HHAT p.Ala89=
c.267A>G · rs145344074 · VCV709535
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.702%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.8 | GERP -4.1 |
| Overall | ||
| CADD | 1.599 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.702%
Admixed American · 421/60,012 alleles
Filtering AF
0.646%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.624%
Overall
0.0266%
428/1,611,972 alleles · rare
exomes 384/1,459,652 · genomes 44/152,320 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.702% | 143 |
| Remaining individualsnot grpmax-eligible | 0.00961% | 10,405 |
| European (non-Finnish) | 8.49e-05% | 1,178,051 |
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
- HHAT
- Protein
- p.Ala89=
- Coding
- c.267A>G
- MANE Select
- NM_018194
- dbSNP
- rs145344074
- Type
- single nucleotide variant
- Location
- chr1:210387575 (GRCh38)
- Gene constraint
- LOEUF 0.785 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.07 · 10 PDB
- Residue 89
- a UniProt-annotated variant site (in nnms; uncertain significance)
Similar variants
- HHAT p.Ala308Thr Uncertain significance ★★ ⚠ same type
- HHAT p.Arg176His Uncertain significance ★★ ⚠ same type
- HHAT p.Arg403Trp Uncertain significance ★★ ⚠ same type
- HHAT p.His379Tyr Uncertain significance ★★ ⚠ same type
- HHAT c.1245+19G>C Benign ★★ same type
- HHAT c.159+15C>A Benign ★★ same type
- HHAT p.Ala389= Benign ★★ same type
- HHAT p.Arg176Cys Benign ★★ ⚠ 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/hhat-p-ala89 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown