NM_000070.3(CAPN3):c.2105C>T (p.Ala702Val) AND not provided

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Mar 24, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000725206.6

Allele description [Variation Report for NM_000070.3(CAPN3):c.2105C>T (p.Ala702Val)]

NM_000070.3(CAPN3):c.2105C>T (p.Ala702Val)

Gene:

CAPN3:calpain 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q15.1

Genomic location:

Preferred name:

NM_000070.3(CAPN3):c.2105C>T (p.Ala702Val)

HGVS:

NC_000015.10:g.42409985C>T
NG_008660.1:g.66883C>T
NM_000070.3:c.2105C>TMANE SELECT
NM_024344.2:c.2087C>T
NM_173087.2:c.1829C>T
NM_173088.2:c.569C>T
NM_173089.2:c.110C>T
NM_173090.2:c.110C>T
NP_000061.1:p.Ala702Val
NP_077320.1:p.Ala696Val
NP_775110.1:p.Ala610Val
NP_775111.1:p.Ala190Val
NP_775112.1:p.Ala37Val
NP_775113.1:p.Ala37Val
LRG_849t1:c.2105C>T
LRG_849:g.66883C>T
LRG_849p1:p.Ala702Val
NC_000015.9:g.42702183C>T
NM_000070.2:c.2105C>T
P20807:p.Ala702Val

Protein change:

A190V

Links:

UniProtKB: P20807#VAR_009594; dbSNP: rs886042557

NCBI 1000 Genomes Browser:

rs886042557

Molecular consequence:

NM_000070.3:c.2105C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_024344.2:c.2087C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_173087.2:c.1829C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_173088.2:c.569C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_173089.2:c.110C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_173090.2:c.110C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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GLT8D2 [Coturnix japonica]
GLT8D2 [Coturnix japonica]
Gene ID:107314759

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000334984	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Likely pathogenic (Sep 15, 2015)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 10330340, 16141003, 16650086, 9150160 Citation Link,
SCV001765281	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Mar 24, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000334984

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Likely pathogenic
(Sep 15, 2015)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Citation Link,

SCV001765281

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Mar 24, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	4	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Calpainopathy-a survey of mutations and polymorphisms.

Richard I, Roudaut C, Saenz A, Pogue R, Grimbergen JE, Anderson LV, Beley C, Cobo AM, de Diego C, Eymard B, Gallano P, Ginjaar HB, Lasa A, Pollitt C, Topaloglu H, Urtizberea JA, de Visser M, van der Kooi A, Bushby K, Bakker E, Lopez de Munain A, Fardeau M, et al.

Am J Hum Genet. 1999 Jun;64(6):1524-40.

PubMed [citation]

PMID:: 10330340
PMCID:: PMC1377896

Extensive scanning of the calpain-3 gene broadens the spectrum of LGMD2A phenotypes.

Piluso G, Politano L, Aurino S, Fanin M, Ricci E, Ventriglia VM, Belsito A, Totaro A, Saccone V, Topaloglu H, Nascimbeni AC, Fulizio L, Broccolini A, Canki-Klain N, Comi LI, Nigro G, Angelini C, Nigro V.

J Med Genet. 2005 Sep;42(9):686-93.

PubMed [citation]

PMID:: 16141003
PMCID:: PMC1736133

See all PubMed Citations (4)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000334984.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	4	not provided	not provided	clinical testing	PubMed (4)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		4	not provided	not provided	not provided

From GeneDx, SCV001765281.2

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

Description

Not observed at a significant frequency in large population cohorts (gnomAD); 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: 30056071, 27234031, 10330340, 9150160, 19556129, 16411092, 16650086, 15757244, 9266733, 27262448, 17994539, 17236769, 16141003, 35741838)

#	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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