HHAT p.Phe17=
c.51C>T · rs141741088 · VCV2912854
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0867%, afr)
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 2.6 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 12.05 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0867%
African / African-American · 65/75,008 alleles
Filtering AF
0.0697%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0636%
Overall
0.00483%
78/1,614,078 alleles · ultra-rare
exomes 47/1,461,828 · genomes 31/152,250 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0867% | 1,154 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,814 |
| Admixed American | 0.005% | 19,997 |
| South Asian | 0.0022% | 45,543 |
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.Phe17=
- Coding
- c.51C>T
- MANE Select
- NM_018194
- dbSNP
- rs141741088
- Type
- single nucleotide variant
- Location
- chr1:210349026 (GRCh38)
- Gene constraint
- LOEUF 0.785 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.07 · 10 PDB
- Residue 17
- an α-helix
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-phe17 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown