Is ITGA3 p.Ser130Asn (c.389G>A) pathogenic?

ITGA3 p.Ser130Asn (c.389G>A) is classified Uncertain significance in ITGA3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-24). AlphaMissense: likely pathogenic (0.9392); Very rare (popmax 8.48e-05%, nfe); Associated with Inborn genetic diseases.

What condition is associated with ITGA3 p.Ser130Asn (c.389G>A)?

ITGA3 p.Ser130Asn (c.389G>A) is associated with Inborn genetic diseases (ClinVar).

How common is ITGA3 p.Ser130Asn (c.389G>A) in the general population?

ITGA3 p.Ser130Asn (c.389G>A) is very rare (popmax 8.48e-05%, nfe) (gnomAD).

What do computational predictors say about ITGA3 p.Ser130Asn (c.389G>A)?

AlphaMissense predicts likely pathogenic (score 0.9392) — an in-silico prediction, not a clinical call.

ITGA3 p.Ser130Asn

c.389G>A · rs372201503 · VCV2478437

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9392 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.48e-05%, nfe)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9392	likely pathogenic
REVEL	0.429	indeterminate
SaProt	LLR -12.68	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.8, phastCons 1
Regional constraint	o/e 0.67	unconstrained · MANE · 18 kb · p 5.2e-14 · regional, not allelic
Overall
CADD	28.3	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 8.48e-05% European (non-Finnish) · 1/1,179,774 alleles

Overall 6.2e-05% 1/1,613,006 alleles · very rare exomes 1/1,460,744 · genomes 0/152,262 · 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.Ser130Asn
Coding: c.389G>A
MANE Select: NM_002204
dbSNP: rs372201503
Type: single nucleotide variant
Location: chr17:50064582 (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

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ITGA3 p.Arg293Trp Uncertain significance ★★ ⚠ same condition
ITGA3 p.Arg524His Uncertain significance ★★ ⚠ same condition
ITGA3 p.Arg525Trp Uncertain significance ★★ ⚠ same condition
ITGA3 p.Arg589Pro Uncertain significance ★★ ⚠ same condition
ITGA3 p.Arg932Gln Uncertain significance ★★ ⚠ same condition
ITGA3 p.Glu668Asp Uncertain significance ★★ same condition
ITGA3 p.Gly533Ser Uncertain significance ★★ ⚠ same condition
ITGA3 p.Leu410Phe 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/itga3-p-ser130asn (accessed [today's date]).

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