HSD11B2 p.Arg147=
c.441C>T · rs143819538 · VCV2079330
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0156%, eas)
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 -4.8 | GERP -4.9 |
| Overall | ||
| CADD | 3.044 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0156%
East Asian · 7/44,880 alleles
Filtering AF
0.0106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00997%
Overall
0.0101%
163/1,614,044 alleles · ultra-rare
exomes 155/1,461,758 · genomes 8/152,286 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0156% | 6,411 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,946 |
| European (non-Finnish) | 0.0123% | 8,138 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
| Admixed American | 0.00167% | 60,018 |
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
- HSD11B2
- Protein
- p.Arg147=
- Coding
- c.441C>T
- MANE Select
- NM_000196
- dbSNP
- rs143819538
- Type
- single nucleotide variant
- Location
- chr16:67435803 (GRCh38)
- Gene constraint
- LOEUF 1.204 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.49
- Residue 147
- a UniProt-annotated variant site (in)
Similar variants
- HSD11B2 p.Arg147His Uncertain significance ★★ ⚠ same residue
- HSD11B2 p.Arg147Cys Uncertain significance ★ ⚠ same residue
- HSD11B2 p.Ala328Val Likely pathogenic ★★ same type
- HSD11B2 p.Arg208His Pathogenic/Likely pathogenic ★★ same type
- HSD11B2 c.664+14C>T Uncertain significance ★★ same type
- HSD11B2 c.802+5G>C Uncertain significance ★★ same type
- HSD11B2 p.Ala196Thr Uncertain significance ★★ ⚠ same type
- HSD11B2 p.Ala19Val 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/hsd11b2-p-arg147 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown