AHI1 p.Ser389=
c.1167A>G · rs1188089329 · VCV2777546
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000179%, nfe)
Conditions
1
Joubert 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 -0.39 | GERP -3.6, phastCons 0.21 |
| Overall | ||
| CADD | 6.535 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000179%
European (non-Finnish) · 2/1,114,556 alleles
Filtering AF
3e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000133%
2/1,499,456 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
- AHI1
- Protein
- p.Ser389=
- Coding
- c.1167A>G
- MANE Select
- NM_001134831
- dbSNP
- rs1188089329
- Type
- single nucleotide variant
- Location
- chr6:135455911 (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 389
- the 'interaction with hap1' region
Similar variants
- AHI1 p.Ser389Ter Pathogenic/Likely pathogenic ★★ same residue
- AHI1 p.Ser389fs Pathogenic ★ same residue
- 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
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-ser389 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown