Is ITGA2 p.Pro1002Ser (c.3004C>T) pathogenic?

ITGA2 p.Pro1002Ser (c.3004C>T) is classified Uncertain significance in ITGA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-12). AlphaMissense: likely benign (0.1827); Very rare (popmax 0.00223%, eas); Associated with Inborn genetic diseases.

What condition is associated with ITGA2 p.Pro1002Ser (c.3004C>T)?

ITGA2 p.Pro1002Ser (c.3004C>T) is associated with Inborn genetic diseases (ClinVar).

How common is ITGA2 p.Pro1002Ser (c.3004C>T) in the general population?

ITGA2 p.Pro1002Ser (c.3004C>T) is very rare (popmax 0.00223%, eas) (gnomAD).

What do computational predictors say about ITGA2 p.Pro1002Ser (c.3004C>T)?

AlphaMissense predicts likely benign (score 0.1827) — an in-silico prediction, not a clinical call.

ITGA2 p.Pro1002Ser

c.3004C>T · VCV3861508

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1827 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1827	likely benign
REVEL	0.079	moderately benign-leaning
SaProt	LLR -6.76	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 4.1	GERP 1.6, phastCons 1
Regional constraint	o/e 0.90	unconstrained · MANE · 20 kb · p 0.016 · regional, not allelic
Overall
CADD	22.1	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 0.00223% East Asian · 1/44,850 alleles

Overall 0.000658% 1/152,000 alleles · very rare

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: ITGA2
Protein: p.Pro1002Ser
Coding: c.3004C>T
MANE Select: NM_002203
Type: single nucleotide variant
Location: chr5:53080586 (GRCh38)
Gene constraint: LOEUF 0.789 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.80 · 23 PDB

Full ITGA2 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

ITGA2 p.Pro1002Thr Uncertain significance ★ ⚠ same residue
ITGA2 p.Asn57Lys Uncertain significance ★★ ⚠ same condition
ITGA2 p.Gly201Asp Uncertain significance ★★ ⚠ same condition
ITGA2 p.Gly205Val Uncertain significance ★★ ⚠ same condition
ITGA2 p.Ala1053Thr Uncertain significance ★ ⚠ same condition
ITGA2 p.Ala1085Pro Uncertain significance ★ ⚠ same condition
ITGA2 p.Ala1085Thr Uncertain significance ★ ⚠ same condition
ITGA2 p.Ala1151Gly 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/itga2-p-pro1002ser (accessed [today's date]).

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