ITGA1 p.Pro83=
c.249A>G · rs61757093 · VCV713618
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.626%, nfe)
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 -1.8 | GERP -3.9 |
| Overall | ||
| CADD | 6.913 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.626%
European (non-Finnish) · 7,384/1,179,740 alleles
Filtering AF
0.614%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.609%
Overall
0.514%
8,293/1,613,816 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.626% | 160 |
| Admixed American | 0.587% | 170 |
| Remaining individualsnot grpmax-eligible | 0.454% | 220 |
| Middle Eastern | 0.313% | 319 |
| Ashkenazi Jewishnot grpmax-eligible | 0.166% | 604 |
| African / African-American | 0.117% | 853 |
| Finnishnot grpmax-eligible | 0.1% | 1,000 |
| South Asian | 0.0582% | 1,718 |
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
- ITGA1
- Protein
- p.Pro83=
- Coding
- c.249A>G
- MANE Select
- NM_181501
- dbSNP
- rs61757093
- Type
- single nucleotide variant
- Location
- chr5:52861513 (GRCh38)
- Gene constraint
- LOEUF 0.771 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.68 · 7 PDB
- Residue 83
- a disulfide bond
Similar variants
- ITGA1 p.Pro83Ser Uncertain significance ★ ⚠ same residue
- ITGA1 p.Ala823Thr Uncertain significance ★★ ⚠ same type
- ITGA1 p.Asn966Ser Uncertain significance ★★ ⚠ same type
- ITGA1 c.1455+7T>C Benign ★★ same type
- ITGA1 p.Glu221= Benign ★★ same type
- ITGA1 p.Phe737= Benign ★★ same type
- ITGA1 p.Ser1096= Benign ★★ same type
- ITGA1 p.Ser1121Arg 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/itga1-p-pro83 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown