ClinVar Miner

Submissions for variant NM_000053.4(ATP7B):c.3646G>A (p.Val1216Met) (rs776280797)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000169211 SCV000220467 likely pathogenic Wilson disease 2014-07-02 criteria provided, single submitter literature only
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000725176 SCV000334638 likely pathogenic not provided 2015-08-28 criteria provided, single submitter clinical testing
Fulgent Genetics,Fulgent Genetics RCV000169211 SCV000894014 likely pathogenic Wilson disease 2018-10-31 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000169211 SCV001158551 likely pathogenic Wilson disease 2019-06-13 criteria provided, single submitter clinical testing The ATP7B c.3646G>A; p.Val1216Met variant (rs776280797) is reported in the literature in multiple individuals affected with Wilson disease (Haas 1999, Liu 2004, Loudianos 1998, Mak 2008, Margarit 2005, Qian 2019). Multiple affected individuals with this variant were also found to carry an additional pathogenic variant (Liu 2004, Margarit 2005, Qian 2019). The p.Val1216Met variant is found in the general population with the low overall allele frequency of 0.01% (24/280998 alleles) in the Genome Aggregation Database, and it is reported as likely pathogenic by multiple laboratories in ClinVar (Variation ID: 188859). The valine at codon 1216 is highly conserved, occurs in the functionally important ATP-binding loop (Loudianos 1998, Mak 2008), and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Based on available information, this variant is considered to be likely pathogenic. References: Haas R et al. Mutation analysis in patients with Wilson disease: identification of 4 novel mutations. Mutation in brief no. 250. Online. Hum Mutat. 1999;14(1):88. Liu XQ et al. Correlation of ATP7B genotype with phenotype in Chinese patients with Wilson disease. World J Gastroenterol. 2004 Feb 15;10(4):590-3. Loudianos G et al. Further delineation of the molecular pathology of Wilson disease in the Mediterranean population. Hum Mutat. 1998;12(2):89-94. Mak CM et al. Mutational analysis of 65 Wilson disease patients in Hong Kong Chinese: identification of 17 novel mutations and its genetic heterogeneity. J Hum Genet. 2008;53(1):55-63. Margarit E et al. Mutation analysis of Wilson disease in the Spanish population -- identification of a prevalent substitution and eight novel mutations in the ATP7B gene. Clin Genet. 2005 Jul;68(1):61-8. Qian Z et al. Novel mutations found in the ATP7B gene in Chinese patients with Wilson's disease. Mol Genet Genomic Med. 2019 May;7(5):e649.
Baylor Genetics RCV000169211 SCV001163728 pathogenic Wilson disease criteria provided, single submitter clinical testing
Invitae RCV000169211 SCV001234718 pathogenic Wilson disease 2020-08-20 criteria provided, single submitter clinical testing This sequence change replaces valine with methionine at codon 1216 of the ATP7B protein (p.Val1216Met). The valine residue is highly conserved and there is a small physicochemical difference between valine and methionine. This variant is present in population databases (rs776280797, ExAC 0.03%). This variant has been observed in several individuals affected with Wilson disease (PMID: 10447265, 14966923, 15952988, 26253413). ClinVar contains an entry for this variant (Variation ID: 188859). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: Deleterious; PolyPhen-2: Probably Damaging; Align-GVGD: Class C0). For these reasons, this variant has been classified as Pathogenic.

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