DMRT2 p.Ser430=
c.1290C>A · rs113111105 · VCV3039062
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.726%, afr)
Conditions
1
DMRT2-related disorder
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 1.1 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 7.295 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.726%
African / African-American · 545/75,034 alleles
Filtering AF
0.676%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.656%
Overall
0.0485%
783/1,614,158 alleles · rare
exomes 466/1,461,890 · genomes 317/152,268 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.726% | 138 |
| Ashkenazi Jewishnot grpmax-eligible | 0.189% | 529 |
| Middle Eastern | 0.132% | 758 |
| Admixed American | 0.095% | 1,053 |
| Remaining individualsnot grpmax-eligible | 0.08% | 1,250 |
| South Asian | 0.00659% | 15,179 |
| European (non-Finnish) | 0.00517% | 19,345 |
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.Ser430=
- Coding
- c.1290C>A
- MANE Select
- NM_181872
- dbSNP
- rs113111105
- Type
- single nucleotide variant
- Location
- chr9:1056877 (GRCh38)
- Gene constraint
- LOEUF 1.279 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 54.37
- Residue 430
- the 'disordered' region
Disease context
DMRT2-related disorder
Similar variants
- DMRT2 p.Arg127Pro Uncertain significance ★ ⚠ same condition
- DMRT2 p.Ala286Pro Uncertain significance ⚠ same condition
- DMRT2 p.Asn247= Likely benign same condition
- DMRT2 p.Gly221= Likely benign same condition
- DMRT2 p.Ser396Leu Likely benign same condition
- DMRT2 p.Thr557Ala Likely benign same condition
- DMRT2 p.Pro41_Ala42insPro Uncertain significance same condition
- DMRT2 p.Ala112Glu 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-ser430 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown