DMRT2 p.Pro107=
c.321C>G · rs1002253152 · VCV2822083
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00459%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.094 | GERP -3.6, phastCons 0.006 |
| Overall | ||
| CADD | 5.987 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00459%
African / African-American · 3/65,412 alleles
Filtering AF
0.00122%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000638%
Overall
0.000367%
5/1,364,024 alleles · very rare
exomes 3/1,212,022 · genomes 2/152,002 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00459% | 21,804 |
| South Asian | 0.00181% | 55,274 |
| European (non-Finnish) | 9.36e-05% | 1,067,834 |
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.Pro107=
- Coding
- c.321C>G
- MANE Select
- NM_181872
- dbSNP
- rs1002253152
- Type
- single nucleotide variant
- Location
- chr9:1051934 (GRCh38)
- Gene constraint
- LOEUF 1.279 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 54.37
- Residue 107
- the 'disordered' region
Similar variants
- DMRT2 p.Pro107Ala Uncertain significance ★ ⚠ same residue
- DMRT2 p.Pro107Ser 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
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-pro107 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown