Is ITGA2 p.Thr1007= (c.3021T>G) pathogenic?

ITGA2 p.Thr1007= (c.3021T>G) is classified Benign/Likely benign in ITGA2 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2024-11-22). Rare (popmax 0.247%, nfe); Associated with platelet-type bleeding disorder 9.

What condition is associated with ITGA2 p.Thr1007= (c.3021T>G)?

ITGA2 p.Thr1007= (c.3021T>G) is associated with platelet-type bleeding disorder 9 (ClinVar).

How common is ITGA2 p.Thr1007= (c.3021T>G) in the general population?

ITGA2 p.Thr1007= (c.3021T>G) is rare (popmax 0.247%, nfe) (gnomAD).

ITGA2 p.Thr1007=

c.3021T>G · rs55980302 · VCV353776

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.247%, nfe)

Conditions

platelet-type bleeding disorder 9

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 -5.3	GERP -4.9
Overall
CADD	0.856	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.247% European (non-Finnish) · 2,910/1,179,040 alleles

Filtering AF 0.239% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.236%

Overall 0.196% 3,157/1,612,866 alleles · rare exomes 2,918/1,460,700 · genomes 239/152,166 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.247%	405
Finnishnot grpmax-eligible	0.212%	471
Remaining individualsnot grpmax-eligible	0.102%	976
Admixed American	0.035%	2,856
African / African-American	0.0227%	4,408
Ashkenazi Jewishnot grpmax-eligible	0.0101%	9,860
South Asian	0.00549%	18,213
East Asian	0.00223%	44,844

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.Thr1007=
Coding: c.3021T>G
MANE Select: NM_002203
dbSNP: rs55980302
Type: single nucleotide variant
Location: chr5:53080603 (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

platelet-type bleeding disorder 9 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ITGA2 p.Asn57Lys Uncertain significance ★★ ⚠ same condition
ITGA2 p.Gln690Arg Uncertain significance ★★ ⚠ same condition
ITGA2 p.Gly201Asp Uncertain significance ★★ ⚠ same condition
ITGA2 p.Gly205Val Uncertain significance ★★ ⚠ same condition
ITGA2 c.1312+12T>C Benign/Likely benign ★★ same condition
ITGA2 c.1807-6T>C Benign/Likely benign ★★ same condition
ITGA2 c.2236-62T>C Benign ★★ same condition
ITGA2 c.2742-4A>G Benign/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/itga2-p-thr1007 (accessed [today's date]).

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