ClinVar Miner

Submissions for variant NM_144631.6(ZNF513):c.1015T>C (p.Cys339Arg)

gnomAD frequency: 0.00005  dbSNP: rs267607182
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000778613 SCV000914924 uncertain significance Retinitis Pigmentosa, Dominant 2017-10-20 criteria provided, single submitter clinical testing The ZNF513 c.1015T>C (p.Cys339Arg) variant has been reported in a homozygous state in four siblings from a consanguineous family with retinitis pigmentosa (Li et al. 2010). The unaffected parents and three unaffected siblings were heterozygous for this variant. This variant was absent from 242 control chromosomes, but is reported at a frequency of 0.001637 in the South Asian population from the Exome Aggregation Consortium. In zebrafish, the p.Cys339Arg variant showed reduced rescue of retinal phenotype compared to wildtype (31% vs. 86%). The evidence for this variant is limited, therefore the p.Cys339Arg variant is classified as a variant of unknown significance but is suspicious for pathogenicity for autosomal recessive retinitis pigmentosa. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Invitae RCV001239265 SCV001412123 uncertain significance not provided 2023-11-07 criteria provided, single submitter clinical testing This sequence change replaces cysteine, which is neutral and slightly polar, with arginine, which is basic and polar, at codon 339 of the ZNF513 protein (p.Cys339Arg). This variant is present in population databases (rs267607182, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with autosmal recessive retinitis pigmentosa (PMID: 20797688). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 28). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. Experimental studies have shown that this missense change affects ZNF513 function (PMID: 20797688). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
OMIM RCV000000045 SCV000020188 pathogenic Retinitis pigmentosa 58 2010-09-10 no assertion criteria provided literature only

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