DMRT2 p.Lys139=
c.417G>A · rs964673440 · VCV2779509
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00256%, sas)
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 4.4 | GERP 0.29, phastCons 1 |
| Overall | ||
| CADD | 13.47 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00256%
South Asian · 2/78,186 alleles
Filtering AF
0.000425%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000159%
Overall
0.000339%
5/1,476,232 alleles · very rare
exomes 4/1,323,894 · genomes 1/152,338 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00256% | 39,093 |
| European (non-Finnish) | 0.000268% | 373,427 |
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.Lys139=
- Coding
- c.417G>A
- MANE Select
- NM_181872
- dbSNP
- rs964673440
- Type
- single nucleotide variant
- Location
- chr9:1052030 (GRCh38)
- Gene constraint
- LOEUF 1.279 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 54.37
- Residue 139
- a DNA-binding 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-lys139 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown