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NM_000093.5(COL5A1):c.514G>T (p.Val172Phe)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(5);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
9 (Most recent: Sep 23, 2021)
Last evaluated:
Jul 1, 2021
Accession:
VCV000180298.17
Variation ID:
180298
Description:
single nucleotide variant
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NM_000093.5(COL5A1):c.514G>T (p.Val172Phe)

Allele ID
178594
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q34.3
Genomic location
9: 134701193 (GRCh38) GRCh38 UCSC
9: 137593039 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.137593039G>T
NC_000009.12:g.134701193G>T
NG_008030.1:g.64388G>T
... more HGVS
Protein change
V172F
Other names
p.V172F:GTC>TTC
Canonical SPDI
NC_000009.12:134701192:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00049
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00100
Links
ClinGen: CA324337
dbSNP: rs150147262
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 criteria provided, multiple submitters, no conflicts Nov 25, 2020 RCV001085122.3
Likely benign 1 criteria provided, single submitter Sep 30, 2020 RCV000619401.2
Likely benign 1 criteria provided, single submitter Nov 1, 2016 RCV000659439.1
Conflicting interpretations of pathogenicity 4 criteria provided, conflicting interpretations Jul 1, 2021 RCV000199784.12
Uncertain significance 1 no assertion criteria provided Apr 8, 2014 RCV000157144.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
COL5A1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1544 2077

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Dec 18, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000249872.14
Submitted: (Jan 29, 2019)
Evidence details
Comment:
A variant of uncertain significance has been identified in the COL5A1 gene. The V172F variant has not been published as pathogenic or been reported as … (more)
Likely benign
(Nov 01, 2016)
criteria provided, single submitter
Method: clinical testing
Connective tissue disease
Allele origin: germline
Center for Human Genetics, Inc,Center for Human Genetics, Inc
Accession: SCV000781253.1
Submitted: (Dec 20, 2017)
Evidence details
Likely benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Ehlers-Danlos syndrome, classic type I
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001329746.1
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)
Likely benign
(Sep 30, 2020)
criteria provided, single submitter
Method: clinical testing
Cardiovascular phenotype
Allele origin: germline
Ambry Genetics
Accession: SCV000738565.3
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (2)
Comment:
In silico models in agreement (benign);Subpopulation frequency in support of benign classification
Likely benign
(Nov 25, 2020)
criteria provided, single submitter
Method: clinical testing
Ehlers-Danlos syndrome, classic type I
Allele origin: germline
Invitae
Accession: SCV000631540.6
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Likely benign
(Jul 01, 2021)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001155816.7
Submitted: (Jul 04, 2021)
Evidence details
Uncertain significance
(Apr 08, 2014)
no assertion criteria provided
Method: clinical testing
Thoracic aortic aneurysms and aortic dissections
Aortic valve disorder
Allele origin: germline
Blueprint Genetics
Accession: SCV000206867.1
Submitted: (Feb 02, 2015)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV001808838.1
Submitted: (Aug 24, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001931512.1
Submitted: (Sep 23, 2021)
Evidence details

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
Rare genetic variants in patients with cervical artery dissection. Traenka C European stroke journal 2019 PMID: 31903434
New variants in <i>COL5A1</i> gene among Polish patients with Ehlers-Danlos syndrome: analysis of nine cases. Junkiert-Czarnecka A Postepy dermatologii i alergologii 2019 PMID: 30858776
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532

Text-mined citations for rs150147262...

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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 Dec 04, 2021