DMRT2 p.Arg158=
c.474G>T · VCV3633573
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0325%, 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 1 | GERP -4.6, phastCons 1 |
| Overall | ||
| CADD | 11.09 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0325%
African / African-American · 22/67,646 alleles
Filtering AF
0.022%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0185%
Overall
0.00179%
26/1,454,300 alleles · ultra-rare
exomes 12/1,302,096 · genomes 14/152,204 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0325% | 3,075 |
| Remaining individualsnot grpmax-eligible | 0.00358% | 27,957 |
| Admixed American | 0.00252% | 39,688 |
| European (non-Finnish) | 9.01e-05% | 1,109,330 |
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
- DMRT2
- Protein
- p.Arg158=
- Coding
- c.474G>T
- MANE Select
- NM_181872
- Type
- single nucleotide variant
- Location
- chr9:1052087 (GRCh38)
- Gene constraint
- LOEUF 1.279 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 54.37
- Residue 158
- a DNA-binding region
Similar variants
- DMRT2 p.Arg158Leu Uncertain significance ★ ⚠ same residue
- DMRT2 p.Ala112Glu Uncertain significance ★★ ⚠ same type
- DMRT2 p.Ala29Ser Uncertain significance ★★ ⚠ same type
- DMRT2 p.Asp176Gly Uncertain significance ★★ ⚠ same type
- DMRT2 p.Asp48Glu Uncertain significance ★★ ⚠ same type
- DMRT2 p.Cys105Tyr Uncertain significance ★★ ⚠ same type
- DMRT2 p.Glu60Gln Uncertain significance ★★ ⚠ same type
- DMRT2 p.Gly110Asp 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/dmrt2-p-arg158 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown