Is ITGA3 p.Pro987Arg (c.2960C>G) pathogenic?

ITGA3 p.Pro987Arg (c.2960C>G) is classified Benign/Likely benign in ITGA3 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-06). AlphaMissense: likely benign (0.2223); Low-frequency (popmax 1.33%, amr).

How common is ITGA3 p.Pro987Arg (c.2960C>G) in the general population?

ITGA3 p.Pro987Arg (c.2960C>G) is low-frequency (popmax 1.33%, amr) (gnomAD).

What do computational predictors say about ITGA3 p.Pro987Arg (c.2960C>G)?

AlphaMissense predicts likely benign (score 0.2223) — an in-silico prediction, not a clinical call.

ITGA3 p.Pro987Arg

c.2960C>G · rs146126922 · VCV770643

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.2223 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.33%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2223	likely benign
REVEL	0.284	benign-leaning
SaProt	LLR -8.67	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 5.9	GERP 0.52, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 14 kb · p 6.1e-06 · regional, not allelic
Overall
CADD	26.2	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.33% Admixed American · 799/59,994 alleles

Filtering AF 1.26% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.22%

Overall 0.0722% 1,164/1,613,250 alleles · low-frequency exomes 979/1,461,004 · genomes 185/152,246 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	1.33%	75
East Asian	0.232%	432
Ashkenazi Jewishnot grpmax-eligible	0.166%	604
Remaining individualsnot grpmax-eligible	0.0977%	1,024
South Asian	0.0549%	1,821
Middle Eastern	0.0344%	2,903
Finnishnot grpmax-eligible	0.0204%	4,906
African / African-American	0.0133%	7,499
European (non-Finnish)	0.00644%	15,524

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.Pro987Arg
Coding: c.2960C>G
MANE Select: NM_002204
dbSNP: rs146126922
Type: single nucleotide variant
Location: chr17:50087784 (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

Similar variants

ITGA3 p.Pro987= Likely benign ★ same residue
ITGA3 c.2070+1G>A Pathogenic ★★ same type
ITGA3 p.Arg274Gln Likely pathogenic ★★ ⚠ same type
ITGA3 p.Arg875Ter Likely pathogenic ★★ same type
ITGA3 c.*48G>A Uncertain significance ★★ same type
ITGA3 c.*96G>A Uncertain significance ★★ same type
ITGA3 p.Ala1026Val Uncertain significance ★★ ⚠ same type
ITGA3 p.Ala1035Val Uncertain significance ★★ ⚠ same type

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-pro987arg (accessed [today's date]).

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