DMRT2

doublesex and mab-3 related transcription factor 2

Basic information

Region (hg38): 9:1049858-1057552

Links

ENSG00000173253 ∙ NCBI:10655 ∙ OMIM:604935 ∙ HGNC:2935 ∙ Uniprot:Q9Y5R5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spondylocostal dysostosis (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DMRT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DMRT2 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			2	20	3	25
missense			84	7	5	96
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				5		5
Total	0	0	87	32	8

Variants in DMRT2

This is a list of pathogenic ClinVar variants found in the DMRT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-1051614-A-T			Uncertain significance (Aug 03, 2021)
9-1051624-C-G			Uncertain significance (Mar 26, 2023)
9-1051630-C-G			Uncertain significance (Apr 30, 2022)
9-1051636-C-T		not specified	Uncertain significance (Jan 08, 2024)
9-1051642-C-A			Uncertain significance (Sep 08, 2023)
9-1051684-A-C		Gonadal agenesis	Uncertain significance (-)
9-1051687-A-C			Uncertain significance (Nov 28, 2023)
9-1051688-C-T			Likely benign (Jun 17, 2023)
9-1051695-G-C			Uncertain significance (Dec 23, 2023)
9-1051698-G-T		not specified	Uncertain significance (Jun 02, 2024)
9-1051703-G-A			Likely benign (Jul 12, 2022)
9-1051703-G-T			Likely benign (Aug 17, 2023)
9-1051704-C-A			Likely benign (Sep 19, 2023)
9-1051713-C-A		DMRT2-related disorder	Benign (Jan 21, 2024)
9-1051719-G-A		not specified	Uncertain significance (Oct 08, 2024)
9-1051727-CC-AT			Uncertain significance (Jan 30, 2024)
9-1051727-C-CCCG		DMRT2-related disorder	Uncertain significance (Apr 23, 2024)
9-1051732-C-T			Uncertain significance (Oct 24, 2022)
9-1051734-C-G		not specified	Uncertain significance (Aug 04, 2023)
9-1051735-C-G			Uncertain significance (Sep 18, 2021)
9-1051736-G-T			Likely benign (Jun 04, 2023)
9-1051740-G-A		not specified	Uncertain significance (Jan 02, 2024)
9-1051741-A-C		not specified	Uncertain significance (Jun 11, 2021)
9-1051755-G-T			Uncertain significance (Jan 13, 2023)
9-1051756-A-C		not specified	Uncertain significance (Sep 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DMRT2	protein_coding	protein_coding	ENST00000382251	3	7199

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00966	0.981	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.06	350	257	1.36	0.0000128	3592
Missense in Polyphen		74	66.362	1.1151		981
Synonymous	-2.74	140	104	1.34	0.00000561	1136
Loss of Function	2.26	6	15.7	0.383	7.96e-7	225

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional activator that directly regulates early activation of the myogenic determination gene MYF5 by binding in a sequence-specific manner to the early epaxial enhancer element of it. Involved in somitogenesis during embryogenesis and somite development and differentiation into sclerotome and dermomyotome. Required for the initiation and/or maintenance of proper organization of the sclerotome, dermomyotome and myotome (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.103

Haploinsufficiency Scores

• pHI: 0.284
• hipred: Y
• hipred_score: 0.699

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.921

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dmrt2
• Phenotype: limbs/digits/tail phenotype; skeleton phenotype; respiratory system phenotype; embryo 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); craniofacial phenotype; muscle phenotype

Zebrafish Information Network

• Gene name: dmrt2a
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: curved ventral

Gene ontology

• Biological process: biological_process;regulation of somitogenesis;positive regulation of transcription by RNA polymerase II;embryonic skeletal system development;positive regulation of myotome development
• Cellular component: cellular_component;nucleus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;molecular_function;protein homodimerization activity;metal ion binding