ClinVar Miner

Submissions for variant NM_001384140.1(PCDH15):c.3656A>G (p.Lys1219Arg)

gnomAD frequency: 0.00001  dbSNP: rs763978654
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001552066 SCV001772686 uncertain significance not provided 2020-09-24 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Labcorp Genetics (formerly Invitae), Labcorp RCV001552066 SCV003498880 uncertain significance not provided 2022-09-06 criteria provided, single submitter clinical testing This sequence change replaces lysine, which is basic and polar, with arginine, which is basic and polar, at codon 1219 of the PCDH15 protein (p.Lys1219Arg). This variant is present in population databases (rs763978654, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with PCDH15-related conditions. ClinVar contains an entry for this variant (Variation ID: 1191114). 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: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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.
Ambry Genetics RCV004952978 SCV005470191 uncertain significance Inborn genetic diseases 2024-07-17 criteria provided, single submitter clinical testing The c.3656A>G (p.K1219R) alteration is located in exon 27 (coding exon 26) of the PCDH15 gene. This alteration results from a A to G substitution at nucleotide position 3656, causing the lysine (K) at amino acid position 1219 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Natera, Inc. RCV001832752 SCV002094884 uncertain significance Usher syndrome type 1F 2020-03-17 no assertion criteria provided clinical testing

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