NM_000070.3(CAPN3):c.1622G>A (p.Arg541Gln) AND not provided

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Feb 16, 2022
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:: RCV000790834.16

Allele description [Variation Report for NM_000070.3(CAPN3):c.1622G>A (p.Arg541Gln)]

NM_000070.3(CAPN3):c.1622G>A (p.Arg541Gln)

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.1622G>A (p.Arg541Gln)

HGVS:

NC_000015.10:g.42402879G>A
NG_008660.1:g.59777G>A
NM_000070.3:c.1622G>AMANE SELECT
NM_024344.2:c.1622G>A
NM_173087.2:c.1478G>A
NM_173088.2:c.86G>A
NP_000061.1:p.Arg541Gln
NP_000061.1:p.Arg541Gln
NP_077320.1:p.Arg541Gln
NP_775110.1:p.Arg493Gln
NP_775111.1:p.Arg29Gln
LRG_849t1:c.1622G>A
LRG_849:g.59777G>A
LRG_849p1:p.Arg541Gln
NC_000015.9:g.42695077G>A
NM_000070.2:c.1622G>A
P20807:p.Arg541Gln

Protein change:

R29Q

Links:

UniProtKB: P20807#VAR_009588; dbSNP: rs398123143

NCBI 1000 Genomes Browser:

rs398123143

Molecular consequence:

NM_000070.3:c.1622G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_024344.2:c.1622G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_173087.2:c.1478G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_173088.2:c.86G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Rattus norvegicus insulin-like 6 (Insl6), mRNA
Rattus norvegicus insulin-like 6 (Insl6), mRNA
gi|12018233|ref|NM_022583.1|

Nucleotide
ARSB [Eublepharis macularius]
ARSB [Eublepharis macularius]
Gene ID:129335000

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000331404	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions)	Likely pathogenic (Sep 18, 2015)	germline	clinical testing	Citation Link,
SCV002770909	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Likely pathogenic (Feb 16, 2022)	unknown	clinical testing	PubMed (6) [See all records that cite these PMIDs] 16411092, 16141003, 32668095, 31555977, 10330340, 26467025

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000331404

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions)

Likely pathogenic
(Sep 18, 2015)

germline

clinical testing

Citation Link,

SCV002770909

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Likely pathogenic
(Feb 16, 2022)

unknown

clinical testing

PubMed (6)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	3	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Calpain-3 mutations in Turkey.

Balci B, Aurino S, Haliloglu G, Talim B, Erdem S, Akcören Z, Tan E, Caglar M, Richard I, Nigro V, Topaloglu H, Dincer P.

Eur J Pediatr. 2006 May;165(5):293-8. Epub 2006 Jan 13.

PubMed [citation]

PMID:: 16411092

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 (6)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000331404.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	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	unknown	not provided	not provided	not provided		3	not provided	not provided	not provided

From Athena Diagnostics, SCV002770909.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

The frequency of this variant in the general population is consistent with pathogenicity (http://gnomad.broadinstitute.org). This variant is statistically more frequent in affected individuals than in the general population and/or healthy controls. In multiple individuals, this variant has been seen with a single recessive pathogenic variant in the same gene, suggesting this variant may also be pathogenic. Computational tools predict that this variant is damaging.

#	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		not provided	not provided	not provided	not provided

Last Updated: Nov 3, 2024

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