Is ITGA4 p.Ala960= (c.2880G>A) pathogenic?

ITGA4 p.Ala960= (c.2880G>A) is classified Likely benign in ITGA4 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-08-16). Very rare (popmax 0.0095%, afr); Associated with ITGA4-related disorder.

What condition is associated with ITGA4 p.Ala960= (c.2880G>A)?

ITGA4 p.Ala960= (c.2880G>A) is associated with ITGA4-related disorder (ClinVar).

How common is ITGA4 p.Ala960= (c.2880G>A) in the general population?

ITGA4 p.Ala960= (c.2880G>A) is very rare (popmax 0.0095%, afr) (gnomAD).

ITGA4 p.Ala960=

c.2880G>A · rs201433950 · VCV3052620

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0095%, afr)

Conditions

ITGA4-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 1.6	GERP -2.6, phastCons 0.96
Overall
CADD	6.906	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0095% African / African-American · 7/73,664 alleles

Filtering AF 0.00444% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00398%

Overall 0.00534% 83/1,553,678 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0095%	10,523
East Asian	0.009%	11,105
Admixed American	0.00668%	14,964
European (non-Finnish)	0.00551%	18,164
Remaining individualsnot grpmax-eligible	0.00498%	20,100
South Asian	0.00336%	29,775

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: ITGA4
Protein: p.Ala960=
Coding: c.2880G>A
MANE Select: NM_000885
dbSNP: rs201433950
Type: single nucleotide variant
Location: chr2:181534367 (GRCh38)
Gene constraint: LOEUF 0.603 · pLI 0.20 (gnomAD)
Structure: AlphaFold pLDDT 84.11 · 7 PDB

Full ITGA4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ITGA4-related disorder

Similar variants

ITGA4 p.Ala960Thr Uncertain significance ★ ⚠ same residue
ITGA4 p.Ala960Val Uncertain significance ★ ⚠ same residue
ITGA4 p.Ser547Gly Uncertain significance ⚠ same condition
ITGA4 c.1340-8T>A Likely benign same condition
ITGA4 p.Leu358= Likely benign same condition
ITGA4 p.Thr673= Likely benign same condition
ITGA4 c.3004-11_3004-3dup Likely benign same condition
ITGA4 c.1042-6A>G 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/itga4-p-ala960 (accessed [today's date]).

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