DMRT3

doublesex and mab-3 related transcription factor 3

Basic information

Region (hg38): 9:976654-991732

Previous symbols: [ "DMRTA3" ]

Links

ENSG00000064218 ∙ NCBI:58524 ∙ OMIM:614754 ∙ HGNC:13909 ∙ Uniprot:Q9NQL9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DMRT3 gene.

• Inborn genetic diseases (24 variants)
• not provided (14 variants)
• Premature ovarian failure (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DMRT3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	3	7
missense		1	21	6	4	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	21	10	7

Highest pathogenic variant AF is 0.00000657

Variants in DMRT3

This is a list of pathogenic ClinVar variants found in the DMRT3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-977042-C-G		not specified	Uncertain significance (Dec 26, 2023)
9-977043-G-A			Likely benign (Jun 11, 2018)
9-977045-T-G		not specified	Uncertain significance (Dec 16, 2021)
9-977054-C-A			Benign (Dec 31, 2019)
9-977131-C-T		not specified	Uncertain significance (Jun 11, 2021)
9-977138-G-A		not specified	Uncertain significance (Apr 11, 2023)
9-977161-A-G		not specified	Uncertain significance (Apr 07, 2022)
9-977177-T-G		not specified	Uncertain significance (Feb 21, 2024)
9-977225-G-A		not specified	Uncertain significance (Jul 13, 2022)
9-977253-G-A			Benign (May 24, 2018)
9-977295-G-C			Benign (Dec 31, 2019)
9-977318-C-A		not specified	Uncertain significance (Jun 24, 2022)
9-977337-C-T			Likely benign (Jul 07, 2018)
9-977348-C-G		not specified	Uncertain significance (Jan 04, 2024)
9-977357-A-C		not specified	Likely benign (Jul 28, 2021)
9-977365-C-T		not specified	Uncertain significance (Oct 30, 2023)
9-977374-G-C		not specified	Uncertain significance (Nov 13, 2023)
9-977395-G-T		not specified	Uncertain significance (Oct 22, 2021)
9-990109-A-G		not specified	Uncertain significance (Jun 12, 2023)
9-990112-G-A		not specified	Uncertain significance (Jun 21, 2022)
9-990121-A-C		not specified	Uncertain significance (Jan 19, 2022)
9-990134-T-C		not specified	Uncertain significance (Jan 09, 2024)
9-990154-T-C		not specified	Uncertain significance (Jun 24, 2022)
9-990228-C-T			Likely benign (May 25, 2018)
9-990235-C-T			Likely benign (Apr 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DMRT3	protein_coding	protein_coding	ENST00000190165	2	14768

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000615	0.710	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.69	335	258	1.30	0.0000147	2993
Missense in Polyphen		147	115.5	1.2727		1269
Synonymous	-2.09	154	124	1.24	0.00000843	1010
Loss of Function	1.09	10	14.5	0.691	9.55e-7	153

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000374	0.000354
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000162	0.000158
Middle Eastern	0.0000544	0.0000544
South Asian	0.000199	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable transcription factor that plays a role in configuring the spinal circuits controlling stride in vertebrates. Involved in neuronal specification within specific subdivision of spinal cord neurons and in the development of a coordinated locomotor network controlling limb movements. May regulate transcription during sexual development (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.579
• rvis_EVS: 0.64
• rvis_percentile_EVS: 84.1

Haploinsufficiency Scores

• pHI: 0.177
• hipred: N
• hipred_score: 0.342
• ghis: 0.420

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.795

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Dmrt3
• Phenotype: craniofacial phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;sex differentiation;adult walking behavior;transmission of nerve impulse;ventral spinal cord interneuron specification;regulation of odontogenesis of dentin-containing tooth;male sex differentiation
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding;sequence-specific DNA binding;metal ion binding;protein heterodimerization activity