DMRT3 p.Ala112=
c.336C>T · rs1586681295 · VCV757499
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000496%, nfe)
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 -0.73 | GERP -2.2 |
| Overall | ||
| CADD | 8.987 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000496%
European (non-Finnish) · 5/1,007,720 alleles
Filtering AF
0.000145%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000106%
Overall
0.000395%
5/1,264,646 alleles · very rare
exomes 5/1,113,590 · genomes 0/151,056 · joint denominator
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
- DMRT3
- Protein
- p.Ala112=
- Coding
- c.336C>T
- MANE Select
- NM_021240
- dbSNP
- rs1586681295
- Type
- single nucleotide variant
- Location
- chr9:977337 (GRCh38)
- Gene constraint
- LOEUF 1.273 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 57.72
- Residue 112
- the 'disordered' region
Similar variants
- DMRT3 p.Arg217Cys Likely benign ★★ same type
- DMRT3 p.Asn261Thr Benign ★★ same type
- DMRT3 p.Pro18Gln Benign ★★ same type
- DMRT3 p.Pro98= Benign ★★ same type
- DMRT3 p.Ser463Pro Benign ★★ same type
- DMRT3 p.Val424Ile Likely benign ★★ same type
- DMRT3 p.Pro443Ser Likely pathogenic ★ ⚠ same type
- DMRT3 p.Ala103Thr 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/dmrt3-p-ala112 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown