HYPK p.Thr92=
c.276T>C · rs11554827 · VCV730909
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.966%, afr)
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 -0.058 | GERP -3.8, phastCons 0.012 |
| Overall | ||
| CADD | 3.93 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.966%
African / African-American · 725/75,064 alleles
Filtering AF
0.908%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.884%
Overall
0.0507%
819/1,614,204 alleles · rare
exomes 406/1,461,862 · genomes 413/152,342 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.966% | 104 |
| Admixed American | 0.075% | 1,334 |
| Remaining individualsnot grpmax-eligible | 0.0608% | 1,645 |
| Middle Eastern | 0.033% | 3,031 |
| European (non-Finnish) | 0.000763% | 131,113 |
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
- HYPK
- Protein
- p.Thr92=
- Coding
- c.276T>C
- MANE Select
- NM_016400
- dbSNP
- rs11554827
- Type
- single nucleotide variant
- Location
- chr15:43801716 (GRCh38)
- Gene constraint
- LOEUF 1.059 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.87 · 3 PDB
- Residue 92
- an α-helix; the 'required for association with the naa10-naa15 complex' region
Similar variants
- HYPK p.Glu12= Benign ★★ same type
- HYPK c.-11G>A Uncertain significance ★ ⚠ same type
- HYPK c.-17G>A Uncertain significance ★ ⚠ same type
- HYPK c.-18C>T Uncertain significance ★ ⚠ same type
- HYPK p.Ala115Val Uncertain significance ★ same type
- HYPK p.Ala118Thr Uncertain significance ★ ⚠ same type
- HYPK p.Ala118Val Uncertain significance ★ ⚠ same type
- HYPK p.Ala99Thr Uncertain significance ★ ⚠ 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/hypk-p-thr92 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown