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NM_001844.5(COL2A1):c.4264C>T (p.Arg1422Trp)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Jul 13, 2020
Accession:
VCV000308904.3
Variation ID:
308904
Description:
single nucleotide variant
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NM_001844.5(COL2A1):c.4264C>T (p.Arg1422Trp)

Allele ID
325001
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12q13.11
Genomic location
12: 47974142 (GRCh38) GRCh38 UCSC
12: 48367925 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000012.11:g.48367925G>A
NC_000012.12:g.47974142G>A
NM_001844.5:c.4264C>T MANE Select NP_001835.3:p.Arg1422Trp missense
... more HGVS
Protein change
R1422W, R1353W
Other names
-
Canonical SPDI
NC_000012.12:47974141:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Exome Aggregation Consortium (ExAC) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00002
Links
ClinGen: CA6534511
dbSNP: rs754466377
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 criteria provided, single submitter Jan 12, 2018 RCV000350564.2
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV000396722.2
Uncertain significance 1 criteria provided, single submitter Jul 13, 2020 RCV001344740.1
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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
1045 1056

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Type II Collagenopathies
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000378956.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Stickler syndrome type 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000378957.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Uncertain significance
(Jul 13, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001538816.1
Submitted: (Jan 07, 2021)
Evidence details
Comment:
This sequence change replaces arginine with tryptophan at codon 1422 of the COL2A1 protein (p.Arg1422Trp). The arginine residue is highly conserved and there is a … (more)

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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs754466377...

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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 Apr 08, 2021