AHI1 p.Lys799=
c.2397G>A · rs747639578 · VCV1587795
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0036%, sas)
Conditions
1
Joubert syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.19 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.9 | GERP -2.5, phastCons 0.002 |
| Overall | ||
| CADD | 1.569 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0036%
South Asian · 3/83,370 alleles
Filtering AF
0.000956%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000465%
Overall
0.000382%
6/1,570,174 alleles · very rare
exomes 6/1,418,430 · genomes 0/151,744 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0036% | 27,790 |
| Remaining individualsnot grpmax-eligible | 0.00164% | 60,864 |
| European (non-Finnish) | 0.000173% | 577,477 |
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
- AHI1
- Protein
- p.Lys799=
- Coding
- c.2397G>A
- MANE Select
- NM_001134831
- dbSNP
- rs747639578
- Type
- single nucleotide variant
- Location
- chr6:135429977 (GRCh38)
- Gene constraint
- LOEUF 1.069 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 62.03 · 1 PDB
- Residue 799
- a UniProt-annotated variant site (in jbts3)
Similar variants
- AHI1 c.1152-1G>A Pathogenic/Likely pathogenic ★★ same condition
- AHI1 c.1152-2A>G Pathogenic ★★ same condition
- AHI1 c.1626+1G>A Pathogenic/Likely pathogenic ★★ same condition
- AHI1 c.1779+1G>T Pathogenic/Likely pathogenic ★★ same condition
- AHI1 c.2492+1G>A Pathogenic/Likely pathogenic ★★ same condition
- AHI1 c.2623+1G>A Pathogenic ★★ same condition
- AHI1 c.2623+1G>T Pathogenic ★★ same condition
- AHI1 c.3426+2T>C Likely 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/ahi1-p-lys799 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown