Is ITGA3 p.Ile962Met (c.2886C>G) pathogenic?

ITGA3 p.Ile962Met (c.2886C>G) is classified Uncertain significance in ITGA3 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-28). AlphaMissense: likely benign (0.1219); Ultra-rare (popmax 0.0159%, amr); Associated with Inborn genetic diseases.

What condition is associated with ITGA3 p.Ile962Met (c.2886C>G)?

ITGA3 p.Ile962Met (c.2886C>G) is associated with Inborn genetic diseases (ClinVar).

How common is ITGA3 p.Ile962Met (c.2886C>G) in the general population?

ITGA3 p.Ile962Met (c.2886C>G) is ultra-rare (popmax 0.0159%, amr) (gnomAD).

What do computational predictors say about ITGA3 p.Ile962Met (c.2886C>G)?

AlphaMissense predicts likely benign (score 0.1219) — an in-silico prediction, not a clinical call.

ITGA3 p.Ile962Met

c.2886C>G · rs771100368 · VCV2239841

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1219 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0159%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1219	likely benign
REVEL	0.067	moderately benign-leaning
SaProt	LLR -6.24	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.13	GERP -3.8, phastCons 0.013
Regional constraint	o/e 0.84	unconstrained · MANE · 14 kb · p 6.1e-06 · regional, not allelic
Overall
CADD	11.73	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0159% Admixed American · 9/56,664 alleles

Filtering AF 0.00825% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00618%

Overall 0.00101% 16/1,588,130 alleles · ultra-rare exomes 14/1,435,972 · genomes 2/152,158 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0159%	6,296
Remaining individualsnot grpmax-eligible	0.00325%	30,768
European (non-Finnish)	0.000429%	233,120

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.Ile962Met
Coding: c.2886C>G
MANE Select: NM_002204
dbSNP: rs771100368
Type: single nucleotide variant
Location: chr17:50081375 (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

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ITGA3 p.Arg293Trp Uncertain significance ★★ ⚠ same condition
ITGA3 p.Arg524His Uncertain significance ★★ ⚠ same condition
ITGA3 p.Arg525Trp Uncertain significance ★★ ⚠ same condition
ITGA3 p.Arg589Pro Uncertain significance ★★ ⚠ same condition
ITGA3 p.Arg932Gln Uncertain significance ★★ ⚠ same condition
ITGA3 p.Glu668Asp Uncertain significance ★★ same condition
ITGA3 p.Gly533Ser Uncertain significance ★★ ⚠ same condition
ITGA3 p.Leu410Phe Uncertain significance ★★ ⚠ 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-ile962met (accessed [today's date]).

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