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NM_000090.4(COL3A1):c.560C>T (p.Thr187Ile)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Sep 25, 2021)
Last evaluated:
May 26, 2020
Accession:
VCV000199711.6
Variation ID:
199711
Description:
single nucleotide variant
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NM_000090.4(COL3A1):c.560C>T (p.Thr187Ile)

Allele ID
196767
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q32.2
Genomic location
2: 188988112 (GRCh38) GRCh38 UCSC
2: 189852838 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_3:g.18740C>T
LRG_3t1:c.560C>T LRG_3p1:p.Thr187Ile
NC_000002.11:g.189852838C>T
... more HGVS
Protein change
T187I
Other names
p.T187I:ACA>ATA
Canonical SPDI
NC_000002.12:188988111:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00017
The Genome Aggregation Database (gnomAD) 0.00010
Trans-Omics for Precision Medicine (TOPMed) 0.00018
The Genome Aggregation Database (gnomAD), exomes 0.00004
Exome Aggregation Consortium (ExAC) 0.00007
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Trans-Omics for Precision Medicine (TOPMed) 0.00025
Links
ClinGen: CA006991
dbSNP: rs371583734
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter May 26, 2020 RCV000698663.4
Uncertain significance 1 criteria provided, single submitter Jan 15, 2020 RCV001190472.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 4, 2019 RCV000586266.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
COL3A1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1881 1932

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Dec 04, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000233345.10
Submitted: (Sep 25, 2021)
Evidence details
Comment:
In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Reported in ClinVar with conflicting classifications … (more)
Benign
(Jul 10, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000695377.1
Submitted: (Jan 25, 2018)
Evidence details
Publications
PubMed (1)
Uncertain significance
(Jan 15, 2020)
criteria provided, single submitter
Method: clinical testing
Familial thoracic aortic aneurysm and aortic dissection
Allele origin: germline
Color Health, Inc
Accession: SCV001357972.1
Submitted: (May 19, 2020)
Comment:
This missense variant replaces threonine with isoleucine at codon 187 of the COL3A1 protein. Computational prediction suggests that this variant may not impact protein structure … (more)
Evidence details
Uncertain significance
(May 26, 2020)
criteria provided, single submitter
Method: clinical testing
Ehlers-Danlos syndrome, type 4
Allele origin: germline
Invitae
Accession: SCV000827343.4
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change replaces threonine with isoleucine at codon 187 of the COL3A1 protein (p.Thr187Ile). The threonine residue is weakly 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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Title Author Journal Year Link
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
Clinical utility of a next generation sequencing panel assay for Marfan and Marfan-like syndromes featuring aortopathy. Wooderchak-Donahue W American journal of medical genetics. Part A 2015 PMID: 25944730

Text-mined citations for rs371583734...

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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