ITGA4 p.Ala15=
c.45C>A · rs201902294 · VCV2651732
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00835%, amr)
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 0.7 | GERP -2.3, phastCons 0.98 |
| Overall | ||
| CADD | 6.995 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00835%
Admixed American · 5/59,888 alleles
Filtering AF
0.00324%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00207%
Overall
0.00143%
23/1,611,950 alleles · very rare
exomes 22/1,459,986 · genomes 1/151,964 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00835% | 11,978 |
| European (non-Finnish) | 0.00153% | 65,536 |
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.Ala15=
- Coding
- c.45C>A
- MANE Select
- NM_000885
- dbSNP
- rs201902294
- Type
- single nucleotide variant
- Location
- chr2:181457699 (GRCh38)
- Gene constraint
- LOEUF 0.603 · pLI 0.20 (gnomAD)
- Structure
- AlphaFold pLDDT 84.11 · 7 PDB
Similar variants
- ITGA4 c.1042-6A>G Benign ★★ same type
- ITGA4 c.2884-7C>G Likely benign ★★ same type
- ITGA4 c.754+10A>C Benign ★★ same type
- ITGA4 c.841-15T>C Benign ★★ same type
- ITGA4 p.Ser634Thr Benign ★★ same type
- ITGA4 c.*2719T>C Likely pathogenic ★ same type
- CERKL c.*1212A>G Uncertain significance ★ same type
- CERKL c.*25G>T Uncertain significance ★ 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-ala15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown