Activity
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21 actions
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| Cystic kidney disease v9.3 | CFAP47 | Achchuthan Shanmugasundram Mode of pathogenicity for gene: CFAP47 was changed from Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments to None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v9.2 | CFAP47 |
Ida Ertmanska changed review comment from: The association between CFAP47 and X-linked polycystic kidney disease was classified as Disputed on 02/10/2025 by the ClinGen Kidney Cystic and Ciliopathy Disorders Expert panel (see https://search.clinicalgenome.org/kb/gene-validity/CGGV:assertion_da276c83-09e0-428f-a58e-6cd3bf517d00-2025-02-10T170000.000Z). The disputing evidence relates to PMID:39698362 and includes "non-specific genetically heterogenous phenotype, missense variant with no convincing functional data" for the 3 male patients with polycystic kidney disease. 2/3 variants are common in gnomAD v4, with homozygous and numerous hemizygous individuals reported. The curation summary states that "the gene may be associated with a susceptibility phenotype that could manifest with age-dependent incomplete penetrance." There is also conflicting functional evidence: PMID: 36571501 describes a knockout 40-week-old mice model with "larger kidneys, cyst-like histological changes in the kidneys, including tubular cell vacuolation and dilatation, and they had significantly shorter cilia compared to wild types. However, another study published later reported that 10-week-old knockout mice showed no apparent histological kidney problems (PMID: 40473901)."; to: The association between CFAP47 and X-linked polycystic kidney disease was classified as Disputed on 02/10/2025 by the ClinGen Kidney Cystic and Ciliopathy Disorders Expert panel (see https://search.clinicalgenome.org/kb/gene-validity/CGGV:assertion_da276c83-09e0-428f-a58e-6cd3bf517d00-2025-02-10T170000.000Z). The disputing evidence relates to PMID:39698362 and includes "non-specific genetically heterogenous phenotype, missense variant with no convincing functional data" for the 3 male patients with polycystic kidney disease. 2/3 variants are common in gnomAD v4, with homozygous and numerous hemizygous individuals reported. The curation summary states that "the gene may be associated with a susceptibility phenotype that could manifest with age-dependent incomplete penetrance." There is also conflicting functional evidence: PMID: 36571501 describes a knockout 40-week-old mice model with "larger kidneys, cyst-like histological changes in the kidneys, including tubular cell vacuolation and dilatation, and they had significantly shorter cilia compared to wild types. However, another study published later reported that 10-week-old knockout mice showed no apparent histological kidney problems (PMID: 40473901)." - consistent with later onset? |
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| Cystic kidney disease v9.2 | CFAP47 |
Ida Ertmanska changed review comment from: The association between CFAP47 and X-linked polycystic kidney disease was classified as Disputed on 02/10/2025 by the ClinGen Kidney Cystic and Ciliopathy Disorders Expert panel (see https://search.clinicalgenome.org/kb/gene-validity/CGGV:assertion_da276c83-09e0-428f-a58e-6cd3bf517d00-2025-02-10T170000.000Z). The disputing evidence relates to PMID:39698362 and includes "non-specific genetically heterogenous phenotype, missense variant with no convincing functional data" for the 3 male patients with polycystic kidney disease. 2/3 variants are common in gnomAD v4, with homozygous and numerous hemizygous individuals reported. The curation summary states that "the gene may be associated with a susceptibility phenotype that could manifest with age-dependent incomplete penetrance." There is also conflicting functional evidence: PMID: 36401472, 36571501 describe a knockout 40-week-old mice model with "larger kidneys, cyst-like histological changes in the kidneys, including tubular cell vacuolation and dilatation, and they had significantly shorter cilia compared to wild types. However, another study published later reported that 10-week-old knockout mice showed no apparent histological kidney problems (PMID: 40473901)."; to: The association between CFAP47 and X-linked polycystic kidney disease was classified as Disputed on 02/10/2025 by the ClinGen Kidney Cystic and Ciliopathy Disorders Expert panel (see https://search.clinicalgenome.org/kb/gene-validity/CGGV:assertion_da276c83-09e0-428f-a58e-6cd3bf517d00-2025-02-10T170000.000Z). The disputing evidence relates to PMID:39698362 and includes "non-specific genetically heterogenous phenotype, missense variant with no convincing functional data" for the 3 male patients with polycystic kidney disease. 2/3 variants are common in gnomAD v4, with homozygous and numerous hemizygous individuals reported. The curation summary states that "the gene may be associated with a susceptibility phenotype that could manifest with age-dependent incomplete penetrance." There is also conflicting functional evidence: PMID: 36571501 describes a knockout 40-week-old mice model with "larger kidneys, cyst-like histological changes in the kidneys, including tubular cell vacuolation and dilatation, and they had significantly shorter cilia compared to wild types. However, another study published later reported that 10-week-old knockout mice showed no apparent histological kidney problems (PMID: 40473901)." |
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| Cystic kidney disease v9.2 | CFAP47 | Ida Ertmanska Tag Q3_26_expert_review tag was added to gene: CFAP47. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v9.2 | CFAP47 |
Ida Ertmanska Tag disputed tag was added to gene: CFAP47. Tag Q3_26_demote_red tag was added to gene: CFAP47. |
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| Cystic kidney disease v9.2 | CFAP47 | Ida Ertmanska changed review comment from: Comment on list classification: Based on conflicting and disputing evidence outlined in the ClinGen curation of evidence linking CFAP47 and X-linked polycystic kidney disease, the rating should be demoted to Red on this panel.; to: Comment on list classification: Based on conflicting and disputing evidence outlined in the ClinGen curation of evidence linking CFAP47 and X-linked polycystic kidney disease, the rating should be demoted to Red on this panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v9.2 | CFAP47 | Ida Ertmanska commented on gene: CFAP47: Comment on list classification: Based on conflicting and disputing evidence outlined in the ClinGen curation of evidence linking CFAP47 and X-linked polycystic kidney disease, the rating should be demoted to Red on this panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v9.2 | CFAP47 | Ida Ertmanska edited their review of gene: CFAP47: Changed rating: RED; Changed publications to: 39698362; Changed phenotypes to: polycystic kidney disease, MONDO:0020642; Changed mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v9.2 | CFAP47 | Ida Ertmanska commented on gene: CFAP47 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v8.8 | CFAP47 | Ida Ertmanska Tag gene-checked tag was added to gene: CFAP47. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v8.7 | CFAP47 | Arina Puzriakova Tag Q4_24_promote_green was removed from gene: CFAP47. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v8.7 | CFAP47 | Achchuthan Shanmugasundram commented on gene: CFAP47: The rating of this gene has been updated to green following NHS Genomic Medicine Service approval. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v8.6 | CFAP47 |
Arina Puzriakova Source NHS GMS was added to CFAP47. Source Expert Review Green was added to CFAP47. Rating Changed from Amber List (moderate evidence) to Green List (high evidence) |
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| Cystic kidney disease v7.10 | CFAP47 | Achchuthan Shanmugasundram Tag Q4_24_promote_green tag was added to gene: CFAP47. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v7.10 | CFAP47 | Achchuthan Shanmugasundram Classified gene: CFAP47 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v7.10 | CFAP47 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence available (three unrelated cases and functional work) for the promotion of this gene to green rating in the next GMS update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v7.10 | CFAP47 | Achchuthan Shanmugasundram Gene: cfap47 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v7.9 | CFAP47 | Achchuthan Shanmugasundram Phenotypes for gene: CFAP47 were changed from PKD to polycystic kidney disease, MONDO:0020642 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v7.8 | CFAP47 | Achchuthan Shanmugasundram Publications for gene: CFAP47 were set to PMID: 38633811 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v7.7 | CFAP47 | Achchuthan Shanmugasundram reviewed gene: CFAP47: Rating: GREEN; Mode of pathogenicity: None; Publications: 39698362; Phenotypes: polycystic kidney disease, MONDO:0020642; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v7.7 | CFAP47 |
Dmitrijs Rots gene: CFAP47 was added gene: CFAP47 was added to Cystic kidney disease. Sources: Literature Mode of inheritance for gene: CFAP47 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: CFAP47 were set to PMID: 38633811 Phenotypes for gene: CFAP47 were set to PKD Penetrance for gene: CFAP47 were set to unknown Mode of pathogenicity for gene: CFAP47 was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments Review for gene: CFAP47 was set to GREEN Added comment: Three cases & some functional work described in PMID: 38633811 (now published). Sources: Literature |
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