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NM_004370.6(COL12A1):c.9050C>T (p.Thr3017Ile) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 26, 2020
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:
RCV001304433.7

Allele description [Variation Report for NM_004370.6(COL12A1):c.9050C>T (p.Thr3017Ile)]

NM_004370.6(COL12A1):c.9050C>T (p.Thr3017Ile)

Gene:
COL12A1:collagen type XII alpha 1 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6q13
Genomic location:
Preferred name:
NM_004370.6(COL12A1):c.9050C>T (p.Thr3017Ile)
HGVS:
  • NC_000006.12:g.75087708G>A
  • NG_042181.1:g.123200C>T
  • NM_004370.6:c.9050C>TMANE SELECT
  • NM_080645.3:c.5558C>T
  • NP_004361.3:p.Thr3017Ile
  • NP_542376.2:p.Thr1853Ile
  • NC_000006.11:g.75797424G>A
Protein change:
T1853I
Links:
dbSNP: rs1767573014
NCBI 1000 Genomes Browser:
rs1767573014
Molecular consequence:
  • NM_004370.6:c.9050C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_080645.3:c.5558C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Ullrich congenital muscular dystrophy 2 (UCMD2)
Identifiers:
MONDO: MONDO:0014654; MedGen: C4225314; Orphanet: 75840; OMIM: 616470
Name:
Bethlem myopathy 2 (BTHLM2)
Identifiers:
MONDO: MONDO:0034022; MedGen: C4225313; Orphanet: 610; OMIM: 616471

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001493713Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jun 26, 2020) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001493713.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant has not been reported in the literature in individuals with COL12A1-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant is not present in population databases (ExAC no frequency). This sequence change replaces threonine with isoleucine at codon 3017 of the COL12A1 protein (p.Thr3017Ile). The threonine residue is highly conserved and there is a moderate physicochemical difference between threonine and isoleucine.

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

Last Updated: Sep 29, 2024