HK2 p.Thr331=
c.993C>T · rs61751209 · VCV3039056
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.83%, sas)
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 -5.3 | GERP -4.1 |
| Overall | ||
| CADD | 0.139 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.83%
South Asian · 1,670/91,088 alleles
Filtering AF
1.76%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.73%
Overall
0.797%
12,871/1,614,152 alleles · low-frequency
exomes 12,021/1,461,880 · genomes 850/152,272 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.83% | 55 |
| European (non-Finnish) | 0.869% | 115 |
| Remaining individualsnot grpmax-eligible | 0.619% | 162 |
| Admixed American | 0.568% | 176 |
| Middle Eastern | 0.445% | 225 |
| African / African-American | 0.145% | 688 |
| Finnishnot grpmax-eligible | 0.0765% | 1,307 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0743% | 1,346 |
| East Asian | 0.0379% | 2,639 |
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.Thr331=
- Coding
- c.993C>T
- MANE Select
- NM_000189
- dbSNP
- rs61751209
- Type
- single nucleotide variant
- Location
- chr2:74877283 (GRCh38)
- Structure
- AlphaFold pLDDT 82.81
- Residue 331
- the 'sufficient for interaction with microtubules' 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-thr331 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown