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Unexplained kidney failure in young people v1.122 SIX5 Arina Puzriakova Phenotypes for gene: SIX5 were changed from Branchiootorenal syndrome 2, 610896 to Branchiootorenal syndrome 2, OMIM:610896
Unexplained kidney failure in young people v1.121 SIX5 Arina Puzriakova Added comment: Comment on list classification: This gene-disease association has been rated as 'DISPUTED' by ClinGen (https://search.clinicalgenome.org/CCID:006145) Multiple families reported but reported variants are high in frequency in population databases, have no evidence of pathogenicity, and/or an alternate cause of disease has later been reported (21280147). Two independent SIX5 mouse models have cataracts and no ear or kidney abnormalities (10802667, 10802668) which are typical of branchio-oto-renal syndrome.

As the evidence for the association of SIX5 with branchio-oto-renal syndrome is disputed, downgraded this gene from Green to Red.
Unexplained kidney failure in young people v1.120 VIPAS39 Arina Puzriakova Phenotypes for gene: VIPAS39 were changed from Arthrogryposis, renal dysfunction, and cholestasis 2, 613404 to Arthrogryposis, renal dysfunction, and cholestasis 2, OMIM:613404; ARC syndrome
Unexplained kidney failure in young people v1.117 COX10 Arina Puzriakova Phenotypes for gene: COX10 were changed from Encephalopathy, progressive mitochondrial, with proximal renal tubulopathy due tocytochrome c oxidase deficiency to Mitochondrial complex IV deficiency, nuclear type 3, OMIM:619046; Encephalopathy, progressive mitochondrial, with proximal renal tubulopathy due tocytochrome c oxidase deficiency
Unexplained kidney failure in young people v1.113 CFHR5 Eleanor Williams Phenotypes for gene: CFHR5 were changed from Haematuria; C3 glomerulopathy; kidney failure; macroscopic haematuria to C3 glomerulopathy; C3G; Immune complex MPGN; IC-MPGN; Nephropathy due to CFHR5 deficiency, OMIM:614809; Immune-complex-mediated MPGN; CFHR5 nephropathy; Haematuria; Chronic Kidney Disease; Proteinuria; End stage renal disease
Unexplained kidney failure in young people v1.111 CFHR5 Eleanor Williams Added comment: Comment on list classification: Promoting to green in light of external review and the fact that it is already green on the 'Unexplained paediatric onset end-stage renal disease' panel.
Unexplained kidney failure in young people v1.108 CFI Sarah Leigh changed review comment from: Renal insufficiency, glomerulonephritis and pyelonephritis has been reported in Complement factor I deficiency (OMIM:610984)(PMID:17018561; 10352206), therefore it would be appropriate for the mode of inheritance to be changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to BOTH monoallelic and biallelic, autosomal or pseudoautosomal.; to: Renal insufficiency, glomerulonephritis and pyelonephritis has been reported in Complement factor I deficiency (OMIM:610984)(PMID:17018561; 10352206), therefore it would be appropriate for the mode of inheritance to be changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to BOTH monoallelic and biallelic, autosomal or pseudoautosomal on this panel.
Unexplained kidney failure in young people v1.106 CFI Sarah Leigh edited their review of gene: CFI: Added comment: Renal insufficiency, glomerulonephritis and pyelonephritis has been reported in Complement factor I deficiency (OMIM:610984)(PMID:17018561; 10352206), therefore it would be appropriate for the mode of inheritance to be changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to BOTH monoallelic and biallelic, autosomal or pseudoautosomal.; Changed publications to: 17018561, 10352206; Changed mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Unexplained kidney failure in young people v1.106 CFHR5 Daniel Gale reviewed gene: CFHR5: Rating: GREEN; Mode of pathogenicity: Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments; Publications: PMID: 20800271, 21566112, 30844074, 28729035, 32928961, 24067434, 27490940, 33753502, 30197990, 24067434; Phenotypes: Haematuria, C3 glomerulopathy, Chronic Kidney Disease, Proteinuria, End stage renal disease; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Unexplained kidney failure in young people v1.91 SARS2 Sarah Leigh Added comment: Comment on list classification: Associated with Hyperuricemia, pulmonary hypertension, renal failure, and alkalosis 613845 in OMIM, but not associated with phenotype in Gen2Phen. At least 3 variants reported in at least 3 unrelated cases, together with supportive functional studies and segregation with the phenotype.
Unexplained kidney failure in young people v1.90 SARS2 Sarah Leigh gene: SARS2 was added
gene: SARS2 was added to Unexplained kidney failure in young people. Sources: Literature
Mode of inheritance for gene: SARS2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SARS2 were set to 21255763; 24034276; 27279129
Phenotypes for gene: SARS2 were set to Hyperuricemia, pulmonary hypertension, renal failure, and alkalosis 613845; Progressive Spastic Paresis
Review for gene: SARS2 was set to AMBER
Added comment: Sources: Literature
Unexplained kidney failure in young people v1.89 CD151 Eleanor Williams changed review comment from: Comment on list classification: Changing rating from red to amber as 2 cases have been reported with end stage renal disease, although the same variant is reported and the families are from the same ethnic origin.; to: Comment on list classification: Changing rating from red to amber as 2 cases have been reported with end stage renal disease, although the same variant is reported and the families are from the same ethnic origin. Also the presentation is syndromic so end-stage renal disease is unlikely to be the only phenotype picked up.
Unexplained kidney failure in young people v1.85 CD151 Eleanor Williams Added comment: Comment on list classification: Changing rating from red to amber as 2 cases have been reported with end stage renal disease, although the same variant is reported and the families are from the same ethnic origin.
Unexplained kidney failure in young people v1.84 CD151 Eleanor Williams changed review comment from: Associated with Nephropathy with pretibial epidermolysis bullosa and deafness #609057 in OMIM.

The 3 patients from 2 families described in PMID: 15265795 - Karamatic Crew et al 2004 all had end-stage kidney disease and homozygous insertion in the CD151 gene. Although they are described as unrelated both families are of Indian Jewish origin.; to: Associated with Nephropathy with pretibial epidermolysis bullosa and deafness #609057 in OMIM.

The 3 patients from 2 families described in PMID: 15265795 - Karamatic Crew et al 2004 all had end-stage kidney disease and homozygous insertion in the CD151 gene. Although they are described as unrelated both families are of Indian Jewish origin. The ages of the patients are not reported.

Another case is described in PMID: 29138120 - Vahidnezhad et al 2018 where the patient had history of nephropathy with proteinuria.

PMID: 17015618 - Sachs et al 2006 - report the generation of Cd151-null mice that recapitulate the renal pathology of human patients, i.e., with age they develop massive proteinuria
Unexplained kidney failure in young people v1.84 VIPAS39 Rebecca Foulger Added comment: Comment on list classification: Updated rating from Red to Green following review by Zornitza Stark, and curation of PMID:20190753. Sufficient (>3) cases of ARC being caused by VIPAS39 variants in PMID:20190753. Although only one paper, the patients are from multiple ethnicities and functional studies support the phenotype: VIPAS39 & VPS33B form a complex, and have roles in apical junction formation. Variants in VPS33B cause 'Arthrogryposis, renal dysfunction, and cholestasis 1, MIM:208085', and VPS33B is Green on this panel. VIPAS39-ARC also has a Confirmed Disease confidence in Gene2Phenotype.
Unexplained kidney failure in young people v1.82 VIPAS39 Zornitza Stark reviewed gene: VIPAS39: Rating: GREEN; Mode of pathogenicity: None; Publications: 20190753; Phenotypes: Arthrogryposis, renal dysfunction, and cholestasis 2, MIM# 613404; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Unexplained kidney failure in young people v1.80 FAN1 Eleanor Williams Added comment: Comment on list classification: Downgrading from green to amber while consulting with the Genomics England clinical team as to the suitability of this gene as the age of onset for renal disease is from 30 year old onwards.
Unexplained kidney failure in young people v1.78 FAN1 Eleanor Williams changed review comment from: FAN1 associated with Interstitial nephritis, karyomegalic #614817 (AR) in OMIM.

PMID: 22772369 - Zhou et al 2012 - 9 unrelated families with karyomegalic interstitial nephritis which can result in Chronic kidney disease. They identified 12 different homozygous or compound heterozygous mutations in the FAN1 gene. Eight of the 12 mutations resulted in a truncated protein. (Summary from OMIM).

Sufficient cases with likely disease causing mutations to rate this gene green. ; to: FAN1 associated with Interstitial nephritis, karyomegalic #614817 (AR) in OMIM.

PMID: 22772369 - Zhou et al 2012 - 9 unrelated families with karyomegalic interstitial nephritis which can result in Chronic kidney disease. They identified 12 different homozygous or compound heterozygous mutations in the FAN1 gene. Eight of the 12 mutations resulted in a truncated protein. (Summary from OMIM). End-stage kidney failure ensued by a median age of 45 years in the 12 individuals with KIN and FAN1 mutations.

Sufficient cases with likely disease causing mutations to rate this gene green.
Unexplained kidney failure in young people v1.77 APRT Eleanor Williams Added comment: Comment on list classification: There are more than 3 cases where homozygous or compound heterozygous variants in APRT have been reported in patients with Adenine phosphoribosyltransferase deficiency. PMID: 30106368 and PMID: 25307253 report cases in which end-stage renal disease has been observed under the age of 50.
Unexplained kidney failure in young people v1.76 APRT Eleanor Williams Phenotypes for gene: APRT were changed from interstitial nephritis; chronic kidney disease; end stage renal disease; nephrolithiaisis to interstitial nephritis; chronic kidney disease; end stage renal disease; nephrolithiaisis; Adenine phosphoribosyltransferase deficiency 614723
Unexplained kidney failure in young people v1.74 APRT John Sayer gene: APRT was added
gene: APRT was added to Unexplained kidney failure in young people. Sources: Expert list
Mode of inheritance for gene: APRT was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: APRT were set to 30355577
Phenotypes for gene: APRT were set to interstitial nephritis; chronic kidney disease; end stage renal disease; nephrolithiaisis
Penetrance for gene: APRT were set to Complete
Review for gene: APRT was set to GREEN
Added comment: Sources: Expert list
Unexplained kidney failure in young people v1.73 FAN1 Eleanor Williams changed review comment from: FAN1 associated with Interstitial nephritis, karyomegalic #614817 (AR) in OMIM.

PMID: 22772369 - Zhou et al 2012 - 9 unrelated families with karyomegalic interstitial nephritis which can result in Chronic kidney disease. They identified 12 different homozygous or compound heterozygous mutations in the FAN1 gene. Eight of the 12 mutations resulted in a truncated protein. (Summary from OMIM).

Sufficient cases with likely disease causing mutations to rate this gene green. ; to: FAN1 associated with Interstitial nephritis, karyomegalic #614817 (AR) in OMIM.

PMID: 22772369 - Zhou et al 2012 - 9 unrelated families with karyomegalic interstitial nephritis which can result in Chronic kidney disease. They identified 12 different homozygous or compound heterozygous mutations in the FAN1 gene. Eight of the 12 mutations resulted in a truncated protein. (Summary from OMIM).

Sufficient cases with likely disease causing mutations to rate this gene green.
Unexplained kidney failure in young people v1.73 FAN1 Eleanor Williams changed review comment from: FAN1 associated with Interstitial nephritis, karyomegalic #614817 (AR) in OMIM.

PMID: 22772369 - Zhou et al 2012 - 9 unrelated families with karyomegalic interstitial nephritis which can result in Chronic kidney disease. They identified 12 different homozygous or compound heterozygous mutations in the FAN1 gene. Eight of the 12 mutations resulted in a truncated protein. (Summary from OMIM).

Sufficient cases with likely disease causing mutations to rate this gene green.; to: FAN1 associated with Interstitial nephritis, karyomegalic #614817 (AR) in OMIM.

PMID: 22772369 - Zhou et al 2012 - 9 unrelated families with karyomegalic interstitial nephritis which can result in Chronic kidney disease. They identified 12 different homozygous or compound heterozygous mutations in the FAN1 gene. Eight of the 12 mutations resulted in a truncated protein. (Summary from OMIM).

Sufficient cases with likely disease causing mutations to rate this gene green.
Unexplained kidney failure in young people v1.73 Eleanor Williams Panel name changed from End-stage renal disease - childhood onset to Unexplained kidney failure in young people
List of related panels changed from Unexplained kidney failure in young people; Familial IgA nephropathy and IgA vasculitis; End-stage renal disease - childhood onset to Familial IgA nephropathy and IgA vasculitis; End-stage renal disease - childhood onset
Unexplained kidney failure in young people v1.72 Eleanor Williams List of related panels changed from Unexplained kidney failure in young people; Familial IgA nephropathy and IgA vasculitis to Unexplained kidney failure in young people; Familial IgA nephropathy and IgA vasculitis; End-stage renal disease - childhood onset
Unexplained kidney failure in young people v1.70 GLA Eleanor Williams Phenotypes for gene: GLA were changed from to renal insufficiency; renal failure; Fabry disease, 301500
Unexplained kidney failure in young people v1.68 GLA Eleanor Williams changed review comment from: This gene has been reviewed by Daniel Gale on the Unexplained paediatric onset end-stage renal disease panel 2019-05-08.; to: This gene has been reviewed by Daniel Gale on the Unexplained paediatric onset end-stage renal disease panel 2019-05-08. He states that "Fabry disease may present with renal limited disease, including presentation at end stage renal failure with no other clinical features (typically in young adults in their 20s). This has been repeatedly described in cohorts of people with kidney failure, ascertained either using biochemical or genetic screening."
Unexplained kidney failure in young people v1.68 GLA Eleanor Williams commented on gene: GLA: GLA is associated with Fabry disease (#301500) in OMIM

PMID: 28006774 - Turkmen et al 2016 - 3 out of 313 chronic kidney disease patients not receiving renal replacement therapy (0.95%) were diagnosed of Fabry disease by GLA gene mutation analysis. The age of the patients and their family members with Fabry disease ( total number =11) was 41.3 +/- 14.5.

PMID: 15861341 - Cybulla et al 2005 - describe a family presenting with chronic renal failure and proteinuria in which classic skin and neurological features were absent and the diagnosis of Fabry disease was difficult and not established until a second family member developed renal abnormalities. The index patient was 35 years old. Analysis of the alpha-GLA gene showed the mutation E66K. The mutation also was found in another asymptomatic 30-year-old brother who also had chronic renal failure and proteinuria, but normal extrarenal findings. Mutation carriers also included the mother, a sister (both without abnormalities), and a nephew (with episodic pains in his feet).

PMID: 15100373 - Kotanko et al 2004 - Nationwide screening of Anderson-Fabry disease among dialysis patients in Austria. Individuals with decreased leukocyte AGAL activity were subjected to mutation testing in the GLA gene, Genetic testing revealed mutations associated with Fabry disease in all four men with severely decreased AGAL activity resulting in a prevalence of 0.161% for the entire study population. Age at start of dialysis ranged from 27 to 53.
Unexplained kidney failure in young people v1.61 VPS33B Eleanor Williams Phenotypes for gene: VPS33B were changed from Arthrogryposis, renal dysfunction, and cholestasis 1 208085 to Arthrogryposis, renal dysfunction, and cholestasis 1 208085
Unexplained kidney failure in young people v1.50 SCARB2 Eleanor Williams Phenotypes for gene: SCARB2 were changed from Epilepsy, progressive myoclonic 4, with or without renal failure 254900 to Epilepsy, progressive myoclonic 4, with or without renal failure 254900
Unexplained kidney failure in young people v1.49 RRM2B Eleanor Williams Phenotypes for gene: RRM2B were changed from Mitochondrial DNA depletion syndrome 8A (encephalomyopathic type with renal tubulopathy) 612075; Mitochondrial DNA depletion syndrome 8B (MNGIE type) 612075 to Mitochondrial DNA depletion syndrome 8A (encephalomyopathic type with renal tubulopathy) 612075; Mitochondrial DNA depletion syndrome 8B (MNGIE type) 612075
Unexplained kidney failure in young people v1.24 BSND Eleanor Williams Phenotypes for gene: BSND were changed from Bartter syndrome, type 4a, 602522Sensorineural deafness with mild renal dysfunction, 602522 to Bartter syndrome, type 4a, 602522; Sensorineural deafness with mild renal dysfunction, 602522
Unexplained kidney failure in young people v1.20 Ellen McDonagh Panel name changed from Unexplained kidney failure in young people to End-stage renal disease - childhood onset
List of related panels changed from Familial IgA nephropathy and IgA vasculitis to Unexplained kidney failure in young people; Familial IgA nephropathy and IgA vasculitis
Panel types changed to Rare Disease 100K; GMS Rare Disease Virtual
Unexplained kidney failure in young people v1.15 ISCA-37432-Loss Louise Daugherty Region: ISCA-37432-Loss was added
Region: ISCA-37432-Loss was added to Unexplained kidney failure in young people. Sources: ClinGen,Expert Review Green
Mode of inheritance for Region: ISCA-37432-Loss was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for Region: ISCA-37432-Loss were set to RCAD syndrome; utero-vaginal atresia; Schizophrenia; 614527; delayed development, intellectual disability; Renal cysts and diabetes syndrome; Autism Spectrum Disorder; Mayer-Rokitansky-Kster-Hauser (MRKH) syndrome in females; Chromosome 17q12 deletion syndrome; global developmental delay
Unexplained kidney failure in young people REN Sarah Leigh marked REN as ready
Unexplained kidney failure in young people REN Sarah Leigh commented on REN