ABI3 p.Pro299=
c.897T>G · VCV4874395
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.008%, afr)
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 -20 | GERP -3 |
| Overall | ||
| CADD | 0.006 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.008%
African / African-American · 6/75,024 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00228%
Overall
0.000744%
12/1,613,790 alleles · very rare
exomes 10/1,461,516 · genomes 2/152,274 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.008% | 12,504 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,622 |
| Admixed American | 0.00167% | 59,968 |
| European (non-Finnish) | 8.48e-05% | 1,179,864 |
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
- ABI3
- Protein
- p.Pro299=
- Coding
- c.897T>G
- MANE Select
- NM_016428
- Type
- single nucleotide variant
- Location
- chr17:49222185 (GRCh38)
- Gene constraint
- LOEUF 1.113 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.31
- Residue 299
- the 'disordered' region
Similar variants
- ABI3 p.Glu87= Benign ★★ same type
- ABI3 p.Pro174= Benign ★★ same type
- ABI3 p.Ala126Ser Uncertain significance ★ ⚠ same type
- ABI3 p.Ala173Gly Uncertain significance ★ ⚠ same type
- ABI3 p.Ala173Ser Uncertain significance ★ ⚠ same type
- ABI3 p.Ala178Thr Uncertain significance ★ ⚠ same type
- ABI3 p.Ala18Thr Uncertain significance ★ ⚠ same type
- ABI3 p.Ala204Val 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/abi3-p-pro299 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown