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NM_004369.4(COL6A3):c.5059C>T (p.Pro1687Ser)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Sep 25, 2021)
Last evaluated:
Dec 3, 2020
Accession:
VCV000094942.6
Variation ID:
94942
Description:
single nucleotide variant
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NM_004369.4(COL6A3):c.5059C>T (p.Pro1687Ser)

Allele ID
100842
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q37.3
Genomic location
2: 237367128 (GRCh38) GRCh38 UCSC
2: 238275771 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.12:g.237367128G>A
NG_008676.1:g.52080C>T
NM_004369.4:c.5059C>T MANE Select NP_004360.2:p.Pro1687Ser missense
... more HGVS
Protein change
P1080S, P1481S
Other names
-
Canonical SPDI
NC_000002.12:237367127:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00739 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00682
1000 Genomes Project 0.00739
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00838
Trans-Omics for Precision Medicine (TOPMed) 0.00682
Links
ClinGen: CA147980
UniProtKB: P12111#VAR_058256
dbSNP: rs35273032
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, multiple submitters, no conflicts Jan 2, 2013 RCV000080947.8
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000385545.2
Benign 1 criteria provided, single submitter Dec 3, 2020 RCV000545987.5
Benign 1 criteria provided, single submitter May 9, 2018 RCV001703998.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
COL6A3 - - GRCh38
GRCh37
1882 1962

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jan 02, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000112854.8
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000310184.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Collagen VI-related myopathy
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000428790.3
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)
Benign
(Dec 03, 2020)
criteria provided, single submitter
Method: clinical testing
Bethlem myopathy 1
Allele origin: germline
Invitae
Accession: SCV000657333.5
Submitted: (Jan 07, 2021)
Evidence details
Benign
(May 09, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000530269.4
Submitted: (Sep 25, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 15689448)

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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=COL6A3 - - - -

Text-mined citations for rs35273032...

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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 Nov 20, 2021