HK2 p.Ser155=
c.465G>A · rs61755708 · VCV3052840
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.409%, afr)
Conditions
1
HK2-related disorder
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 -15 | GERP -4.1 |
| Overall | ||
| CADD | 0.039 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.409%
African / African-American · 307/75,006 alleles
Filtering AF
0.372%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.357%
Overall
0.0437%
705/1,613,890 alleles · rare
exomes 454/1,461,678 · genomes 251/152,212 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.409% | 244 |
| Admixed American | 0.252% | 397 |
| Middle Eastern | 0.099% | 1,010 |
| Remaining individualsnot grpmax-eligible | 0.0448% | 2,232 |
| East Asian | 0.0201% | 4,985 |
| European (non-Finnish) | 0.0169% | 5,929 |
| South Asian | 0.00549% | 18,213 |
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
- HK2
- Protein
- p.Ser155=
- Coding
- c.465G>A
- MANE Select
- NM_000189
- dbSNP
- rs61755708
- Type
- single nucleotide variant
- Location
- chr2:74872389 (GRCh38)
- Structure
- AlphaFold pLDDT 82.81
- Residue 155
- the 'sufficient for interaction with microtubules' region; the 'required for localization to the centrosome and induction of aggresome formation' region
Disease context
HK2-related disorder
Similar variants
- HK2 c.591+10G>A Benign same condition
- HK2 p.Ala113= Likely benign same condition
- HK2 p.Ala387= Likely benign same condition
- HK2 p.Ala387Ser Benign same condition
- HK2 p.Ala424= Likely benign same condition
- HK2 p.Ala831= Benign same condition
- HK2 p.Arg844Lys Benign same condition
- HK2 p.Asn692= Benign 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/hk2-p-ser155 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown