DMRT2 p.Thr99=
c.297C>G · rs183524725 · VCV776400
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.46%, 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 -5.5 | GERP -3.8 |
| Overall | ||
| CADD | 2.725 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.46%
African / African-American · 2,253/65,122 alleles
Filtering AF
3.34%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.29%
Overall
0.228%
3,101/1,361,772 alleles · low-frequency
exomes 1,541/1,209,672 · genomes 1,560/152,100 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.46% | 29 |
| Ashkenazi Jewishnot grpmax-eligible | 0.665% | 150 |
| Admixed American | 0.468% | 214 |
| Middle Eastern | 0.43% | 233 |
| Remaining individualsnot grpmax-eligible | 0.339% | 295 |
| European (non-Finnish) | 0.0378% | 2,643 |
| South Asian | 0.00182% | 54,972 |
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.Thr99=
- Coding
- c.297C>G
- MANE Select
- NM_181872
- dbSNP
- rs183524725
- Type
- single nucleotide variant
- Location
- chr9:1051910 (GRCh38)
- Gene constraint
- LOEUF 1.279 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 54.37
- Residue 99
- the 'disordered' region
Similar variants
- 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
- DMRT2 p.Gly36Arg 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-thr99 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown