HSD17B2 p.Pro130=
c.390G>A · rs34731990 · VCV713204
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.318%, sas)
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 0.88 | GERP -3 |
| Overall | ||
| CADD | 7.007 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.318%
South Asian · 290/91,058 alleles
Filtering AF
0.288%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.277%
Overall
0.162%
2,607/1,614,066 alleles · rare
exomes 2,413/1,461,836 · genomes 194/152,230 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.318% | 314 |
| Middle Eastern | 0.182% | 549 |
| European (non-Finnish) | 0.177% | 566 |
| Remaining individualsnot grpmax-eligible | 0.157% | 638 |
| Finnishnot grpmax-eligible | 0.0921% | 1,085 |
| Admixed American | 0.0517% | 1,936 |
| African / African-American | 0.0373% | 2,679 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0169% | 5,922 |
| East Asian | 0.00446% | 22,432 |
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
- HSD17B2
- Protein
- p.Pro130=
- Coding
- c.390G>A
- MANE Select
- NM_002153
- dbSNP
- rs34731990
- Type
- single nucleotide variant
- Location
- chr16:82068294 (GRCh38)
- Gene constraint
- LOEUF 1.567 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.62
Similar variants
- HSD17B2 p.Pro130Leu Uncertain significance ★ ⚠ same residue
- HSD17B2 p.Ala121Thr Benign ★★ ⚠ same type
- HSD17B2 p.Ala331Val Likely benign ★★ ⚠ same type
- HSD17B2 p.Met226Val Benign ★★ same type
- HSD17B2 p.Thr240Ser Benign ★★ same type
- HSD17B2 p.Ala230Thr Uncertain significance ★ same type
- HSD17B2 p.Ala270Thr Uncertain significance ★ ⚠ same type
- HSD17B2 p.Ala289Ser 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/hsd17b2-p-pro130 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown