NM_002206.3(ITGA7):c.3364G>A (p.Gly1122Arg) AND Congenital muscular dystrophy due to integrin alpha-7 deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 10, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001936033.2

Allele description [Variation Report for NM_002206.3(ITGA7):c.3364G>A (p.Gly1122Arg)]

NM_002206.3(ITGA7):c.3364G>A (p.Gly1122Arg)

Gene:

ITGA7:integrin subunit alpha 7 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12q13.2

Genomic location:

Preferred name:

NM_002206.3(ITGA7):c.3364G>A (p.Gly1122Arg)

HGVS:

NC_000012.12:g.55685108C>T
NG_012343.1:g.32198G>A
NM_001144996.2:c.3376G>A
NM_001144997.2:c.3085G>A
NM_001367993.1:c.3037G>A
NM_001367994.1:c.2020G>A
NM_001374465.1:c.3346G>A
NM_001410977.1:c.3496G>A
NM_001414029.1:c.3358G>A
NM_001414030.1:c.3289G>A
NM_001414031.1:c.3277G>A
NM_001414032.1:c.3244G>A
NM_001414033.1:c.3181G>A
NM_001414034.1:c.3139G>A
NM_001414035.1:c.3025G>A
NM_002206.3:c.3364G>AMANE SELECT
NP_001138468.1:p.Gly1126Arg
NP_001138469.1:p.Gly1029Arg
NP_001138469.1:p.Gly1029Arg
NP_001354922.1:p.Gly1013Arg
NP_001354923.1:p.Gly674Arg
NP_001361394.1:p.Gly1116Arg
NP_001397906.1:p.Gly1166Arg
NP_001400958.1:p.Gly1120Arg
NP_001400959.1:p.Gly1097Arg
NP_001400960.1:p.Gly1093Arg
NP_001400961.1:p.Gly1082Arg
NP_001400962.1:p.Gly1061Arg
NP_001400963.1:p.Gly1047Arg
NP_001400964.1:p.Gly1009Arg
NP_002197.2:p.Gly1122Arg
LRG_871t1:c.3364G>A
LRG_871t2:c.3085G>A
LRG_871:g.32198G>A
LRG_871p1:p.Gly1122Arg
LRG_871p2:p.Gly1029Arg
NC_000012.11:g.56078892C>T
NM_001144997.1:c.3085G>A

Protein change:

G1009R

Links:

dbSNP: rs750258372

NCBI 1000 Genomes Browser:

rs750258372

Molecular consequence:

NM_001144996.2:c.3376G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001144997.2:c.3085G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001367993.1:c.3037G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001367994.1:c.2020G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374465.1:c.3346G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001410977.1:c.3496G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001414029.1:c.3358G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001414030.1:c.3289G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001414031.1:c.3277G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001414032.1:c.3244G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001414033.1:c.3181G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001414034.1:c.3139G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001414035.1:c.3025G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002206.3:c.3364G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Congenital muscular dystrophy due to integrin alpha-7 deficiency
Synonyms:: MYOPATHY, CONGENITAL, DUE TO INTEGRIN ALPHA-7 DEFICIENCY; Congenital muscular dystrophy with integrin alpha-7 deficiency; Muscular dystrophy, congenital, due to ITGA7 deficiency
Identifiers:: MONDO: MONDO:0013177; MedGen: C2750786; Orphanet: 34520; OMIM: 613204

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002188393	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 10, 2022)	germline	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

SCV002188393

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 10, 2022)

germline

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV002188393.2

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

Description

This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 1122 of the ITGA7 protein (p.Gly1122Arg). This variant is present in population databases (rs750258372, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with ITGA7-related conditions. ClinVar contains an entry for this variant (Variation ID: 1417080). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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		not provided	not provided	not provided	not provided

Last Updated: Dec 24, 2023

ClinVar

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