DMRT2

gene
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Summary

DMRT2 (doublesex and mab-3 related transcription factor 2, HGNC:2935) is a protein-coding gene on chromosome 9p24.3, encoding Doublesex- and mab-3-related transcription factor 2 (Q9Y5R5). 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.

The protein encoded by this gene belongs to the DMRT gene family, sharing a DM DNA-binding domain with Drosophila ‘doublesex’ (dsx) and C. elegans mab3, genes involved in sex determination in these organisms. Also, this gene is located in a region of the human genome (chromosome 9p24.3) associated with gonadal dysgenesis and XY sex reversal. Hence this gene is one of the candidates for sex-determining gene(s) on chr 9.

Source: NCBI Gene 10655 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): spondylocostal dysostosis (Limited, GenCC)
  • GWAS associations: 20
  • Clinical variants (ClinVar): 256 total — 2 pathogenic, 1 likely-pathogenic
  • Dosage sensitivity (ClinGen): haploinsufficiency no evidence, triplosensitivity no evidence
  • MANE Select transcript: NM_181872

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2935
Approved symbolDMRT2
Namedoublesex and mab-3 related transcription factor 2
Location9p24.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000173253
Ensembl biotypeprotein_coding
OMIM604935
Entrez10655

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 10 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000259622, ENST00000302441, ENST00000358146, ENST00000382251, ENST00000382255, ENST00000412350, ENST00000634526, ENST00000634824, ENST00000635183, ENST00000910808, ENST00000910809, ENST00000910810

RefSeq mRNA: 10 — MANE Select: NM_181872 NM_001130865, NM_001370531, NM_001370532, NM_001370533, NM_001387557, NM_001387558, NM_001387559, NM_001387560, NM_006557, NM_181872

CCDS: CCDS6444, CCDS6445

Canonical transcript exons

ENST00000358146 — 4 exons

ExonStartEnd
ENSE0000092782910515701052138
ENSE0000120304610537221053824
ENSE0000140917210562161057552
ENSE0000391666510503571050775

Expression profiles

Bgee: expression breadth ubiquitous, 174 present calls, max score 92.78.

FANTOM5 (CAGE): breadth broad, TPM avg 1.2239 / max 84.4928, expressed in 372 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
958191.0861347
958210.057833
958220.040714
958200.039217

Top tissues by expression

233 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
kidney epitheliumUBERON:000481992.78gold quality
metanephros cortexUBERON:001053391.78gold quality
adult mammalian kidneyUBERON:000008289.51gold quality
olfactory segment of nasal mucosaUBERON:000538686.33gold quality
biceps brachiiUBERON:000150784.62silver quality
buccal mucosa cellCL:000233683.21gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450282.48silver quality
kidneyUBERON:000211382.47gold quality
hindlimb stylopod muscleUBERON:000425282.39gold quality
quadriceps femorisUBERON:000137779.32silver quality
cortex of kidneyUBERON:000122578.72gold quality
mucosa of transverse colonUBERON:000499176.53gold quality
nasal cavity mucosaUBERON:000182675.14gold quality
subcutaneous adipose tissueUBERON:000219074.66gold quality
skeletal muscle tissueUBERON:000113474.42gold quality
metanephrosUBERON:000008173.54gold quality
mucosa of paranasal sinusUBERON:000503072.39gold quality
muscle of legUBERON:000138372.19gold quality
gastrocnemiusUBERON:000138871.24gold quality
adipose tissueUBERON:000101370.58gold quality
C1 segment of cervical spinal cordUBERON:000646970.06gold quality
renal medullaUBERON:000036270.02gold quality
muscle tissueUBERON:000238569.96gold quality
thymusUBERON:000237069.86gold quality
apex of heartUBERON:000209869.59gold quality
deltoidUBERON:000147669.43silver quality
endothelial cellCL:000011568.22silver quality
spinal cordUBERON:000224067.85gold quality
bronchial epithelial cellCL:000232867.73gold quality
sural nerveUBERON:001548867.61gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-CURD-119yes39.28
E-CURD-114yes12.05
E-ANND-3yes6.42

