Is ITGA3 p.Asp36Tyr (c.106G>T) pathogenic?

ITGA3 p.Asp36Tyr (c.106G>T) is classified Uncertain significance in ITGA3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-09). AlphaMissense: likely pathogenic (0.9472); Very rare (popmax 0.00136%, afr); Associated with ITGA3-related disorder.

What condition is associated with ITGA3 p.Asp36Tyr (c.106G>T)?

ITGA3 p.Asp36Tyr (c.106G>T) is associated with ITGA3-related disorder (ClinVar).

How common is ITGA3 p.Asp36Tyr (c.106G>T) in the general population?

ITGA3 p.Asp36Tyr (c.106G>T) is very rare (popmax 0.00136%, afr) (gnomAD).

What do computational predictors say about ITGA3 p.Asp36Tyr (c.106G>T)?

AlphaMissense predicts likely pathogenic (score 0.9472) — an in-silico prediction, not a clinical call.

ITGA3 p.Asp36Tyr

c.106G>T · rs1322013575 · VCV2631334

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9472 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00136%, afr)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

ITGA3-related disorder

Computational evidence

Protein change
AlphaMissense	0.9472	likely pathogenic · top 10% in ITGA3
REVEL	0.773	moderately pathogenic-leaning
SaProt	LLR -16.27	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.9, phastCons 1
Regional constraint	o/e 0.67	unconstrained · MANE · 18 kb · p 5.2e-14 · regional, not allelic
Overall
CADD	32.0	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

Grpmax group 0.00136% African / African-American · 1/73,612 alleles

Overall 6.4e-05% 1/1,561,322 alleles · very rare exomes 1/1,408,954 · genomes 0/152,368 · joint denominator

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.Asp36Tyr
Coding: c.106G>T
MANE Select: NM_002204
dbSNP: rs1322013575
Type: single nucleotide variant
Location: chr17:50056545 (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

ITGA3-related disorder

Similar variants

ITGA3 p.Arg276Ter Likely pathogenic ★ same condition
ITGA3 p.Arg932Ter Likely pathogenic ★ same condition
ITGA3 p.Gln348Ter Likely pathogenic ★ same condition
ITGA3 p.Pro506Thr Uncertain significance ⚠ same condition
ITGA3 c.1537+8C>A Likely benign same condition
ITGA3 c.2706+9C>T Likely benign same condition
ITGA3 p.Ala312= Likely benign same condition
ITGA3 p.Arg295= 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/itga3-p-asp36tyr (accessed [today's date]).

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