DMRT2 p.Arg81=
c.243G>T · rs541403055 · VCV1586014
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.181%, 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 -0.017 | GERP -0.24 |
| Overall | ||
| CADD | 4.979 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.181%
African / African-American · 119/65,592 alleles
Filtering AF
0.155%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.145%
Overall
0.0119%
166/1,399,602 alleles · rare
exomes 81/1,247,566 · genomes 85/152,036 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.181% | 551 |
| Middle Eastern | 0.05% | 2,001 |
| Admixed American | 0.0368% | 2,718 |
| Remaining individualsnot grpmax-eligible | 0.0187% | 5,358 |
| European (non-Finnish) | 0.00221% | 45,319 |
| South Asian | 0.00162% | 61,730 |
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.Arg81=
- Coding
- c.243G>T
- MANE Select
- NM_181872
- dbSNP
- rs541403055
- Type
- single nucleotide variant
- Location
- chr9:1051856 (GRCh38)
- Gene constraint
- LOEUF 1.279 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 54.37
- Residue 81
- the 'disordered' region
Similar variants
- DMRT2 p.Arg81fs 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-arg81 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown