Is ITGA7 p.Asp573= (c.1719C>T) pathogenic?

ITGA7 p.Asp573= (c.1719C>T) is classified Likely benign in ITGA7 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-31). Ultra-rare (popmax 0.0165%, mid); Associated with congenital muscular dystrophy due to integrin alpha-7 deficiency.

What condition is associated with ITGA7 p.Asp573= (c.1719C>T)?

ITGA7 p.Asp573= (c.1719C>T) is associated with congenital muscular dystrophy due to integrin alpha-7 deficiency (ClinVar).

How common is ITGA7 p.Asp573= (c.1719C>T) in the general population?

ITGA7 p.Asp573= (c.1719C>T) is ultra-rare (popmax 0.0165%, mid) (gnomAD).

ITGA7 p.Asp573=

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.1719C>T · rs530050340 · VCV718839

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

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.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.14	GERP -2.6
Overall
CADD	6.198	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0165% Middle Eastern · 1/6,046 alleles

Filtering AF 0.0105% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00994%

Overall 0.0096% 155/1,614,156 alleles · ultra-rare exomes 147/1,461,826 · genomes 8/152,330 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0165%	6,046
European (non-Finnish)	0.0122%	8,195
Admixed American	0.005%	20,005
African / African-American	0.004%	25,019
Remaining individualsnot grpmax-eligible	0.0032%	31,252
South Asian	0.0022%	45,542

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.Asp573=
Coding: c.1719C>T
MANE Select: NM_002206
dbSNP: rs530050340
Type: single nucleotide variant
Location: chr12:55696917 (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.Asp573Glu Uncertain significance ★ ⚠ same residue
ITGA7 c.1887+2T>C Likely pathogenic ★★ same condition
ITGA7 p.Arg143Ter Pathogenic/Likely pathogenic ★★ same condition
ITGA7 p.Arg149Ter Pathogenic/Likely pathogenic ★★ same condition
ITGA7 p.Arg569Ter Pathogenic/Likely pathogenic ★★ same condition
ITGA7 p.Arg604Ter Pathogenic/Likely pathogenic ★★ same condition
ITGA7 p.Arg798Ter Pathogenic/Likely pathogenic ★★ same condition
ITGA7 p.Gln76Ter Pathogenic/Likely 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-asp573 (accessed [today's date]).

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