ; to: Associated with Hypouricemia, renal, 2\t#612076\t(AD, AR) in OMIM. \r\n\r\nCases with nepthrolithiasis:\r\nPMID: 19926891 - Dinour et al 2010 - studied two unrelated consanguineous families who had severe hereditary hypouricemia and did not have a URAT1 defect. Both families had homozygous SLC2A9 mutations: A missense mutation (L75R) in six affected members of one family and a 36-kb deletion, resulting in a truncated protein, in the other. Nephrolithiasis was seen in some members of both families. \r\n\r\nPMID: 21256783 - Stiburkova et al 2011 - proband and her brother from a Czech family with renal hypouricemia have a one nucleotide homozygous insertion in exon 3 in the SLC2A9 gene resulting in a truncated protein (p.Ile118HisfsX27). The brother showed urolithiasis. \r\n\r\nCases with no report of nepthrolithiasis:\r\nPMID: 19026395 - Matsuo et al 2008 - report two loss-of-function heterozygous mutations in GLUT9 (SLC2A9)(R380W and R198C) in renal hypouricemic patients who have no URAT1 mutations but it is not reported whether they have Nephrocalcinosis/nephrolithiasis.\r\n\r\nPMID: 21810765 - 2 cases renal hypouricemia and variants in SLC2A9 - no nephrolithiasis reported\r\nPMID: 29486147 - 2 cases with renal hypouricemia and variants in SLC2A9 - no nephrolithiasis reported\r\nPMID: 27116386 - 1 case with renal hypouricemia and variant in SLC2A9 - no nephrolithiasis reported\r\nPMID: 24940677 - 1 case with renal hypouricaemia and variant in SLC2A9 - no mention of nepthrolithiasis\r\n\r\nSummary, clear association of variants in SLC2A9 with renal hypouricaemia . 3 cases reported with nepthrolithiasis/urothilthiasis but many more cases where it is not mentioned. ",
"entity_name": "SLC2A9",
"entity_type": "gene"
},
{
"created": "2019-10-30T14:54:57.084558Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.31",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "changed review comment from: Associated with Hypouricemia, renal, 2\t#612076\t(AD, AR) in OMIM. \r\n\r\nPMID: 19926891 - Dinour et al 2010 - studied two unrelated consanguineous families who had severe hereditary hypouricemia and did not have a URAT1 defect. Both families had homozygous SLC2A9 mutations: A missense mutation (L75R) in six affected members of one family and a 36-kb deletion, resulting in a truncated protein, in the other. Nephrolithiasis was seen in some members of both families. \r\n\r\nPMID: 21256783 - Stiburkova et al 2011 - proband and her brother from a Czech family with renal hypouricemia have a one nucleotide homozygote insertion in exon 3 in the SLC2A9 gene resulting in a truncated protein (p.Ile118HisfsX27). The brother showed urolithiasis. \r\n\r\nPMID: 19026395 - Matsuo et al 2008 - report two loss-of-function heterozygous mutations in GLUT9 (SLC2A9)(R380W and R198C) in renal hypouricemic patients who have no URAT1 mutations but it is not reported whether they have Nephrocalcinosis/nephrolithiasis.\r\nPMID: 21810765 - 2 cases renal hypouricemia and variants in SLC2A9 - no nephrolithiasis reported\r\nPMID: 29486147 - 2 cases with renal hypouricemia and variants in SLC2A9 - no nephrolithiasis reported\r\nPMID: 27116386 - 1 case with renal hypouricemia and variant in SLC2A9 - no nephrolithiasis reported\r\nPMID: 24940677 - 1 case with renal hypouricaemia and variant in SLC2A9 - no mention of nepthrolithiasis\r\n\r\nSummary, clear association of variants in SLC2A9 with renal hypouricaemia . 3 cases reported with nepthrolithiasis/urothilthiasis but many more cases where it is not mentioned. ; to: Associated with Hypouricemia, renal, 2\t#612076\t(AD, AR) in OMIM. \r\n\r\nPMID: 19926891 - Dinour et al 2010 - studied two unrelated consanguineous families who had severe hereditary hypouricemia and did not have a URAT1 defect. Both families had homozygous SLC2A9 mutations: A missense mutation (L75R) in six affected members of one family and a 36-kb deletion, resulting in a truncated protein, in the other. Nephrolithiasis was seen in some members of both families. \r\n\r\nPMID: 21256783 - Stiburkova et al 2011 - proband and her brother from a Czech family with renal hypouricemia have a one nucleotide homozygote insertion in exon 3 in the SLC2A9 gene resulting in a truncated protein (p.Ile118HisfsX27). The brother showed urolithiasis. \r\n\r\nPMID: 19026395 - Matsuo et al 2008 - report two loss-of-function heterozygous mutations in GLUT9 (SLC2A9)(R380W and R198C) in renal hypouricemic patients who have no URAT1 mutations but it is not reported whether they have Nephrocalcinosis/nephrolithiasis.\r\n\r\nPMID: 21810765 - 2 cases renal hypouricemia and variants in SLC2A9 - no nephrolithiasis reported\r\nPMID: 29486147 - 2 cases with renal hypouricemia and variants in SLC2A9 - no nephrolithiasis reported\r\nPMID: 27116386 - 1 case with renal hypouricemia and variant in SLC2A9 - no nephrolithiasis reported\r\nPMID: 24940677 - 1 case with renal hypouricaemia and variant in SLC2A9 - no mention of nepthrolithiasis\r\n\r\nSummary, clear association of variants in SLC2A9 with renal hypouricaemia . 3 cases reported with nepthrolithiasis/urothilthiasis but many more cases where it is not mentioned. ",
"entity_name": "SLC2A9",
"entity_type": "gene"
},
{
"created": "2019-10-30T14:50:43.625499Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.31",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Classified gene: SLC22A12 as Green List (high evidence)",
"entity_name": "SLC22A12",
"entity_type": "gene"
},
{
"created": "2019-10-30T14:50:43.620485Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.31",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Added comment: Comment on list classification: Promoting from red to green. Sufficient number of cases with biallelic or compound heterozygous variants in this gene and a relevant phenotype reported. A few heterozygous cases also reported but the evidence is not so strong (asymptomatic family members with the same variant, only the SLC22A12 gene looked at).",
"entity_name": "SLC22A12",
"entity_type": "gene"
},
{
"created": "2019-10-30T14:50:43.595092Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.31",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Gene: slc22a12 has been classified as Green List (High Evidence).",
"entity_name": "SLC22A12",
"entity_type": "gene"
},
{
"created": "2019-10-30T14:43:32.386889Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.30",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Phenotypes for gene: SLC22A12 were changed from to Hypouricemia, renal, 220150",
"entity_name": "SLC22A12",
"entity_type": "gene"
},
{
"created": "2019-10-30T14:42:16.875287Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.29",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "changed review comment from: Associated with Hypouricemia, renal #220150 (AR) in OMIM with Uric acid nephrolithiasis listed as a clinical feature. \r\n\r\nPMID: 29486147 - Claverie-Martin et al 2018 - report patients from 6 unrelated Spanish families with Renal hypouricemia and variants in SLC22A12. Nephrolithiasis was reported in one Roma patient with compound heterozygous variants in this gene. \r\n\r\nPMID: 29958533 - Vidanapathirana et al 2018 - report a 9 year old Sri Lankan boy with renal hypouricemia who presented with nephrolithiasis and haematuria. He was found to have a potentially deleterious missense variant c.1400C > T (p.T467 M, rs200104135) in heterozygous state. This variant has been previously identified in homozygous and/or compound heterozygous state with other causative SLC22A12 variant c.1245_1253del (p.L415_G417del) in Roma population. The genotype c.[1400C > T] was found in the proband, his sister and father (both asymptomatic). \r\n\r\nPMID: 18492088 - Ichida et al 2008 - identified SLC22A12 mutations in 66 of 71 Japanese patients with hypouricemia. A total of 13 mutations, including 3 novel mutations, were identified. Urolithiasis occurred in 5 of the patients with variants in SLC22A12. 4 were homozygous or compound heterozygous, one was heterozygous. One variant G774A/W258X was the most common variant and is thought to be a founder mutation. \r\n\r\nPMID: 15912381 - Cheong et al 2005 - studied the SLC22A12 gene in five Korean patients with idiopathic renal hypouricemia, 1 patient with a R90H substitution had uric acid urolithiasis. The variant was heterozygous.; to: Associated with Hypouricemia, renal #220150 (AR) in OMIM with Uric acid nephrolithiasis listed as a clinical feature. \r\n\r\nPMID: 29486147 - Claverie-Martin et al 2018 - report patients from 6 unrelated Spanish families with Renal hypouricemia and variants in SLC22A12. Nephrolithiasis was reported in one Roma patient with compound heterozygous variants in this gene (L415_G417del, T467M). \r\n\r\nPMID: 29958533 - Vidanapathirana et al 2018 - report a 9 year old Sri Lankan boy with renal hypouricemia who presented with nephrolithiasis and haematuria. He was found to have a potentially deleterious missense variant c.1400C > T (p.T467 M, rs200104135) in heterozygous state. This variant has been previously identified in homozygous and/or compound heterozygous state with other causative SLC22A12 variant c.1245_1253del (p.L415_G417del) in Roma population. The genotype c.[1400C > T] was found in the proband, his sister and father (both asymptomatic). \r\n\r\nPMID: 18492088 - Ichida et al 2008 - identified SLC22A12 mutations in 66 of 71 Japanese patients with hypouricemia. A total of 13 mutations, including 3 novel mutations, were identified. Urolithiasis occurred in 5 of the patients with variants in SLC22A12. 4 were homozygous or compound heterozygous, one was heterozygous. One variant G774A/W258X was the most common variant and is thought to be a founder mutation. \r\n\r\nPMID: 15912381 - Cheong et al 2005 - studied the SLC22A12 gene in five Korean patients with idiopathic renal hypouricemia, 1 patient with a R90H substitution had uric acid urolithiasis. The variant was heterozygous.",
"entity_name": "SLC22A12",
"entity_type": "gene"
},
{
"created": "2019-10-30T14:34:16.206137Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.29",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Publications for gene: SLC22A12 were set to ",
"entity_name": "SLC22A12",
"entity_type": "gene"
},
{
"created": "2019-10-30T14:34:07.877684Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.28",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Added comment: Comment on mode of inheritance: The evidence for biallelic inheritance is stronger so setting to this for now.",
"entity_name": "SLC22A12",
"entity_type": "gene"
},
{
"created": "2019-10-30T14:34:07.865577Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.28",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Mode of inheritance for gene: SLC22A12 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal",
"entity_name": "SLC22A12",
"entity_type": "gene"
},
{
"created": "2019-10-30T14:26:35.742723Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.27",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: PHEX: Personal communication from Detlef Bockenhauer. They see nephrocalcinosis in ~50% patients. It clearly is also related to treatment, but probably an intrinsic part of the disease.",
"entity_name": "PHEX",
"entity_type": "gene"
},
{
"created": "2019-10-30T14:22:19.245587Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.27",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Classified gene: HPRT1 as Green List (high evidence)",
"entity_name": "HPRT1",
"entity_type": "gene"
},
{
"created": "2019-10-30T14:22:19.240781Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.27",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Added comment: Comment on list classification: Promoting from red to green. > 3 unrelated cases with variants in this gene and Lesch-Nyhan syndrome with nephrocalcinosis as a feature are reported. Numerous variants are reported. Two publications.",
"entity_name": "HPRT1",
"entity_type": "gene"
},
{
"created": "2019-10-30T14:22:19.214759Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.27",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Gene: hprt1 has been classified as Green List (High Evidence).",
"entity_name": "HPRT1",
"entity_type": "gene"
},
{
"created": "2019-10-30T14:15:03.384352Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.26",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Phenotypes for gene: HPRT1 were changed from to Lesch-Nyhan syndrome, 300322",
"entity_name": "HPRT1",
"entity_type": "gene"
},
{
"created": "2019-10-30T14:14:47.406862Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.25",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Publications for gene: HPRT1 were set to ",
"entity_name": "HPRT1",
"entity_type": "gene"
},
{
"created": "2019-10-30T14:10:54.520663Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.24",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Classified gene: HNF4A as Amber List (moderate evidence)",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2019-10-30T14:10:54.517805Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.24",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Added comment: Comment on list classification: Promoting from red to amber. Only one paper (PMID: 24285859) reporting variants in this gene associated with Fanconi syndrome and nephrocalcinosis and all patients have the same variant. Another paper reports that individuals with that variant have congenital hyperinsulinism and Fanconi syndrome but no nephrocalcinosis, however they are younger than the previously reported patients. Rating amber for now until another report confirms the association.",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2019-10-30T14:10:54.503780Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.24",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Gene: hnf4a has been classified as Amber List (Moderate Evidence).",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2019-10-30T13:49:42.839822Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: FGF23: Leaving this gene red as no published evidence to date to associate variants in this gene with Nephrocalcinosis or nephrolithiasis. However, it is a likely contender so added the watchlist tag.",
"entity_name": "FGF23",
"entity_type": "gene"
},
{
"created": "2019-10-30T13:43:53.234512Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Tag watchlist tag was added to gene: FGF23.",
"entity_name": "FGF23",
"entity_type": "gene"
},
{
"created": "2019-10-30T13:00:45.336524Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: STRADA: Despite red rating from reviewer, there is some published evidence that nephrocalcinosis is reported in patients with Polyhydramnios, so keeping green rating for now.",
"entity_name": "STRADA",
"entity_type": "gene"
},
{
"created": "2019-10-30T12:56:49.378944Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: CLCN5",
"entity_name": "CLCN5",
"entity_type": "gene"
},
{
"created": "2019-10-30T11:59:52.401433Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "reviewed gene: ZNF365: Rating: RED; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: ",
"entity_name": "ZNF365",
"entity_type": "gene"
},
{
"created": "2019-10-30T11:59:52.390488Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "reviewed gene: VDR: Rating: RED; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: ",
"entity_name": "VDR",
"entity_type": "gene"
},
{
"created": "2019-10-30T11:59:52.379645Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "reviewed gene: TRPM6: Rating: RED; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: ",
"entity_name": "TRPM6",
"entity_type": "gene"
},
{
"created": "2019-10-30T11:59:52.368316Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "reviewed gene: STRADA: Rating: RED; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: ",
"entity_name": "STRADA",
"entity_type": "gene"
},
{
"created": "2019-10-30T11:59:52.357326Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "reviewed gene: SLC9A3: Rating: RED; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: ",
"entity_name": "SLC9A3",
"entity_type": "gene"
},
{
"created": "2019-10-30T11:59:52.346543Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "reviewed gene: SLC6A20: Rating: RED; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: ",
"entity_name": "SLC6A20",
"entity_type": "gene"
},
{
"created": "2019-10-30T11:59:52.335723Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "reviewed gene: SLC6A19: Rating: RED; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: ",
"entity_name": "SLC6A19",
"entity_type": "gene"
},
{
"created": "2019-10-30T11:59:52.324774Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "reviewed gene: SLC36A2: Rating: RED; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: ",
"entity_name": "SLC36A2",
"entity_type": "gene"
},
{
"created": "2019-10-30T11:59:52.312021Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "reviewed gene: GNA11: Rating: RED; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: ",
"entity_name": "GNA11",
"entity_type": "gene"
},
{
"created": "2019-10-30T11:59:52.301276Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "reviewed gene: CLCNKA: Rating: RED; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: ",
"entity_name": "CLCNKA",
"entity_type": "gene"
},
{
"created": "2019-10-30T11:59:52.289917Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "reviewed gene: AP2S1: Rating: RED; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: ",
"entity_name": "AP2S1",
"entity_type": "gene"
},
{
"created": "2019-10-30T11:59:52.278594Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "reviewed gene: AGK: Rating: RED; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: ",
"entity_name": "AGK",
"entity_type": "gene"
},
{
"created": "2019-10-30T11:59:52.265586Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "reviewed gene: ADCY10: Rating: RED; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: ",
"entity_name": "ADCY10",
"entity_type": "gene"
},
{
"created": "2019-10-30T11:59:52.254810Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "reviewed gene: HNF4A: Rating: AMBER; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: ",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2019-10-30T11:59:52.243844Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "reviewed gene: SLC2A9: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: ",
"entity_name": "SLC2A9",
"entity_type": "gene"
},
{
"created": "2019-10-30T11:59:52.232327Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "reviewed gene: SLC22A12: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal",
"entity_name": "SLC22A12",
"entity_type": "gene"
},
{
"created": "2019-10-30T11:59:52.220950Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "reviewed gene: PHEX: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: ",
"entity_name": "PHEX",
"entity_type": "gene"
},
{
"created": "2019-10-30T11:59:52.209967Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "reviewed gene: HPRT1: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: ",
"entity_name": "HPRT1",
"entity_type": "gene"
},
{
"created": "2019-10-30T11:59:52.198491Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "reviewed gene: FGF23: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: ",
"entity_name": "FGF23",
"entity_type": "gene"
},
{
"created": "2019-10-30T11:59:52.187351Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.23",
"user_name": "Detlef Bockenhauer",
"item_type": "entity",
"text": "reviewed gene: FAM20A: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: ",
"entity_name": "FAM20A",
"entity_type": "gene"
},
{
"created": "2019-10-21T04:46:30.036190Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.22",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "changed review comment from: Associated with Hypophosphatemic rickets, X-linked dominant (#307800)(XLD) in OMIM. \r\n\r\nPMID: 31514490 - Şıklar et al 2019 - From 24 centers in Turkey, 166 patients with Hypophosphatemic rickets were included in the study data. Genetic analysis (n:75) showed PHEX mutation in 80% patients (60 patients). 27 patients developed nephrocalcinosis. However, higher treatment dose of phosphate and calcitriol has been detected in nephrocalcinosis group. \r\n\r\nPMID: 29460029 - Chesher et al 2018 - clinical records of 59 adult patients from 35 kindreds with X-linked hypophosphatemia attending a single inherited metabolic disease service from 1998 were retrospectively reviewed. All had PHEX mutations (either directly obtained or inferred from the result of a first degree relative). 37 distinct variants were identified (14 not previously reported). Nephrocalcinosis was reported in 16/38 patients (42%) with at least one renal ultrasound performed. Treatment with vitamin D was associated with a small increase in urine calcium but there was no association between the presence or absence of nephrocalcinosis and whether or not the patient was currently being treated with vitamin D. \r\n\r\nWill consult with Genomics England Clinical team with regards to nephrocalcinosis being associated with PHEX variants or a result of treatment for Hypophosphatemic rickets.; to: Associated with Hypophosphatemic rickets, X-linked dominant (#307800)(XLD) in OMIM. \r\n\r\nPMID: 31514490 - Şıklar et al 2019 - Study of 166 patients with Hypophosphatemic rickets from 24 centers in Turkey. Genetic analysis (n:75) showed PHEX mutation in 80% patients (60 patients). 27 patients developed nephrocalcinosis. However, higher treatment dose of phosphate and calcitriol has been detected in nephrocalcinosis group. \r\n\r\nPMID: 29460029 - Chesher et al 2018 - clinical records of 59 adult patients from 35 kindreds with X-linked hypophosphatemia attending a single inherited metabolic disease service from 1998 were retrospectively reviewed. All had PHEX mutations (either directly obtained or inferred from the result of a first degree relative). 37 distinct variants were identified (14 not previously reported). Nephrocalcinosis was reported in 16/38 patients (42%) with at least one renal ultrasound performed. Treatment with vitamin D was associated with a small increase in urine calcium but there was no association between the presence or absence of nephrocalcinosis and whether or not the patient was currently being treated with vitamin D. \r\n\r\nWill consult with Genomics England Clinical team with regards to nephrocalcinosis being associated with PHEX variants or a result of treatment for Hypophosphatemic rickets.",
"entity_name": "PHEX",
"entity_type": "gene"
},
{
"created": "2019-10-21T01:00:48.747970Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.22",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: HNF4A",
"entity_name": "HNF4A",
"entity_type": "gene"
},
{
"created": "2019-10-21T00:36:40.798671Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.22",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: FGF23",
"entity_name": "FGF23",
"entity_type": "gene"
},
{
"created": "2019-10-21T00:20:17.954449Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.22",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "gene: FGF23 was added\ngene: FGF23 was added to Nephrocalcinosis or nephrolithiasis. Sources: Expert list\nMode of inheritance for gene: FGF23 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown",
"entity_name": "FGF23",
"entity_type": "gene"
},
{
"created": "2019-10-21T00:17:17.999044Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.21",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "reviewed gene: PHEX: Rating: ; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)",
"entity_name": "PHEX",
"entity_type": "gene"
},
{
"created": "2019-10-20T23:52:36.840636Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.21",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "gene: PHEX was added\ngene: PHEX was added to Nephrocalcinosis or nephrolithiasis. Sources: Expert list,Literature\nMode of inheritance for gene: PHEX was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females",
"entity_name": "PHEX",
"entity_type": "gene"
},
{
"created": "2019-10-20T23:43:17.189507Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.20",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "changed review comment from: Provisional association with {Nephrolithiasis, uric acid, susceptibility to} #605990 in OMIM. \r\nPubMed search did not find any further papers beyond the association study of 2003 (PMID: 12740763)\r\nKeep red rating.; to: Provisional association with {Nephrolithiasis, uric acid, susceptibility to} #605990 in OMIM. \r\nPubMed search did not find any further papers beyond the study of 2003 (PMID: 12740763)\r\nKeep red rating.",
"entity_name": "ZNF365",
"entity_type": "gene"
},
{
"created": "2019-10-20T23:42:57.651028Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.20",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: ZNF365",
"entity_name": "ZNF365",
"entity_type": "gene"
},
{
"created": "2019-10-20T23:35:47.289349Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.20",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: TRPM6",
"entity_name": "TRPM6",
"entity_type": "gene"
},
{
"created": "2019-10-20T22:35:43.720136Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.20",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: STRADA",
"entity_name": "STRADA",
"entity_type": "gene"
},
{
"created": "2019-10-20T21:46:54.024236Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.20",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "changed review comment from: Associated with Hypouricemia, renal, 2\t#612076\t(AD, AR) in OMIM. \r\n\r\nPMID: 19926891 - Dinour et al 2010 - studied two unrelated consanguineous families who had severe hereditary hypouricemia and did not have a URAT1 defect. Both families had homozygous SLC2A9 mutations: A missense mutation (L75R) in six affected members of one family and a 36-kb deletion, resulting in a truncated protein, in the other. Nephrolithiasis was seen in some members of both families. \r\n\r\nPMID: 21256783 - Stiburkova et al 2011 - proband and her brother from a Czech family with renal hypouricemia have a one nucleotide homozygote insertion in exon 3 in the SLC2A9 gene resulting in a truncated protein (p.Ile118HisfsX27). The brother showed urolithiasis. \r\n\r\nPMID: 19026395 - Matsuo et al 2008 - report two loss-of-function heterozygous mutations in GLUT9 (SLC2A9) in renal hypouricemic patients who have no URAT1 mutations (R380W and R198C) but it is not reported whether they have Nephrocalcinosis/nephrolithiasis.\r\nPMID: 21810765 - 2 cases renal hypouricemia and variants in SLC2A9 - no nephrolithiasis reported\r\nPMID: 29486147 - 2 cases with renal hypouricemia and variants in SLC2A9 - no nephrolithiasis reported\r\nPMID: 27116386 - 1 case renal hypouricemia and with variant in SLC2A9 - no nephrolithiasis reported; to: Associated with Hypouricemia, renal, 2\t#612076\t(AD, AR) in OMIM. \r\n\r\nPMID: 19926891 - Dinour et al 2010 - studied two unrelated consanguineous families who had severe hereditary hypouricemia and did not have a URAT1 defect. Both families had homozygous SLC2A9 mutations: A missense mutation (L75R) in six affected members of one family and a 36-kb deletion, resulting in a truncated protein, in the other. Nephrolithiasis was seen in some members of both families. \r\n\r\nPMID: 21256783 - Stiburkova et al 2011 - proband and her brother from a Czech family with renal hypouricemia have a one nucleotide homozygote insertion in exon 3 in the SLC2A9 gene resulting in a truncated protein (p.Ile118HisfsX27). The brother showed urolithiasis. \r\n\r\nPMID: 19026395 - Matsuo et al 2008 - report two loss-of-function heterozygous mutations in GLUT9 (SLC2A9)(R380W and R198C) in renal hypouricemic patients who have no URAT1 mutations but it is not reported whether they have Nephrocalcinosis/nephrolithiasis.\r\nPMID: 21810765 - 2 cases renal hypouricemia and variants in SLC2A9 - no nephrolithiasis reported\r\nPMID: 29486147 - 2 cases with renal hypouricemia and variants in SLC2A9 - no nephrolithiasis reported\r\nPMID: 27116386 - 1 case with renal hypouricemia and variant in SLC2A9 - no nephrolithiasis reported\r\nPMID: 24940677 - 1 case with renal hypouricaemia and variant in SLC2A9 - no mention of nepthrolithiasis\r\n\r\nSummary, clear association of variants in SLC2A9 with renal hypouricaemia . 3 cases reported with nepthrolithiasis/urothilthiasis but many more cases where it is not mentioned. ",
"entity_name": "SLC2A9",
"entity_type": "gene"
},
{
"created": "2019-10-20T21:08:30.650893Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.20",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: SLC2A9",
"entity_name": "SLC2A9",
"entity_type": "gene"
},
{
"created": "2019-10-20T15:09:18.281556Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.20",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "edited their review of gene: SLC22A12: Changed publications: 29486147, 29958533, 18492088, 15912381; Changed mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal",
"entity_name": "SLC22A12",
"entity_type": "gene"
},
{
"created": "2019-10-20T15:08:25.822190Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.20",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: SLC22A12",
"entity_name": "SLC22A12",
"entity_type": "gene"
},
{
"created": "2019-10-20T13:12:55.682744Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.20",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "changed review comment from: Associated with HPRT-related gout #300323\t(XLR) and Lesch-Nyhan syndrome\t#300322\t(XLR) in OMIM, both of which have Nephrolithiasis listed as a clinical feature. \r\n\r\nHPRT encodes the Hypoxanthine-guanine phosphoribosyltransferase enzyme. Partial deficiency can result in the overproduction of uric acid leading to a severe form of gout, whilst a virtual absence of HPRT activity causes the Lesch-Nyhan syndrome. \r\n\r\nPMID: 31129767 - Cho et al 2019 - studied 26 Korean LNS patients from 23 unrelated families. Twenty one of the 23 LNS patients with available data (91.3%) showed renal manifestations such as hyperuricemia, nephrocalcinosis, or urinary stones. 16 patients from 13 families had nephrocalcinosis. Twenty different mutations in HPRT1 were identified from the 23 independent pedigrees. \r\n\r\nPMID: 27079129 - Vargiami E et al 2016 - report of two cousins with Lesch-Nyhan syndrome and a confirmed novel HPRT gene mutation: c.65T>C, who both developed nephrocalcinosis and renal failure, findings not been previously published in children with HPRT deficiency.; to: Associated with HPRT-related gout #300323\t(XLR) and Lesch-Nyhan syndrome\t#300322\t(XLR) in OMIM, both of which have Nephrolithiasis listed as a clinical feature. \r\n\r\nHPRT encodes the Hypoxanthine-guanine phosphoribosyltransferase enzyme. Partial deficiency can result in the overproduction of uric acid leading to a severe form of gout, whilst a virtual absence of HPRT activity causes Lesch-Nyhan syndrome. \r\n\r\nPMID: 31129767 - Cho et al 2019 - studied 26 Korean LNS patients from 23 unrelated families. Twenty one of the 23 LNS patients with available data (91.3%) showed renal manifestations such as hyperuricemia, nephrocalcinosis, or urinary stones. 16 patients from 13 families had nephrocalcinosis. Twenty different mutations in HPRT1 were identified from the 23 independent pedigrees. \r\n\r\nPMID: 27079129 - Vargiami E et al 2016 - report of two cousins with Lesch-Nyhan syndrome and a confirmed novel HPRT gene mutation: c.65T>C, who both developed nephrocalcinosis and renal failure, findings not been previously published in children with HPRT deficiency.",
"entity_name": "HPRT1",
"entity_type": "gene"
},
{
"created": "2019-10-19T17:28:16.839440Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.20",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: HPRT1",
"entity_name": "HPRT1",
"entity_type": "gene"
},
{
"created": "2019-10-17T22:30:11.844625Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.20",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Publications for gene: FAM20A were set to ",
"entity_name": "FAM20A",
"entity_type": "gene"
},
{
"created": "2019-10-17T22:29:17.299123Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.19",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Phenotypes for gene: FAM20A were changed from to Amelogenesis imperfecta, type IG (enamel-renal syndrome) 204690",
"entity_name": "FAM20A",
"entity_type": "gene"
},
{
"created": "2019-10-17T22:28:39.694249Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.18",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "changed review comment from: Associated with Amelogenesis imperfecta, type IG (enamel-renal syndrome) (#204690)(AR) in OMIM and AMELOGENESIS IMPERFECTA AND GINGIVAL FIBROMATOSIS SYNDROME (confirmed, biallelic) in Gene2Phenotype. \r\n\r\nPMID: 23468644 - Wang et al 2013 - Characterized three families (from the Carribean, Jordan and Iran) with amelogenesis imperfecta and gingival fibromatosis syndrome (AIGFS) and identified, in each case, recessive FAM20A mutations with different variants in each family. Significantly, a kidney ultrasound of the family 2 proband revealed nephrocalcinosis, revising the diagnosis from AIGFS to Enamel-renal syndrome. Ultrasounds were not possible to obtain from families 1 and 3. \r\n\r\nPMID: 30394349 - Dourado et al 2018 - investigated ERS characteristics in 11 patients from 5 Brazilian families. \r\n All showed hypoplastic amelogenesis imperfecta, microdontia, intra-pulpal calcification, impacted posterior teeth with hyperplastic pericoronal follicles, gingival fibromatosis, ectopic calcifications on gingival and pericoronal tissues, and nephrocalcinosis. A biallelic loss of function variant in FAM20A [NG_029809.1: c.1447delG; p.(Glu483Lysfs*24)], was detected in all patients, strongly suggesting a founder effect.\r\n\r\nPMID: 28298625 - Kantaputra et al 2017 (Abstract only accessed) - report three patients and their families with findings suggestive of Enamel-renal-gingival syndrome. Mutation analysis of FAM20A was performed in all patients and their family members. Patients with homozygous frameshift and compound heterozygous mutations in FAM20A had typical clinical findings along with periodontitis. The other had a novel homozygous missense mutation in exon 10, mild gingival fibromatosis and renal calcifications.\r\n\r\nPMID: 22732358 - Vogel et al 2012 - two-thirds of Fam20a–/– mice had small kidneys with pitted surfaces, which showed widespread calcification (as well as a dental phenotype)\r\n\r\n3 independent cases with nephrocalcinosis plus mouse knockout data. Not full penetrance for the renal phenotype.; to: Associated with Amelogenesis imperfecta, type IG (enamel-renal syndrome) (#204690)(AR) in OMIM and AMELOGENESIS IMPERFECTA AND GINGIVAL FIBROMATOSIS SYNDROME (confirmed, biallelic) in Gene2Phenotype. \r\n\r\nPMID: 23468644 - Wang et al 2013 - Characterized three families (from the Caribbean, Jordan and Iran) with amelogenesis imperfecta and gingival fibromatosis syndrome (AIGFS) and identified, in each case, recessive FAM20A mutations with different variants in each family. Significantly, a kidney ultrasound of the family 2 proband revealed nephrocalcinosis, revising the diagnosis from AIGFS to Enamel-renal syndrome. Ultrasounds were not possible to obtain from families 1 and 3. \r\n\r\nPMID: 30394349 - Dourado et al 2018 - investigated ERS characteristics in 11 patients from 5 Brazilian families. \r\n All showed hypoplastic amelogenesis imperfecta, microdontia, intra-pulpal calcification, impacted posterior teeth with hyperplastic pericoronal follicles, gingival fibromatosis, ectopic calcifications on gingival and pericoronal tissues, and nephrocalcinosis. A biallelic loss of function variant in FAM20A [NG_029809.1: c.1447delG; p.(Glu483Lysfs*24)], was detected in all patients, strongly suggesting a founder effect.\r\n\r\nPMID: 28298625 - Kantaputra et al 2017 (Abstract only accessed) - report three patients and their families with findings suggestive of Enamel-renal-gingival syndrome. Mutation analysis of FAM20A was performed in all patients and their family members. Patients with homozygous frameshift and compound heterozygous mutations in FAM20A had typical clinical findings along with periodontitis. The other had a novel homozygous missense mutation in exon 10, mild gingival fibromatosis and renal calcifications.\r\n\r\nPMID: 22732358 - Vogel et al 2012 - two-thirds of Fam20a–/– mice had small kidneys with pitted surfaces, which showed widespread calcification (as well as a dental phenotype)\r\n\r\n3 independent cases with nephrocalcinosis plus mouse knockout data. Not full penetrance for the renal phenotype.",
"entity_name": "FAM20A",
"entity_type": "gene"
},
{
"created": "2019-10-17T22:28:01.679296Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.18",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: FAM20A",
"entity_name": "FAM20A",
"entity_type": "gene"
},
{
"created": "2019-10-10T16:11:13.504822Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.18",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: CLCNKA",
"entity_name": "CLCNKA",
"entity_type": "gene"
},
{
"created": "2019-10-10T16:04:56.777623Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.18",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "commented on gene: ADCY10",
"entity_name": "ADCY10",
"entity_type": "gene"
},
{
"created": "2019-09-17T20:55:27.165410Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.18",
"user_name": "Eleanor Williams",
"item_type": "panel",
"text": "List of related panels changed from Renal tract calcification (or Nephrolithiasis or nephrocalcinosis); Renal tract calcification (or Nephrolithiasis/nephrocalcinosis) to Renal tract calcification (or Nephrolithiasis or nephrocalcinosis); Renal tract calcification (or Nephrolithiasis/nephrocalcinosis); R256",
"entity_name": null,
"entity_type": null
},
{
"created": "2019-01-30T13:52:59.346675Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.17",
"user_name": "Eleanor Williams",
"item_type": "entity",
"text": "Phenotypes for gene: BSND were changed from Bartter Syndrome; Bartter syndrome, type 4a, 602522Sensorineural deafness with mild renal dysfunction, 602522 to Bartter Syndrome; Bartter syndrome, type 4a, 602522; Sensorineural deafness with mild renal dysfunction, 602522",
"entity_name": "BSND",
"entity_type": "gene"
},
{
"created": "2018-11-16T14:47:39.299653Z",
"panel_name": "Nephrocalcinosis or nephrolithiasis",
"panel_id": 149,
"panel_version": "1.15",
"user_name": "Ellen McDonagh",
"item_type": "panel",
"text": "Panel name changed from Renal tract calcification (or Nephrolithiasis/nephrocalcinosis) to Nephrocalcinosis or nephrolithiasis\nList of related panels changed from Renal tract calcification (or Nephrolithiasis or nephrocalcinosis) to Renal tract calcification (or Nephrolithiasis or nephrocalcinosis); Renal tract calcification (or Nephrolithiasis/nephrocalcinosis)\nPanel types changed to Rare Disease 100K; GMS Rare Disease",
"entity_name": null,
"entity_type": null
},
{
"created": "2018-07-16T10:20:29.314953Z",
"panel_name": "Renal tract calcification (or Nephrolithiasis/nephrocalcinosis)",
"panel_id": 149,
"panel_version": null,
"user_name": "Louise Daugherty",
"item_type": "entity",
"text": "classified STRADA as Green List (high evidence)",
"entity_name": "STRADA",
"entity_type": "gene"
},
{
"created": "2018-07-16T10:20:19.387388Z",
"panel_name": "Renal tract calcification (or Nephrolithiasis/nephrocalcinosis)",
"panel_id": 149,
"panel_version": null,
"user_name": "Louise Daugherty",
"item_type": "entity",
"text": "Added gene to panel",
"entity_name": "STRADA",
"entity_type": "gene"
},
{
"created": "2017-09-22T09:22:50.594000Z",
"panel_name": "Renal tract calcification (or Nephrolithiasis/nephrocalcinosis)",
"panel_id": 149,
"panel_version": null,
"user_name": "Louise Daugherty",
"item_type": "entity",
"text": "reviewed XDH",
"entity_name": "XDH",
"entity_type": "gene"
},
{
"created": "2017-03-31T22:54:36.258000Z",
"panel_name": "Renal tract calcification (or Nephrolithiasis/nephrocalcinosis)",
"panel_id": 149,
"panel_version": null,
"user_name": "Ellen McDonagh",
"item_type": "entity",
"text": "commented on TRPM6",
"entity_name": "TRPM6",
"entity_type": "gene"
},
{
"created": "2017-03-31T22:52:15.036000Z",
"panel_name": "Renal tract calcification (or Nephrolithiasis/nephrocalcinosis)",
"panel_id": 149,
"panel_version": null,
"user_name": "Ellen McDonagh",
"item_type": "entity",
"text": "classified TRPM6 as green",
"entity_name": "TRPM6",
"entity_type": "gene"
},
{
"created": "2017-03-21T11:37:08.992000Z",
"panel_name": "Renal tract calcification (or Nephrolithiasis/nephrocalcinosis)",
"panel_id": 149,
"panel_version": null,
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "classified XDH as green",
"entity_name": "XDH",
"entity_type": "gene"
},
{
"created": "2017-03-21T11:37:08.991000Z",
"panel_name": "Renal tract calcification (or Nephrolithiasis/nephrocalcinosis)",
"panel_id": 149,
"panel_version": null,
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "commented on XDH",
"entity_name": "XDH",
"entity_type": "gene"
},
{
"created": "2017-03-15T15:34:12.056000Z",
"panel_name": "Renal tract calcification (or Nephrolithiasis/nephrocalcinosis)",
"panel_id": 149,
"panel_version": null,
"user_name": "Ellen McDonagh",
"item_type": "entity",
"text": "commented on TRPM6",
"entity_name": "TRPM6",
"entity_type": "gene"
},
{
"created": "2017-02-28T09:58:13.152000Z",
"panel_name": "Renal tract calcification (or Nephrolithiasis/nephrocalcinosis)",
"panel_id": 149,
"panel_version": null,
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "classified APRT as green",
"entity_name": "APRT",
"entity_type": "gene"
},
{
"created": "2017-02-28T09:58:13.151000Z",
"panel_name": "Renal tract calcification (or Nephrolithiasis/nephrocalcinosis)",
"panel_id": 149,
"panel_version": null,
"user_name": "Sarah Leigh",
"item_type": "entity",
"text": "commented on APRT",
"entity_name": "APRT",
"entity_type": "gene"
}
]