DMRT3 p.Pro14=
c.42G>A · rs769336614 · VCV750416
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00189%, amr)
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 0.28 | GERP -3.7, phastCons 0.96 |
| Overall | ||
| CADD | 11.32 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00189%
Admixed American · 1/53,048 alleles
Filtering AF
0.000894%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000731%
Overall
0.00121%
19/1,565,764 alleles · very rare
exomes 16/1,413,708 · genomes 3/152,056 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00189% | 53,048 |
| European (non-Finnish) | 0.00147% | 68,101 |
| South Asian | 0.00116% | 85,986 |
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.Pro14=
- Coding
- c.42G>A
- MANE Select
- NM_021240
- dbSNP
- rs769336614
- Type
- single nucleotide variant
- Location
- chr9:977043 (GRCh38)
- Gene constraint
- LOEUF 1.273 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 57.72
Similar variants
- DMRT3 p.Pro14Arg Uncertain significance ★ ⚠ same residue
- 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
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-pro14 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown