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NM_001105206.3(LAMA4):c.3175G>A (p.Val1059Met)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Likely benign(2);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Jan 7, 2021)
Last evaluated:
Sep 30, 2020
Accession:
VCV000044373.9
Variation ID:
44373
Description:
single nucleotide variant
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NM_001105206.3(LAMA4):c.3175G>A (p.Val1059Met)

Allele ID
53540
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
6q21
Genomic location
6: 112139227 (GRCh38) GRCh38 UCSC
6: 112460429 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000006.11:g.112460429C>T
NC_000006.12:g.112139227C>T
NM_001105206.3:c.3175G>A MANE Select NP_001098676.2:p.Val1059Met missense
... more HGVS
Protein change
V1052M, V1059M
Other names
p.V1052M:GTG>ATG
Canonical SPDI
NC_000006.12:112139226:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00319 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00008
1000 Genomes Project 0.00319
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
The Genome Aggregation Database (gnomAD) 0.00016
Links
ClinGen: CA237257
dbSNP: rs373650093
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 Jun 24, 2013 RCV000171974.3
Likely benign 1 criteria provided, single submitter Jan 5, 2017 RCV000618915.1
Benign 1 criteria provided, single submitter Jul 30, 2018 RCV000769196.2
Premature ventricular contraction
Likely benign 1 criteria provided, single submitter Nov 22, 2018 RCV000853002.1
Benign 1 criteria provided, single submitter Sep 30, 2020 RCV001088319.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Apr 7, 2016 RCV000037361.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
LAMA4 - - GRCh38
GRCh37
805 869

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jun 24, 2013)
criteria provided, single submitter
Method: research
Not provided
Allele origin: unknown
Biesecker Lab/Clinical Genomics Section,National Institutes of Health
Study: ClinSeq
Accession: SCV000055151.1
Submitted: (Mar 10, 2015)
Comments (2):
The study set was not selected for affection status in relation to any cancer. Pathogenicity categories were based on literature curation. See Pubmed ID:23861362 for … (more)
Medical sequencing
Evidence details
Benign
(Apr 07, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000250559.7
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Uncertain significance
(Jun 07, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000061018.5
Submitted: (Mar 21, 2019)
Evidence details
Comment:
Variant classified as Uncertain Significance - Favor Benign. The Val1052Met vari ant in LAMA4 has been identified by our laboratory in 1 Sri Lankan individual … (more)
Benign
(Jul 30, 2018)
criteria provided, single submitter
Method: clinical testing
Cardiomyopathy
Allele origin: germline
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario
Accession: SCV000900572.2
Submitted: (Mar 03, 2020)
Evidence details
Likely benign
(Jan 05, 2017)
criteria provided, single submitter
Method: clinical testing
Cardiovascular phenotype
Allele origin: germline
Ambry Genetics
Accession: SCV000736740.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
In silico models in agreement (benign);Subpopulation frequency in support of benign classification
Benign
(Sep 30, 2020)
criteria provided, single submitter
Method: clinical testing
Dilated cardiomyopathy 1JJ
Allele origin: germline
Invitae
Accession: SCV001006951.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Nov 22, 2018)
criteria provided, single submitter
Method: clinical testing
Premature ventricular contraction
Allele origin: germline
Center for Advanced Laboratory Medicine, UC San Diego Health,University of California San Diego
Accession: SCV000995756.1
Submitted: (Jun 12, 2019)
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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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 rs373650093...

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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 Jul 07, 2021