Is ITGA3 p.Ala312= (c.936C>T) pathogenic?

ITGA3 p.Ala312= (c.936C>T) is classified Likely benign in ITGA3 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-04-23). Ultra-rare (popmax 0.066%, sas); Associated with ITGA3-related disorder.

What condition is associated with ITGA3 p.Ala312= (c.936C>T)?

ITGA3 p.Ala312= (c.936C>T) is associated with ITGA3-related disorder (ClinVar).

How common is ITGA3 p.Ala312= (c.936C>T) in the general population?

ITGA3 p.Ala312= (c.936C>T) is ultra-rare (popmax 0.066%, sas) (gnomAD).

ITGA3 p.Ala312=

c.936C>T · rs771016039 · VCV3036535

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.066%, sas)

Conditions

ITGA3-related disorder

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 2.2	GERP 0.88, phastCons 1
Overall
CADD	14.32	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.066% South Asian · 60/90,914 alleles

Filtering AF 0.0526% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0477%

Overall 0.00441% 71/1,609,562 alleles · ultra-rare exomes 66/1,457,344 · genomes 5/152,218 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.066%	1,515
Admixed American	0.00667%	14,987
East Asian	0.00223%	44,880
Remaining individualsnot grpmax-eligible	0.0016%	62,340
European (non-Finnish)	0.000424%	235,936

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.Ala312=
Coding: c.936C>T
MANE Select: NM_002204
dbSNP: rs771016039
Type: single nucleotide variant
Location: chr17:50071495 (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.Asp36Tyr Uncertain significance ★ ⚠ 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.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-ala312 (accessed [today's date]).

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