Is ITGA7 p.Pro397fs (c.1190del) pathogenic?

ITGA7 p.Pro397fs (c.1190del) is classified Likely pathogenic in ITGA7 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-24). Very rare (popmax 0.00552%, sas); Associated with congenital muscular dystrophy due to integrin alpha-7 deficiency.

What condition is associated with ITGA7 p.Pro397fs (c.1190del)?

ITGA7 p.Pro397fs (c.1190del) is associated with congenital muscular dystrophy due to integrin alpha-7 deficiency (ClinVar).

How common is ITGA7 p.Pro397fs (c.1190del) in the general population?

ITGA7 p.Pro397fs (c.1190del) is very rare (popmax 0.00552%, sas) (gnomAD).

ITGA7 p.Pro397fs

Q: How is Congenital muscular dystrophy with integrin alpha-7 deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.1190del · VCV4081464

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00552%, sas)

Conditions

congenital muscular dystrophy due to integrin alpha-7 deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 7 of 25
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.9	GERP 1.1, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00552% South Asian · 5/90,636 alleles

Filtering AF 0.00211% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00137%

Overall 0.00031% 5/1,610,930 alleles · very rare exomes 5/1,458,830 · genomes 0/152,100 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: ITGA7
Protein: p.Pro397fs
Coding: c.1190del
MANE Select: NM_002206
Type: Deletion
Location: chr12:55698385 (GRCh38)
Gene constraint: LOEUF 0.738 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.14

Full ITGA7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

congenital muscular dystrophy due to integrin alpha-7 deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Congenital muscular dystrophy with integrin alpha-7 deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal
Prevalence: <1 / 1 000 000 (Europe)

Similar variants

ITGA7 p.Pro397= Uncertain significance ★ same residue
ITGA7 p.Gly363fs Pathogenic/Likely pathogenic ★★ same condition
ITGA7 p.Ile483fs Pathogenic/Likely pathogenic ★★ same condition
ITGA7 c.1410-3del Benign/Likely benign ★★ same condition
ITGA7 p.Ala728fs Likely pathogenic ★ same condition
ITGA7 p.Ala940fs Pathogenic ★ same condition
ITGA7 p.Arg173fs Pathogenic ★ same condition
ITGA7 p.Asn289fs Pathogenic ★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/itga7-p-pro397fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown