Is DMRT2 p.Asn247= (c.741C>T) pathogenic?

DMRT2 p.Asn247= (c.741C>T) is classified Likely benign in DMRT2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-07). Ultra-rare (popmax 0.0317%, amr); Associated with DMRT2-related disorder.

What condition is associated with DMRT2 p.Asn247= (c.741C>T)?

DMRT2 p.Asn247= (c.741C>T) is associated with DMRT2-related disorder (ClinVar).

How common is DMRT2 p.Asn247= (c.741C>T) in the general population?

DMRT2 p.Asn247= (c.741C>T) is ultra-rare (popmax 0.0317%, amr) (gnomAD).

DMRT2 p.Asn247=

c.741C>T · rs759993378 · VCV3041906

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0317%, amr)

Conditions

DMRT2-related disorder

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 2.8	GERP 1.4, phastCons 1
Overall
CADD	8.592	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0317% Admixed American · 19/60,004 alleles

Filtering AF 0.0207% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0172%

Overall 0.0026% 42/1,614,054 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0317%	3,158
Middle Eastern	0.0164%	6,084
Remaining individualsnot grpmax-eligible	0.0112%	8,927
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,608
European (non-Finnish)	0.00119%	84,289

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.Asn247=
Coding: c.741C>T
MANE Select: NM_181872
dbSNP: rs759993378
Type: single nucleotide variant
Location: chr9:1056328 (GRCh38)
Gene constraint: LOEUF 1.279 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 54.37

Full DMRT2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DMRT2-related disorder

Similar variants

DMRT2 p.Asn247Thr Uncertain significance ★ ⚠ same residue
DMRT2 p.Arg127Pro Uncertain significance ★ ⚠ same condition
DMRT2 p.Ala286Pro Uncertain significance ⚠ same condition
DMRT2 p.Gly221= Likely benign same condition
DMRT2 p.Ser396Leu Likely benign same condition
DMRT2 p.Ser430= Likely benign same condition
DMRT2 p.Thr557Ala Likely benign same condition
DMRT2 p.Pro41_Ala42insPro Uncertain significance same condition

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-asn247 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown