DMRT1 p.Ser61=
c.183G>C · VCV3715013
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0577%, sas)
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 -0.06 | GERP -4.6 |
| Overall | ||
| CADD | 7.693 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0577%
South Asian · 49/84,910 alleles
Filtering AF
0.0448%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0402%
Overall
0.00323%
50/1,549,518 alleles · ultra-rare
exomes 48/1,397,236 · genomes 2/152,282 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0577% | 1,733 |
| Remaining individualsnot grpmax-eligible | 0.00166% | 60,126 |
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
- DMRT1
- Protein
- p.Ser61=
- Coding
- c.183G>C
- MANE Select
- NM_021951
- Type
- single nucleotide variant
- Location
- chr9:842021 (GRCh38)
- Gene constraint
- LOEUF 0.432 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 57.76 · 1 PDB
- Residue 61
- the 'disordered' region
Similar variants
- DMRT1 p.Asn151Ser Uncertain significance ★★ ⚠ same type
- DMRT1 p.Met275Val Uncertain significance ★★ ⚠ same type
- DMRT1 p.Ser58Cys Uncertain significance ★★ ⚠ same type
- DMRT1 p.Thr366Ser Uncertain significance ★★ ⚠ same type
- DMRT1 p.Val265Met Uncertain significance ★★ ⚠ same type
- DMRT1 c.355-218G>C Benign ★★ same type
- DMRT1 c.355-8G>C Benign ★★ same type
- DMRT1 c.538+65A>G Benign ★★ 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/dmrt1-p-ser61 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown