Is ITGA2 p.Phe307Cys (c.920T>G) pathogenic?

ITGA2 p.Phe307Cys (c.920T>G) is classified Uncertain significance in ITGA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-09-30). AlphaMissense: likely pathogenic (0.9822); Absent from gnomAD v4.1.

How common is ITGA2 p.Phe307Cys (c.920T>G) in the general population?

ITGA2 p.Phe307Cys (c.920T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ITGA2 p.Phe307Cys (c.920T>G)?

AlphaMissense predicts likely pathogenic (score 0.9822) — an in-silico prediction, not a clinical call.

ITGA2 p.Phe307Cys

c.920T>G · VCV4970328

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9822 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9822	likely pathogenic · top 3% in ITGA2
REVEL	0.909	moderately pathogenic-leaning
SaProt	LLR -13.99	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · T>A here scores Δ0.89 · evaluated, not missing
Constraint at this position
Conservation	phyloP 7.9	GERP 2.5, phastCons 1
Regional constraint	o/e 0.94	unconstrained · MANE · 81 kb · p 0.11 · regional, not allelic
Overall
CADD	31.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ITGA2
Protein: p.Phe307Cys
Coding: c.920T>G
MANE Select: NM_002203
Type: single nucleotide variant
Location: chr5:53055678 (GRCh38)
Gene constraint: LOEUF 0.789 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.80 · 23 PDB
Residue 307: a β-strand; the vwfa domain

Full ITGA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ITGA2 p.Asn57Lys Uncertain significance ★★ ⚠ same type
ITGA2 p.Gln690Arg Uncertain significance ★★ ⚠ same type
ITGA2 p.Gly201Asp Uncertain significance ★★ ⚠ same type
ITGA2 p.Gly205Val Uncertain significance ★★ ⚠ same type
ITGA2 c.1173+172A>T Benign ★★ same type
ITGA2 c.1312+12T>C Benign/Likely benign ★★ same type
ITGA2 c.1313-30T>G Benign ★★ same type
ITGA2 c.1313-39T>C Benign ★★ 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/itga2-p-phe307cys (accessed [today's date]).

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