ClinVar Miner

Submissions for variant NM_025132.4(WDR19):c.3722C>T (p.Pro1241Leu)

gnomAD frequency: 0.00003  dbSNP: rs576113399
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000345648 SCV000449436 likely benign Asphyxiating thoracic dystrophy 5 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Illumina Laboratory Services, Illumina RCV000379247 SCV000449437 likely benign Cranioectodermal dysplasia 4 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Labcorp Genetics (formerly Invitae), Labcorp RCV002057928 SCV002485569 benign Asphyxiating thoracic dystrophy 5; Senior-Loken syndrome 8 2023-11-28 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000379247 SCV002514830 benign Cranioectodermal dysplasia 4 2021-12-05 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV002244835 SCV002514832 benign Nephronophthisis 13 2021-12-05 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV002244836 SCV002514833 benign Senior-Loken syndrome 8 2021-12-05 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000345648 SCV002514834 benign Asphyxiating thoracic dystrophy 5 2021-12-05 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV003221952 SCV003916891 likely benign not provided 2023-01-01 criteria provided, single submitter clinical testing WDR19: BS2
Sydney Genome Diagnostics, Children's Hospital Westmead RCV001328232 SCV001449475 uncertain significance Bardet-Biedl syndrome 2019-04-30 no assertion criteria provided clinical testing This individual is heterozygous for the c.3722C>T variant in the WDR19 gene, which results in the amino acid substitution of proline to leucine at residue 1241, p.(Pro1241Leu). To our knowledge, this variant has not been previously reported in the literature or any disease specific databases to be a disease causing variant. This variant has been reported in the gnomAD browser (http://gnomad.broadinstitute.org) with an allele frequency of 0.62% (189 out of 30,426 alleles including 2 homozygotes). In silico analysis of pathogenicity (through Alamut Visual v2.8.1) is inconclusive regarding this change; PolyPhen2 and MutationTaster predict it to be likely pathogenic whereas SIFTpredicts this variant to be benign. This variant is considered to be a variant of uncertain clinical significance (VOUS) according to the ACMG guidelines (Evidence used: nil).
PreventionGenetics, part of Exact Sciences RCV004544652 SCV004762170 likely benign WDR19-related disorder 2023-01-18 no assertion criteria provided clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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