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NM_001854.4(COL11A1):c.4416C>A (p.Asp1472Glu)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Likely benign(4);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Sep 24, 2021)
Last evaluated:
Dec 2, 2020
Accession:
VCV000198019.13
Variation ID:
198019
Description:
single nucleotide variant
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NM_001854.4(COL11A1):c.4416C>A (p.Asp1472Glu)

Allele ID
195180
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p21.1
Genomic location
1: 102889503 (GRCh38) GRCh38 UCSC
1: 103355059 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.103355059G>T
NC_000001.11:g.102889503G>T
NG_008033.2:g.223994C>A
... more HGVS
Protein change
D1484E, D1472E, D1356E, D1433E
Other names
-
Canonical SPDI
NC_000001.11:102889502:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00080 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00306
The Genome Aggregation Database (gnomAD) 0.00284
1000 Genomes Project 0.00080
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00284
Exome Aggregation Consortium (ExAC) 0.00294
The Genome Aggregation Database (gnomAD) 0.00163
Trans-Omics for Precision Medicine (TOPMed) 0.00310
The Genome Aggregation Database (gnomAD), exomes 0.00337
Links
ClinGen: CA203185
dbSNP: rs55821405
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Oct 3, 2014 RCV000179220.4
Likely benign 1 criteria provided, single submitter Jan 13, 2018 RCV000318353.2
Likely benign 1 criteria provided, single submitter Jan 13, 2018 RCV000385330.2
Likely benign 1 criteria provided, single submitter Nov 1, 2016 RCV000659326.1
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Dec 2, 2020 RCV000963059.6
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
COL11A1 Little evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
997 1023

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Oct 03, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000231431.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Dec 02, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001110187.3
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Jun 01, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001147356.7
Submitted: (Jul 04, 2021)
Evidence details
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: SCV000781137.1
Submitted: (Dec 20, 2017)
Evidence details
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Stickler syndrome type 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000346377.3
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)
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Fibrochondrogenesis 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000346375.3
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
(Jul 25, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000516874.4
Submitted: (Sep 24, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 15922184, 27353947, 24036952)

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=COL11A1 - - - -

Text-mined citations for rs55821405...

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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 27, 2021