NM_001849.4(COL6A2):c.2980G>A (p.Ala994Thr) AND not specified

Clinical significance:Benign/Likely benign (Last evaluated: Dec 9, 2016)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
5 submissions [Details]
Record status:
current
Accession:
RCV000116794.7

Allele description [Variation Report for NM_001849.4(COL6A2):c.2980G>A (p.Ala994Thr)]

NM_001849.4(COL6A2):c.2980G>A (p.Ala994Thr)

Genes:
FTCD:formimidoyltransferase cyclodeaminase [Gene - OMIM - HGNC]
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.2980G>A (p.Ala994Thr)
HGVS:
  • NC_000021.9:g.46132472G>A
  • NG_008675.1:g.39354G>A
  • NM_001849.3:c.2980G>A
  • NM_001849.4:c.2980G>AMANE SELECT
  • NP_001840.3:p.Ala994Thr
  • NP_001840.3:p.Ala994Thr
  • LRG_476t1:c.2980G>A
  • LRG_476:g.39354G>A
  • LRG_476p1:p.Ala994Thr
  • NC_000021.8:g.47552386G>A
Protein change:
A994T
Links:
dbSNP: rs117931394
NCBI 1000 Genomes Browser:
rs117931394
Molecular consequence:
  • NM_001849.3:c.2980G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001849.4:c.2980G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
3

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000150818Genetic Services Laboratory,University of Chicagono assertion criteria providedLikely benigngermlineclinical testing

SCV000228613EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Benign
(Mar 31, 2015)
germlineclinical testing

Citation Link,

SCV000308308PreventionGenetics,PreventionGeneticscriteria provided, single submitter
Likely benigngermlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000519953GeneDxcriteria provided, single submitter
Benign
(Jun 10, 2016)
germlineclinical testing

Citation Link,

SCV000613013Athena Diagnostics Inccriteria provided, single submitter
Benign
(Dec 9, 2016)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown3not providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Novel collagen VI mutations identified in Chinese patients with Ullrich congenital muscular dystrophy.

Zhang YZ, Zhao DH, Yang HP, Liu AJ, Chang XZ, Hong DJ, Bonnemann C, Yuan Y, Wu XR, Xiong H.

World J Pediatr. 2014 May;10(2):126-32. doi: 10.1007/s12519-014-0481-1. Epub 2014 May 7.

PubMed [citation]
PMID:
24801232
See all PubMed Citations (3)

Details of each submission

From Genetic Services Laboratory,University of Chicago, SCV000150818.2

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

Description

Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.

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

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000228613.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided3not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided3not providednot providednot provided

From PreventionGenetics,PreventionGenetics, SCV000308308.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV000519953.4

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

Description

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.

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

From Athena Diagnostics Inc, SCV000613013.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 30, 2021

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