HSD17B10 p.Ile150=
c.450C>T · rs2521095913 · VCV2002881
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000165%)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.5 | phastCons 1 |
| Overall | ||
| CADD | 9.244 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000165%
Overall
0.000165%
2/1,211,620 alleles · very rare
exomes 2/1,098,127 · genomes 0/113,493 · joint denominator
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
- HSD17B10
- Protein
- p.Ile150=
- Coding
- c.450C>T
- MANE Select
- NM_004493
- dbSNP
- rs2521095913
- Type
- single nucleotide variant
- Location
- chrX:53432024 (GRCh38)
- Structure
- AlphaFold pLDDT 96.95 · 15 PDB
- Residue 150
- a β-strand
Similar variants
- HSD17B10 p.Arg130Cys Pathogenic ★★ ⚠ same type
- HSD17B10 p.Arg226Gln Pathogenic/Likely pathogenic ★★ same type
- HSD17B10 p.Lys212Glu Pathogenic/Likely pathogenic ★★ ⚠ same type
- HSD17B10 c.486+3G>A Uncertain significance ★★ same type
- HSD17B10 p.Arg116Gln Uncertain significance ★★ ⚠ same type
- HSD17B10 p.Asn139Ser Uncertain significance ★★ ⚠ same type
- HSD17B10 p.Asn152Ser Uncertain significance ★★ ⚠ same type
- HSD17B10 p.Asp229Asn 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/hsd17b10-p-ile150 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown