NM_001844.5(COL2A1):c.2831C>T (p.Pro944Leu) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(1);Uncertain significance(1) (Last evaluated: Oct 27, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000755494.5

Allele description [Variation Report for NM_001844.5(COL2A1):c.2831C>T (p.Pro944Leu)]

NM_001844.5(COL2A1):c.2831C>T (p.Pro944Leu)

Gene:
COL2A1:collagen type II alpha 1 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q13.11
Genomic location:
Preferred name:
NM_001844.5(COL2A1):c.2831C>T (p.Pro944Leu)
HGVS:
  • NC_000012.12:g.47978661G>A
  • NG_008072.1:g.30842C>T
  • NM_001844.5:c.2831C>TMANE SELECT
  • NM_033150.3:c.2624C>T
  • NP_001835.3:p.Pro944Leu
  • NP_149162.2:p.Pro875Leu
  • NC_000012.11:g.48372444G>A
  • NM_001844.4:c.2831C>T
Protein change:
P875L
Links:
dbSNP: rs140368756
NCBI 1000 Genomes Browser:
rs140368756
Molecular consequence:
  • NM_001844.5:c.2831C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033150.3:c.2624C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000603128ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratoriescriteria provided, single submitter
Uncertain significance
(Jan 2, 2018)
germlineclinical testing

Citation Link,

SCV001052949Invitaecriteria provided, single submitter
Likely benign
(Oct 27, 2020)
germlineclinical testing

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

SCV001802810GeneDxno assertion criteria provided
Likely benign
(Nov 24, 2020)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories, SCV000603128.2

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

Description

The c.2831C>T p.Pro944Leu variant (rs140368756), to our knowledge, is not reported in the medical literature or gene specific variation databases. This variant is listed in the genome Aggregation Database (gnomAD) with an overall population frequency of 0.3% (identified on 59 out of 23,816 chromosomes). The proline at position 944 is highly conserved, considering 12 species (Alamut v.2.10.0) and computational analyses of the effects of the p.Pro944Leu variant on protein structure and function provide conflicting results (SIFT: tolerated, MutationTaster: disease causing, PolyPhen-2: benign). Based on the available information, the clinical significance of the p.Pro944Leu variant cannot be predicted with certainty.

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

From Invitae, SCV001052949.3

#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, SCV001802810.1

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

Last Updated: Aug 27, 2021

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