HSD3B7 p.Pro321=
c.963C>T · VCV4693106
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0213%, afr)
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 0.67 | GERP -1.6, phastCons 1 |
| Overall | ||
| CADD | 13.25 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0213%
African / African-American · 16/74,946 alleles
Filtering AF
0.0133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0109%
Overall
0.00118%
19/1,607,342 alleles · ultra-rare
exomes 10/1,455,096 · genomes 9/152,246 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0213% | 4,684 |
| South Asian | 0.0022% | 45,537 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,430 |
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.Pro321=
- Coding
- c.963C>T
- MANE Select
- NM_025193
- Type
- single nucleotide variant
- Location
- chr16:30988036 (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.Pro321Thr Uncertain significance ★ ⚠ same residue
- 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
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-pro321 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown