DMRT2 p.Leu154=
c.462G>T · rs372312394 · VCV1551503
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.45%, 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 0.64 | GERP -2.4, phastCons 1 |
| Overall | ||
| CADD | 10.48 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.45%
African / African-American · 983/67,952 alleles
Filtering AF
1.37%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.34%
Overall
0.0792%
1,157/1,461,652 alleles · low-frequency
exomes 565/1,309,308 · genomes 592/152,344 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.45% | 69 |
| Admixed American | 0.145% | 689 |
| Remaining individualsnot grpmax-eligible | 0.0836% | 1,196 |
| Middle Eastern | 0.0479% | 2,087 |
| European (non-Finnish) | 0.00557% | 17,946 |
| South Asian | 0.00394% | 25,387 |
| Finnishnot grpmax-eligible | 0.00232% | 43,088 |
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.Leu154=
- Coding
- c.462G>T
- MANE Select
- NM_181872
- dbSNP
- rs372312394
- Type
- single nucleotide variant
- Location
- chr9:1052075 (GRCh38)
- Gene constraint
- LOEUF 1.279 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 54.37
- Residue 154
- 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-leu154 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown