NM_001105206.3(LAMA4):c.2398C>T (p.Arg800Cys) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Jul 22, 2021
Review status:: criteria provided, conflicting classifications

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000172549.7

Allele description [Variation Report for NM_001105206.3(LAMA4):c.2398C>T (p.Arg800Cys)]

NM_001105206.3(LAMA4):c.2398C>T (p.Arg800Cys)

Gene:

LAMA4:laminin subunit alpha 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6q21

Genomic location:

Preferred name:

NM_001105206.3(LAMA4):c.2398C>T (p.Arg800Cys)

HGVS:

NC_000006.12:g.112144889G>A
NG_008209.1:g.114738C>T
NM_001105206.3:c.2398C>TMANE SELECT
NM_001105207.3:c.2377C>T
NM_002290.5:c.2377C>T
NP_001098676.2:p.Arg800Cys
NP_001098677.2:p.Arg793Cys
NP_002281.3:p.Arg793Cys
LRG_433t2:c.2377C>T
LRG_433:g.114738C>T
NC_000006.11:g.112466091G>A
NM_001105206.2:c.2398C>T
NM_001105207.2:c.2377C>T
NM_002290.3:c.2377C>T
NM_002290.4:c.2377C>T

Protein change:

R793C

Links:

dbSNP: rs202184174

NCBI 1000 Genomes Browser:

rs202184174

Molecular consequence:

NM_001105206.3:c.2398C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001105207.3:c.2377C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_002290.5:c.2377C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000055153	Biesecker Lab/Clinical Genomics Section, National Institutes of Health - ClinSeq	criteria provided, single submitter (Ng et al. (Circ Cardiovasc Genet. 2013))	Likely benign (Jun 24, 2013)	unknown	research	PubMed (1) [See all records that cite this PMID]
SCV001872905	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Jul 22, 2021)	germline	clinical testing	Citation Link,
SCV001920205	Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Uncertain significance	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000055153

Biesecker Lab/Clinical Genomics Section, National Institutes of Health - ClinSeq

criteria provided, single submitter

(Ng et al. (Circ Cardiovasc Genet. 2013))

Likely benign
(Jun 24, 2013)

unknown

research

PubMed (1)
[See all records that cite this PMID]

SCV001872905

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Jul 22, 2021)

germline

clinical testing

Citation Link,

SCV001920205

Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided

Uncertain significance

germline

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	1	not provided	not provided	not provided	not provided	research
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Interpreting secondary cardiac disease variants in an exome cohort.

Ng D, Johnston JJ, Teer JK, Singh LN, Peller LC, Wynter JS, Lewis KL, Cooper DN, Stenson PD, Mullikin JC, Biesecker LG; NIH Intramural Sequencing Center (NISC) Comparative Sequencing Program..

Circ Cardiovasc Genet. 2013 Aug;6(4):337-46. doi: 10.1161/CIRCGENETICS.113.000039. Epub 2013 Jul 16.

PubMed [citation]

PMID:: 23861362
PMCID:: PMC3887521

Details of each submission

From Biesecker Lab/Clinical Genomics Section, National Institutes of Health - ClinSeq, SCV000055153.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	research	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		1	not provided	not provided	not provided

From GeneDx, SCV001872905.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Reported in an African American patient with Wolff-Parkinson-White, left ventricular non-compaction cardiomyopathy and a ventricular septal defect (Coban-Akdemir et al., 2020); Also reported in one individual from a cohort of individuals not selected for cardiomyopathy, arrhythmia, or family history of sudden cardiac death, who underwent exome sequencing (Ng et al., 2013); Reported in ClinVar as a variant of uncertain significance (ClinVar Variant ID#192119; Landrum et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 32233023, 23861362)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001920205.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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