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NM_001844.5(COL2A1):c.4316C>T (p.Thr1439Met)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Jan 1, 2019
Accession:
VCV000017385.4
Variation ID:
17385
Description:
single nucleotide variant
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NM_001844.5(COL2A1):c.4316C>T (p.Thr1439Met)

Allele ID
32424
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12q13.11
Genomic location
12: 47974090 (GRCh38) GRCh38 UCSC
12: 48367873 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P02458:p.Thr1439Met
NC_000012.11:g.48367873G>A
NC_000012.12:g.47974090G>A
... more HGVS
Protein change
T1370M, T1439M
Other names
-
Canonical SPDI
NC_000012.12:47974089:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00010
The Genome Aggregation Database (gnomAD), exomes 0.00008
Trans-Omics for Precision Medicine (TOPMed) 0.00014
Links
ClinGen: CA204551
UniProtKB: P02458#VAR_017105
OMIM: 120140.0035
dbSNP: rs121912886
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, single submitter Jan 1, 2019 RCV000018928.25
Likely pathogenic 1 criteria provided, single submitter Sep 15, 2014 RCV000190574.1
Uncertain significance 1 criteria provided, single submitter Jul 9, 2018 RCV001299254.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
COL2A1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1089 1100

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Sep 15, 2014)
criteria provided, single submitter
Method: clinical testing
Spondyloperipheral dysplasia
(Autosomal dominant inheritance)
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Study: CSER-MedSeq
Accession: SCV000245593.1
Submitted: (Aug 18, 2015)
Evidence details
Publications
PubMed (1)
Comment:
The Thr1439Met variant in COL2A1 has been reported as de novo in one individual with spondyloepiphyseal dysplasia congenita and was shown to segregate with disease … (more)
Uncertain significance
(Jul 09, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001488338.1
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces threonine with methionine at codon 1439 of the COL2A1 protein (p.Thr1439Met). The threonine residue is moderately conserved and there is a … (more)
Uncertain significance
(Jan 01, 2019)
criteria provided, single submitter
Method: clinical testing
Spondyloepiphyseal dysplasia
Allele origin: unknown
Genomic Research Center,Shahid Beheshti University of Medical Sciences
Accession: SCV000923488.1
Submitted: (Apr 08, 2019)
Evidence details
Pathogenic
(Nov 22, 2001)
no assertion criteria provided
Method: literature only
SPONDYLOEPIPHYSEAL DYSPLASIA CONGENITA
Allele origin: germline
OMIM
Accession: SCV000039213.1
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Double heterozygosity for pseudoachondroplasia and spondyloepiphyseal dysplasia congenita. Unger S American journal of medical genetics 2001 PMID: 11746045

Text-mined citations for rs121912886...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 07, 2021