Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.32 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.81 | GERP -3.4 |
| Overall | ||
| CADD | 0.654 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.19% | 84 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,942 |
| Admixed American | 0.00333% | 29,997 |
| South Asian | 0.0033% | 30,345 |
| African / African-American | 0.00133% | 75,036 |
| European (non-Finnish) | 8.48e-05% | 1,179,798 |
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
- SRD5A2
- Protein
- p.His232=
- Coding
- c.696T>C
- MANE Select
- NM_000348
- dbSNP
- rs9332965
- Type
- single nucleotide variant
- Location
- chr2:31529309 (GRCh38)
- Gene constraint
- LOEUF 1.717 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 94.56 · 1 PDB
- Residue 232
- an α-helix; a UniProt-annotated variant site (found in individual with micropenis)
Disease context
46,XY disorder of sex development due to 5-alpha-reductase 2 deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor 46,XY difference of sex development due to 5-alpha-reductase 2 deficiency (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Childhood, Infancy, Neonatal
Similar variants
- SRD5A2 p.His232Arg Pathogenic/Likely pathogenic ★★ same residue
- SRD5A2 c.282-2A>G Pathogenic ★★ same condition
- SRD5A2 c.698+1G>T Pathogenic/Likely pathogenic ★★ same condition
- SRD5A2 p.Ala207Asp Pathogenic/Likely pathogenic ★★ same condition
- SRD5A2 p.Ala228Thr Pathogenic/Likely pathogenic ★★ same condition
- SRD5A2 p.Ala65Pro Pathogenic/Likely pathogenic ★★ same condition
- SRD5A2 p.Arg103Ter Pathogenic ★★ same condition
- SRD5A2 p.Arg145Trp Pathogenic/Likely pathogenic ★★ ⚠ same condition
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/srd5a2-p-his232 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown