rs547012639
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PM2PP3
The ENST00000355527.8(DHCR7):c.1087C>T(p.Arg363Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000688 in 1,613,076 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R363H) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000355527.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DHCR7 | NM_001360.3 | c.1087C>T | p.Arg363Cys | missense_variant | 9/9 | ENST00000355527.8 | NP_001351.2 | |
DHCR7 | NM_001163817.2 | c.1087C>T | p.Arg363Cys | missense_variant | 9/9 | NP_001157289.1 | ||
DHCR7 | XM_011544777.3 | c.1221C>T | p.Ala407= | synonymous_variant | 9/9 | XP_011543079.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DHCR7 | ENST00000355527.8 | c.1087C>T | p.Arg363Cys | missense_variant | 9/9 | 1 | NM_001360.3 | ENSP00000347717 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152260Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.0000563 AC: 14AN: 248840Hom.: 0 AF XY: 0.0000592 AC XY: 8AN XY: 135164
GnomAD4 exome AF: 0.0000698 AC: 102AN: 1460698Hom.: 0 Cov.: 37 AF XY: 0.0000729 AC XY: 53AN XY: 726660
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152378Hom.: 0 Cov.: 35 AF XY: 0.0000671 AC XY: 5AN XY: 74514
ClinVar
Submissions by phenotype
not provided Pathogenic:1Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 06, 2018 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Nov 29, 2022 | Not observed at significant frequency in large population cohorts (gnomAD); 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: 34426522, 12270273) - |
Smith-Lemli-Opitz syndrome Uncertain:2
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Jan 02, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Dec 10, 2021 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Feb 07, 2023 | Variant summary: DHCR7 c.1087C>T (p.Arg363Cys) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 5.6e-05 in 248840 control chromosomes (gnomAD). This frequency is not significantly higher than expected for a pathogenic variant in DHCR7 causing Smith-Lemli-Opitz Syndrome (5.6e-05 vs 0.0043), allowing no conclusion about variant significance. c.1087C>T has been reported in the literature in at least one compound heterozygous individual affected with Smith-Lemli-Opitz Syndrome; the individual displayed a moderate phenotype and elevated 7DHC levels (Patrono_2002). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Four ClinVar submitters (evaluation after 2014) have cited the variant, and all laboratories classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 14, 2019 | The p.R363C variant (also known as c.1087C>T), located in coding exon 7 of the DHCR7 gene, results from a C to T substitution at nucleotide position 1087. The arginine at codon 363 is replaced by cysteine, an amino acid with highly dissimilar properties. This variant was identified in an individual suspicious for Smith-Lemli-Opitz syndrome who also carried the p.V330M variant; however, this individual did not have elevated levels of 7DHC and cholesterol levels were not measured (Patrono C et al. Mol. Cell. Probes, 2002 Aug;16:315-8). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on available evidence to date, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at