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.

not_specified (113 variants)
not_provided (108 variants)
DMRT2-related_disorder (15 variants)
Gonadal_agenesis (1 variants)
See_cases (1 variants)

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. These statistics are base on transcript: NM_000181872.6. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	32 clinvar	3 clinvar	37
missense			150 clinvar	7 clinvar	5 clinvar	162
nonsense						0
start loss			1			1
frameshift		1 clinvar				1
splice donor/acceptor (+/-2bp)						0
Total	0	1	153	39	8

Loading clinvar variants...

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
ghis

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