HSD17B3 p.Ser288=
c.864C>T · rs552614077 · VCV2904190
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00666%, amr)
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 4 | GERP -0.73, phastCons 1 |
| Overall | ||
| CADD | 13.83 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00666%
Admixed American · 4/60,024 alleles
Filtering AF
0.00225%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00135%
Overall
0.00192%
31/1,614,134 alleles · very rare
exomes 30/1,461,764 · genomes 1/152,370 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00666% | 15,006 |
| East Asian | 0.00223% | 44,888 |
| European (non-Finnish) | 0.00203% | 49,167 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,506 |
| African / African-American | 0.00133% | 75,080 |
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
- HSD17B3
- Protein
- p.Ser288=
- Coding
- c.864C>T
- MANE Select
- NM_000197
- dbSNP
- rs552614077
- Type
- single nucleotide variant
- Location
- chr9:96235529 (GRCh38)
- Gene constraint
- LOEUF 0.903 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 93.59
Similar variants
- HSD17B3 c.194C>T Pathogenic/Likely pathogenic ★★ same type
- HSD17B3 c.201+1G>A Pathogenic ★★ same type
- HSD17B3 c.202-1G>A Pathogenic ★★ same type
- HSD17B3 c.277+4A>T Pathogenic ★★ same type
- HSD17B3 c.278-1G>C Pathogenic ★★ same type
- HSD17B3 p.Ala203Val Pathogenic/Likely pathogenic ★★ ⚠ same type
- HSD17B3 p.Arg80Gln Pathogenic ★★ same type
- HSD17B3 p.Arg80Trp Pathogenic/Likely pathogenic ★★ 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/hsd17b3-p-ser288 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown