AIP p.Asn259=
c.777C>T · rs1242545854 · VCV2741410
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000847%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.21 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.82 | GERP -0.39, phastCons 1 |
| Overall | ||
| CADD | 13.57 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000847%
European (non-Finnish) · 10/1,179,992 alleles
Filtering AF
0.000429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000312%
Overall
0.000685%
10/1,458,920 alleles · very rare
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.Asn259=
- Coding
- c.777C>T
- MANE Select
- NM_017900 · reported on NM_003977
- dbSNP
- rs1242545854
- Type
- single nucleotide variant
- Location
- chr11:67490447 (GRCh38)
- Structure
- AlphaFold pLDDT 70.14 · 81 PDB
Similar variants
- AIP p.Asn259Lys Uncertain significance ★★ ⚠ same residue
- AIP p.Asn259Ser Uncertain significance ★ ⚠ same residue
- AIP p.Arg271Trp Pathogenic/Likely pathogenic ★★ same type
- AIP p.Arg304Ter Pathogenic ★★ same type
- AIP p.Arg81Ter Pathogenic ★★ same type
- AIP p.Cys238Tyr Likely pathogenic ★★ same type
- AIP p.Gln126Ter Pathogenic ★★ same type
- AIP p.Gln14Ter Pathogenic ★★ 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/aip-p-asn259 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown