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NM_001849.4(COL6A2):c.2048C>T (p.Ser683Phe) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 28, 2017
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000522324.1

Allele description [Variation Report for NM_001849.4(COL6A2):c.2048C>T (p.Ser683Phe)]

NM_001849.4(COL6A2):c.2048C>T (p.Ser683Phe)

Gene:
COL6A2:collagen type VI alpha 2 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
21q22.3
Genomic location:
Preferred name:
NM_001849.4(COL6A2):c.2048C>T (p.Ser683Phe)
HGVS:
  • NC_000021.9:g.46125863C>T
  • NG_008675.1:g.32745C>T
  • NM_001849.4:c.2048C>TMANE SELECT
  • NM_058174.3:c.2048C>T
  • NM_058175.3:c.2048C>T
  • NP_001840.3:p.Ser683Phe
  • NP_001840.3:p.Ser683Phe
  • NP_478054.2:p.Ser683Phe
  • NP_478055.2:p.Ser683Phe
  • LRG_476t1:c.2048C>T
  • LRG_476:g.32745C>T
  • LRG_476p1:p.Ser683Phe
  • NC_000021.8:g.47545777C>T
  • NM_001849.3:c.2048C>T
Protein change:
S683F
Links:
dbSNP: rs1258904789
NCBI 1000 Genomes Browser:
rs1258904789
Molecular consequence:
  • NM_001849.4:c.2048C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_058174.3:c.2048C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_058175.3:c.2048C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000619567GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Jul 28, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000619567.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The S683F variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The S683F variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). This variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. However, missense variants in nearby residues have not been reported in the Human Gene Mutation Database in association with COL6A2-related disorders (Stenson et al., 2014).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024