Is ITGA3 p.Arg295= (c.885G>A) pathogenic?

ITGA3 p.Arg295= (c.885G>A) is classified Likely benign in ITGA3 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-11-08). Very rare (popmax 0.005%, amr); Associated with ITGA3-related disorder.

What condition is associated with ITGA3 p.Arg295= (c.885G>A)?

ITGA3 p.Arg295= (c.885G>A) is associated with ITGA3-related disorder (ClinVar).

How common is ITGA3 p.Arg295= (c.885G>A) in the general population?

ITGA3 p.Arg295= (c.885G>A) is very rare (popmax 0.005%, amr) (gnomAD).

ITGA3 p.Arg295=

c.885G>A · rs764721144 · VCV3045792

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.005%, amr)

Conditions

ITGA3-related disorder

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 3.5	GERP -0.27, phastCons 1
Overall
CADD	12.03	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.005% Admixed American · 3/60,034 alleles

Filtering AF 0.00133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000668%

Overall 0.000496% 8/1,613,918 alleles · very rare exomes 8/1,461,564 · genomes 0/152,354 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.005%	20,011
East Asian	0.00223%	44,874
European (non-Finnish)	0.000339%	295,007

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: ITGA3
Protein: p.Arg295=
Coding: c.885G>A
MANE Select: NM_002204
dbSNP: rs764721144
Type: single nucleotide variant
Location: chr17:50071444 (GRCh38)
Gene constraint: LOEUF 0.69 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.88

Full ITGA3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ITGA3-related disorder

Similar variants

ITGA3 p.Arg276Ter Likely pathogenic ★ same condition
ITGA3 p.Arg932Ter Likely pathogenic ★ same condition
ITGA3 p.Gln348Ter Likely pathogenic ★ same condition
ITGA3 p.Asp36Tyr Uncertain significance ★ ⚠ same condition
ITGA3 p.Pro506Thr Uncertain significance ⚠ same condition
ITGA3 c.1537+8C>A Likely benign same condition
ITGA3 c.2706+9C>T Likely benign same condition
ITGA3 p.Ala312= Likely benign 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/itga3-p-arg295 (accessed [today's date]).

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