ClinVar Miner

Submissions for variant NM_020779.4(WDR35):c.3026C>G (p.Thr1009Arg)

gnomAD frequency: 0.00045  dbSNP: rs201153804
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000380540 SCV000425979 uncertain significance Short-rib thoracic dysplasia 7 with or without polydactyly 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Illumina Laboratory Services, Illumina RCV000283688 SCV000425980 uncertain significance Cranioectodermal dysplasia 2 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001731614 SCV001158124 uncertain significance not provided 2021-10-23 criteria provided, single submitter clinical testing The WDR35 c.3059C>G; p.Thr1020Arg variant (rs201153804), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 333372). This variant is found in the non-Finnish European population with an allele frequency of 0.10% (131/129120 alleles) in the Genome Aggregation Database. The threonine at codon 1020 is weakly conserved, but computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.179). Due to limited information, the clinical significance of the p.Thr1020Arg variant is uncertain at this time.
Labcorp Genetics (formerly Invitae), Labcorp RCV001058852 SCV001223448 likely benign Cranioectodermal dysplasia 2; Short-rib thoracic dysplasia 7 with or without polydactyly 2025-01-30 criteria provided, single submitter clinical testing
GeneDx RCV001731614 SCV001982290 uncertain significance not provided 2021-10-01 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
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004782362 SCV005394975 uncertain significance not specified 2024-09-11 criteria provided, single submitter clinical testing Variant summary: WDR35 c.3059C>G (p.Thr1020Arg) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00041 in 251390 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in WDR35 causing WDR35-Related Disorders, allowing no conclusion about variant significance. To our knowledge, no occurrence of c.3059C>G in individuals affected with WDR35-Related Disorders and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 333372). Based on the evidence outlined above, the variant was classified as uncertain significance.
Fulgent Genetics, Fulgent Genetics RCV001058852 SCV005654877 uncertain significance Cranioectodermal dysplasia 2; Short-rib thoracic dysplasia 7 with or without polydactyly 2024-03-29 criteria provided, single submitter clinical testing

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