ClinVar Miner

Submissions for variant NM_033056.4(PCDH15):c.1360G>A (p.Val454Ile) (rs61735473)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000039701 SCV000063390 benign not specified 2010-10-06 criteria provided, single submitter clinical testing This variant is not expected to have clinical significance because this residue is not highly conserved across species and this is not a significant biochemical change. In addition, this variant has been entered 6 times in dbSNP with a 3.6% (6/168) allele frequency in the West African population (rs61735473). Furthermo re, this variant has been identified by our laboratory in 2/15 (13.3%) Black pro bands.
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000039701 SCV000114265 benign not specified 2013-09-23 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000327397 SCV000363212 benign Usher syndrome type 1 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Illumina Clinical Services Laboratory,Illumina RCV000381862 SCV000363213 uncertain significance Nonsyndromic Hearing Loss, Recessive 2016-06-14 criteria provided, single submitter clinical testing
GeneDx RCV000039701 SCV000514042 benign not specified 2016-02-15 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Integrated Genetics/Laboratory Corporation of America RCV000588827 SCV000699755 benign not provided 2016-10-31 criteria provided, single submitter clinical testing Variant summary: The PCDH15 c.1360G>A (p.Val454Ile) variant involves the alteration of a non-conserved nucleotide. 3/4 in silico tools predict a benign outcome for this variant. This variant was found in 397/121340 control chromosomes (including 6 homozygotes), predominantly observed in the African subpopulation at a frequency of 0.0347943 (362/10404). This frequency is about 11 times the estimated maximal expected allele frequency of a pathogenic PCDH15 variant (0.0031623), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. In addition, multiple clinical diagnostic laboratories have classified this variant as benign. Taken together, this variant is classified as Benign.
Invitae RCV000588827 SCV001103615 benign not provided 2019-12-31 criteria provided, single submitter clinical testing

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