HSD3B7 p.Phe142=
c.426C>T · rs199909008 · VCV2091027
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
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 1.8 | GERP -1.2, phastCons 1 |
| Overall | ||
| CADD | 15.36 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,880 alleles
Filtering AF
0.000739%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000276%
Overall
0.000186%
3/1,613,744 alleles · very rare
exomes 2/1,461,416 · genomes 1/152,328 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,440 |
| European (non-Finnish) | 8.48e-05% | 1,179,600 |
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
- HSD3B7
- Protein
- p.Phe142=
- Coding
- c.426C>T
- MANE Select
- NM_025193
- dbSNP
- rs199909008
- Type
- single nucleotide variant
- Location
- chr16:30986526 (GRCh38)
- Gene constraint
- LOEUF 1.411 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 94.01
Similar variants
- HSD3B7 p.Arg27Ter Pathogenic/Likely pathogenic ★★ same type
- HSD3B7 p.Glu147Lys Pathogenic/Likely pathogenic ★★ same type
- HSD3B7 p.Glu167Ter Pathogenic/Likely pathogenic ★★ same type
- HSD3B7 c.167-6G>A Uncertain significance ★★ same type
- HSD3B7 p.Ala364Thr Uncertain significance ★★ ⚠ same type
- HSD3B7 p.Ala76Thr Uncertain significance ★★ ⚠ same type
- HSD3B7 p.Arg110Gln Uncertain significance ★★ ⚠ same type
- HSD3B7 p.Arg203Lys 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/hsd3b7-p-phe142 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown