ClinVar Miner

Submissions for variant NM_025132.4(WDR19):c.3533G>A (p.Arg1178Gln)

gnomAD frequency: 0.00015  dbSNP: rs79436363
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000433622 SCV000516765 likely pathogenic not provided 2023-08-26 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 23559409, 25726036, 27596865, 28621010, 29121203, 26260382, 29145603, 28973083, 29127259, 33875766, 31844813, 31216405, 32165824, 32604935, 34354814, 33323469, 34216551)
Labcorp Genetics (formerly Invitae), Labcorp RCV000653250 SCV000775126 pathogenic Asphyxiating thoracic dystrophy 5; Senior-Loken syndrome 8 2023-09-27 criteria provided, single submitter clinical testing ClinVar contains an entry for this variant (Variation ID: 127158). This missense change has been observed in individual(s) with nephronophthisis (PMID: 23559409, 25726036, 27596865, 28621010). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This variant is present in population databases (rs79436363, gnomAD 0.03%). This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 1178 of the WDR19 protein (p.Arg1178Gln). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on WDR19 protein function. For these reasons, this variant has been classified as Pathogenic.
Rare Disease Group, Clinical Genetics, Karolinska Institutet RCV000754960 SCV000788386 uncertain significance Cranioectodermal dysplasia 2018-05-01 criteria provided, single submitter research
Eurofins Ntd Llc (ga) RCV000433622 SCV000860737 pathogenic not provided 2018-04-24 criteria provided, single submitter clinical testing
Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University RCV000115014 SCV000891658 uncertain significance Senior-Loken syndrome 8 2017-12-30 criteria provided, single submitter curation
Baylor Genetics RCV000850617 SCV000992850 pathogenic Nephronophthisis 13; Senior-Loken syndrome 8 2017-12-31 criteria provided, single submitter clinical testing
Institute of Vision Research, Yonsei University College of Medicine RCV001262101 SCV001371860 likely pathogenic Leber congenital amaurosis 2020-07-09 criteria provided, single submitter clinical testing
OMIM RCV000115014 SCV000148923 pathogenic Senior-Loken syndrome 8 2013-08-01 no assertion criteria provided literature only
OMIM RCV003224149 SCV003920719 pathogenic Nephronophthisis 13 2013-08-01 no assertion criteria provided literature only
OMIM RCV003224150 SCV003920720 pathogenic Cranioectodermal dysplasia 4 2013-08-01 no assertion criteria provided literature only

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