DMRT1 p.Arg258=
c.774G>C · rs146975077 · VCV786903
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.94%, 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 3.5 | GERP -0.19, phastCons 1 |
| Overall | ||
| CADD | 7.534 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.94%
African / African-American · 2,205/75,056 alleles
Filtering AF
2.84%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.79%
Overall
0.167%
2,700/1,614,084 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.94% | 34 |
| Admixed American | 0.355% | 282 |
| Middle Eastern | 0.303% | 330 |
| Remaining individualsnot grpmax-eligible | 0.187% | 534 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0473% | 2,115 |
| European (non-Finnish) | 0.0109% | 9,148 |
| South Asian | 0.00439% | 22,772 |
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.Arg258=
- Coding
- c.774G>C
- MANE Select
- NM_021951
- dbSNP
- rs146975077
- Type
- single nucleotide variant
- Location
- chr9:894147 (GRCh38)
- Gene constraint
- LOEUF 0.432 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 57.76 · 1 PDB
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-arg258 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown