ClinVar Miner

Submissions for variant NM_000093.5(COL5A1):c.3939G>T (p.Glu1313Asp)

gnomAD frequency: 0.00006  dbSNP: rs886063676
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000330772 SCV000478564 uncertain significance Ehlers-Danlos syndrome type 7A 2016-06-14 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002230207 SCV000961030 benign Ehlers-Danlos syndrome, classic type, 1 2024-11-28 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000820322 SCV001158027 uncertain significance Ehlers-Danlos syndrome, classic type 2018-12-05 criteria provided, single submitter clinical testing The COL5A1 c.3939G>T; p.Glu1313Asp variant (rs886063676), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 365725). This variant is found on six chromosomes in the Genome Aggregation Database, indicating it is not a common polymorphism. The glutamate at codon 1313 is highly conserved, but computational analyses (SIFT: tolerated, PolyPhen-2: damaging) predict conflicting effects of this variant on protein structure/function. Due to limited information, the clinical significance of the p.Glu1313Asp variant is uncertain at this time.
GeneDx RCV001567484 SCV001791179 uncertain significance not provided 2021-02-18 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; Reported in ClinVar as a variant of uncertain significance (ClinVar Variant ID# 365725; Landrum et al., 2016); In silico analysis supports that this missense variant does not alter protein structure/function; Occurs in the triple helical domain at the X position in the canonical Gly-X-Y repeat; although this variant may have an effect on normal protein folding and function, missense substitution at the X position is not a common mechanism of disease (Symoens et al., 2012; Stenson et al., 2014)
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV002278630 SCV002565736 uncertain significance Ehlers-Danlos syndrome 2019-03-29 criteria provided, single submitter clinical testing
Ambry Genetics RCV002356502 SCV002621805 uncertain significance Familial thoracic aortic aneurysm and aortic dissection 2020-07-06 criteria provided, single submitter clinical testing The p.E1313D variant (also known as c.3939G>T), located in coding exon 50 of the COL5A1 gene, results from a G to T substitution at nucleotide position 3939. The glutamic acid at codon 1313 is replaced by aspartic acid, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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