NM_002206.3(ITGA7):c.2701A>G (p.Ile901Val) AND Congenital muscular dystrophy due to integrin alpha-7 deficiency

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Jan 29, 2024
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:: RCV001085864.9

Allele description [Variation Report for NM_002206.3(ITGA7):c.2701A>G (p.Ile901Val)]

NM_002206.3(ITGA7):c.2701A>G (p.Ile901Val)

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.2701A>G (p.Ile901Val)

HGVS:

NC_000012.12:g.55693152T>C
NG_012343.1:g.24154A>G
NM_001144996.2:c.2713A>G
NM_001144997.2:c.2422A>G
NM_001367993.1:c.2374A>G
NM_001367994.1:c.1357A>G
NM_001374465.1:c.2683A>G
NM_001410977.1:c.2833A>G
NM_001414029.1:c.2695A>G
NM_001414030.1:c.2626A>G
NM_001414031.1:c.2614A>G
NM_001414032.1:c.2581A>G
NM_001414033.1:c.2518A>G
NM_001414034.1:c.2476A>G
NM_001414035.1:c.2362A>G
NM_002206.3:c.2701A>GMANE SELECT
NP_001138468.1:p.Ile905Val
NP_001138469.1:p.Ile808Val
NP_001138469.1:p.Ile808Val
NP_001354922.1:p.Ile792Val
NP_001354923.1:p.Ile453Val
NP_001361394.1:p.Ile895Val
NP_001397906.1:p.Ile945Val
NP_001400958.1:p.Ile899Val
NP_001400959.1:p.Ile876Val
NP_001400960.1:p.Ile872Val
NP_001400961.1:p.Ile861Val
NP_001400962.1:p.Ile840Val
NP_001400963.1:p.Ile826Val
NP_001400964.1:p.Ile788Val
NP_002197.2:p.Ile901Val
LRG_871t1:c.2701A>G
LRG_871t2:c.2422A>G
LRG_871:g.24154A>G
LRG_871p1:p.Ile901Val
LRG_871p2:p.Ile808Val
NC_000012.11:g.56086936T>C
NM_001144997.1:c.2422A>G
NM_002206.2:c.2701A>G

Protein change:

I453V

Links:

dbSNP: rs113651939

NCBI 1000 Genomes Browser:

rs113651939

Molecular consequence:

NM_001144996.2:c.2713A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001144997.2:c.2422A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001367993.1:c.2374A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001367994.1:c.1357A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374465.1:c.2683A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001410977.1:c.2833A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001414029.1:c.2695A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001414030.1:c.2626A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001414031.1:c.2614A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001414032.1:c.2581A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001414033.1:c.2518A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001414034.1:c.2476A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001414035.1:c.2362A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_002206.3:c.2701A>G - 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
SCV000648324	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 29, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002806122	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Nov 12, 2021)	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

SCV000648324

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 29, 2024)

germline

clinical testing

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

SCV002806122

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Nov 12, 2021)

unknown

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

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 Invitae, SCV000648324.8

#	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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Fulgent Genetics, Fulgent Genetics, SCV002806122.1

#	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

Last Updated: Apr 15, 2024

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