NM_000070.3(CAPN3):c.2092_2095dup (p.Ser699delinsThrTer) AND Muscular dystrophy, limb-girdle, autosomal dominant 4

Germline classification:: no classifications from unflagged records (1 submission)
Last evaluated:: Apr 24, 2024
Review status:: no classifications from unflagged records

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:: RCV003460307.2

Allele description [Variation Report for NM_000070.3(CAPN3):c.2092_2095dup (p.Ser699delinsThrTer)]

NM_000070.3(CAPN3):c.2092_2095dup (p.Ser699delinsThrTer)

Gene:

CAPN3:calpain 3 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

15q15.1

Genomic location:

Preferred name:

NM_000070.3(CAPN3):c.2092_2095dup (p.Ser699delinsThrTer)

HGVS:

NC_000015.10:g.42409972_42409975dup
NG_008660.1:g.66870_66873dup
NM_000070.3:c.2092_2095dupMANE SELECT
NM_024344.2:c.2074_2077dup
NM_173087.2:c.1816_1819dup
NM_173088.2:c.556_559dup
NM_173089.2:c.97_100dup
NM_173090.2:c.97_100dup
NM_212464.2:c.*1190_*1193dup
NM_212467.2:c.*1767_*1770dup
NP_000061.1:p.Ser699delinsThrTer
NP_077320.1:p.Ser693delinsThrTer
NP_775110.1:p.Ser607delinsThrTer
NP_775111.1:p.Ser187delinsThrTer
NP_775112.1:p.Ser34delinsThrTer
NP_775113.1:p.Ser34delinsThrTer
LRG_849t1:c.2092_2095dup
LRG_849:g.66870_66873dup
LRG_849p1:p.Ser699delinsThrTer
NC_000015.9:g.42702170_42702173dup

Molecular consequence:

NM_000070.3:c.2092_2095dup - nonsense - [Sequence Ontology: SO:0001587]
NM_024344.2:c.2074_2077dup - nonsense - [Sequence Ontology: SO:0001587]
NM_173087.2:c.1816_1819dup - nonsense - [Sequence Ontology: SO:0001587]
NM_173088.2:c.556_559dup - nonsense - [Sequence Ontology: SO:0001587]
NM_173089.2:c.97_100dup - nonsense - [Sequence Ontology: SO:0001587]
NM_173090.2:c.97_100dup - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Muscular dystrophy, limb-girdle, autosomal dominant 4
Synonyms:: MUSCULAR DYSTROPHY, LIMB-GIRDLE, TYPE 1I
Identifiers:: MONDO: MONDO:0029133; MedGen: C4748295; OMIM: 618129

Recent activity

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protein ALWAYS EARLY (aly), partial [Graphium agamemnon]
protein ALWAYS EARLY (aly), partial [Graphium agamemnon]
gi|2570953271|gb|WML12653.1|

Protein
eukaryotic translation initiation factor 3 subunit M, partial [Nessaea aglaura]
eukaryotic translation initiation factor 3 subunit M, partial [Nessaea aglaura]
gi|2570992758|gb|WML23204.1|

Protein
protein ALWAYS EARLY (aly), partial [Hesperia comma]
protein ALWAYS EARLY (aly), partial [Hesperia comma]
gi|2570953301|gb|WML12668.1|

Protein
cytochrome oxidase subunit I, partial (mitochondrion) [Cerastoderma glaucum]
cytochrome oxidase subunit I, partial (mitochondrion) [Cerastoderma glaucum]
gi|1870356317|gb|QLI47536.1|

Protein
eukaryotic translation initiation factor 3 subunit M, partial [Riodina lysippus]
eukaryotic translation initiation factor 3 subunit M, partial [Riodina lysippus]
gi|2570992774|gb|WML23212.1|

Protein

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No clinical assertions found. See "Flagged submissions" below.

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Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Baylor Genetics, SCV004213735.1

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

Flagged submissions

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004213735	Baylor Genetics	flagged submission Reason: Other Notes: Flagging candidate with reason of insufficient supporting evidence. This gene has been classified as having a limited gene-disease relationship by a ClinGen Expert Panel. (ACMG Guidelines, 2015)	Likely pathogenic (Aug 14, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004213735

Baylor Genetics

flagged submission

Reason: Other

Notes: Flagging candidate with reason of insufficient supporting evidence. This gene has been classified as having a limited gene-disease relationship by a ClinGen Expert Panel.

(ACMG Guidelines, 2015)

Likely pathogenic
(Aug 14, 2023)

unknown

clinical testing

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

Last Updated: Jul 23, 2024

ClinVar

Relating variation to medicine