AIP p.Pro99=
c.297G>A · rs767511957 · VCV1649033
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.0033%, sas)
Conditions
1
hereditary neoplastic syndrome
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 -12 | GERP -3.9 |
| Overall | ||
| CADD | 1.282 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0033%
South Asian · 3/90,964 alleles
Filtering AF
0.000876%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000443%
Overall
0.000274%
4/1,458,884 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0033% | 30,321 |
| European (non-Finnish) | 8.48e-05% | 1,179,664 |
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
- AIP
- Protein
- p.Pro99=
- Coding
- c.297G>A
- MANE Select
- NM_003977
- dbSNP
- rs767511957
- Type
- single nucleotide variant
- Location
- chr11:67489284 (GRCh38)
- Gene constraint
- LOEUF 0.626 · pLI 0.28 (gnomAD)
- Structure
- AlphaFold pLDDT 91.09 · 5 PDB
- Residue 99
- the ppiase fkbp-type domain; an α-helix
Similar variants
- AIP p.Pro99Leu Uncertain significance ★★ ⚠ same residue
- AIP p.Pro99Gln Uncertain significance ★ ⚠ same residue
- AIP p.Arg271Trp Pathogenic/Likely pathogenic ★★ same condition
- AIP p.Arg304Ter Pathogenic ★★ same condition
- AIP p.Arg81Ter Pathogenic ★★ same condition
- AIP p.Cys238Tyr Likely pathogenic ★★ same condition
- AIP p.Gln126Ter Pathogenic ★★ same condition
- AIP p.Gln14Ter Pathogenic ★★ same condition
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/aip-p-pro99 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown