ABI1 p.Pro264=
c.792T>C · rs781477958 · VCV2640369
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0225%, sas)
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 1.1 | GERP 0.72, phastCons 0.99 |
| Overall | ||
| CADD | 9.242 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0225%
South Asian · 20/88,724 alleles
Filtering AF
0.0149%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0124%
Overall
0.00137%
22/1,606,394 alleles · ultra-rare
exomes 22/1,454,166 · genomes 0/152,228 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0225% | 4,436 |
| Admixed American | 0.00171% | 58,622 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,170 |
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
- ABI1
- Protein
- p.Pro264=
- Coding
- c.792T>C
- MANE Select
- NM_001012750
- dbSNP
- rs781477958
- Type
- single nucleotide variant
- Location
- chr10:26765246 (GRCh38)
- Gene constraint
- LOEUF 0.41 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 66.57 · 1 PDB
- Residue 264
- the 'disordered' region
Similar variants
- ABI1 p.Pro387= Benign ★★ same type
- PDSS1 c.*157T>G Benign/Likely benign ★★ same type
- ABI1 c.820+1285G>T Uncertain significance ★ ⚠ same type
- ABI1 c.820+1311C>T Uncertain significance ★ ⚠ same type
- ABI1 c.820+1315T>A Uncertain significance ★ ⚠ same type
- ABI1 p.Ala275Val Uncertain significance ★ ⚠ same type
- ABI1 p.Arg138Trp Uncertain significance ★ ⚠ same type
- ABI1 p.Arg189Pro 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/abi1-p-pro264 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown