ClinVar Miner

Submissions for variant NM_001163817.2(DHCR7):c.1012G>A (p.Val338Met) (rs72954276)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000079638 SCV000111521 likely benign not specified 2018-02-19 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000585931 SCV000697850 uncertain significance not provided 2016-09-26 criteria provided, single submitter clinical testing Variant summary: The DHCR7 c.1012G>A (p.Val338Met) variant involves the alteration of a non-conserved nucleotide. 3/3 in silico tools predict a benign outcome for this variant. This variant was found in 99/113632 control chromosomes at a frequency of 0.0008712, which does not exceed the estimated maximal expected allele frequency of a pathogenic DHCR7 variant (0.0043301). In addition, one clinical diagnostic laboratory has classified this variant as uncertain significance. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories, nor evaluated for functional impact by in vivo/vitro studies. Because of the absence of clinical information and the lack of functional studies, the variant is classified as a variant of uncertain significance (VUS) until additional information becomes available.
Invitae RCV001027947 SCV000754776 likely benign Smith-Lemli-Opitz syndrome 2020-12-05 criteria provided, single submitter clinical testing
Ambry Genetics RCV000717914 SCV000848774 uncertain significance History of neurodevelopmental disorder 2018-01-30 criteria provided, single submitter clinical testing The p.V338M variant (also known as c.1012G>A), located in coding exon 7 of the DHCR7 gene, results from a G to A substitution at nucleotide position 1012. The valine at codon 338 is replaced by methionine, an amino acid with highly similar properties. This alteration has been reported in a cohort of subjects with autism (Saskin A et al. J. Hum. Genet., 2017 Jun;62:657-659). One functional study demonstrated that this alteration performed similar to the wild type in response to treatment in cholesterol biosynthesis (Korade Z et al. J. Lipid Res., 2017 Nov;58:2139-2146). This amino acid position is poorly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
GeneDx RCV000585931 SCV000981133 likely benign not provided 2018-05-07 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.
Illumina Clinical Services Laboratory,Illumina RCV001027947 SCV001271953 uncertain significance Smith-Lemli-Opitz syndrome 2018-01-12 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.
Centre for Mendelian Genomics,University Medical Centre Ljubljana RCV001027947 SCV001367630 benign Smith-Lemli-Opitz syndrome 2018-10-31 criteria provided, single submitter clinical testing This variant was classified as: Benign. The following ACMG criteria were applied in classifying this variant: BS1,BS2.
Baylor Genetics RCV001027947 SCV001524150 uncertain significance Smith-Lemli-Opitz syndrome 2019-01-20 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].

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