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

151 targeting DMRT2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-3163100.0077.238605
HSA-MIR-4481100.0066.421669
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-428299.9975.366408
HSA-MIR-450099.9972.722367
HSA-MIR-366299.9973.825684
HSA-MIR-6870-5P99.9968.552115
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-4745-5P99.9865.951028
HSA-LET-7A-5P99.9872.291790
HSA-LET-7B-5P99.9872.311790
HSA-LET-7C-5P99.9872.291790
HSA-LET-7E-5P99.9872.291790
HSA-LET-7F-5P99.9872.561784
HSA-LET-7G-5P99.9872.371784
HSA-LET-7I-5P99.9872.371788
HSA-MIR-98-5P99.9872.331787
HSA-MIR-50799.9770.111915
HSA-MIR-807599.9767.20962
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-55799.9670.011640

Functional genomics

ClinGen dosage: haploinsufficiency 0 (no evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 6)

  • Evidence for the essential function of HSF1 in the transcriptional activation of TERRA and in telomere protection upon stress. (PMID:28369628)
  • This study showed that 18p TERRA expression was marginally significantly associated with preoperative CEA and significantly associated with telomere length, rendering it a potential prognostic factor for long-term oncologic outcomes in CRC. (PMID:30946316)
  • study confirms that TERRA corresponds to a large gene family transcribed from multiple chromosome ends where we identified two types of TERRA promoters, only one of which is regulated by DNA methylation (PMID:31350341)
  • Long interspersed element-1 ribonucleoprotein particles protect telomeric ends in alternative lengthening of telomeres dependent cells. (PMID:31846834)
  • TRF2 recruits nucleolar protein TCOF1 to coordinate telomere transcription and replication. (PMID:33082515)
  • Protein Phosphatase 2A-Dependent Mitotic hnRNPA1 Dephosphorylation and TERRA Formation Facilitate Telomere Capping. (PMID:34933911)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriodmrt2aENSDARG00000015072
mus_musculusDmrt2ENSMUSG00000048138
rattus_norvegicusDmrt2ENSRNOG00000016301
drosophila_melanogasterdmrt11EFBGN0030477
caenorhabditis_elegansWBGENE00019521
caenorhabditis_elegansWBGENE00022060

Paralogs (8): DMRT3 (ENSG00000064218), DMRT1 (ENSG00000137090), DMRTC2 (ENSG00000142025), DMRTA2 (ENSG00000142700), DMRTB1 (ENSG00000143006), DMRTA1 (ENSG00000176399), DMRTC1B (ENSG00000184911), DMRTC1 (ENSG00000269502)

Protein

Protein identifiers

Doublesex- and mab-3-related transcription factor 2Q9Y5R5 (reviewed: Q9Y5R5)

Alternative names: Doublesex-like 2 protein

All UniProt accessions (3): Q9Y5R5, A0A0A0MR18, Q05C20

UniProt curated annotations — full annotation on UniProt →

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.

Subunit / interactions. Homodimer.

Subcellular location. Nucleus.

Tissue specificity. Expressed in testis, kidney and skeletal muscle.

Miscellaneous. Produced by DMRT2 bicistronic transcripts (AF284223/AF284224) from non-overlapping reading frame, according to PubMed:10729224. Produced by DMRT2 bicistronic transcripts (AF284223/AF284224) from non-overlapping reading frame, according to PubMed:10729224.

Similarity. Belongs to the DMRT family.

Isoforms (3)

UniProt IDNamesCanonical?
Q9Y5R5-11yes
Q9Y5R5-22
Q9Y5R5-33

RefSeq proteins (9): NP_001124337, NP_001357460, NP_001357461, NP_001357462, NP_001374486, NP_001374487, NP_001374488, NP_006548, NP_870987* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001275DM_DNA-bdDomain
IPR026607DMRTFamily
IPR036407DM_DNA-bd_sfHomologous_superfamily

Pfam: PF00751

UniProt features (15 total): compositionally biased region 4, splice variant 3, sequence variant 2, sequence conflict 2, region of interest 2, chain 1, DNA-binding region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y5R5-F154.370.10

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 123 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_DN, GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_DN, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, AAGCAAT_MIR137, GOBP_EPITHELIUM_DEVELOPMENT, BENPORATH_ES_WITH_H3K27ME3, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_EMBRYONIC_SKELETAL_SYSTEM_DEVELOPMENT, TGACCTY_ERR1_Q2, TAKADA_GASTRIC_CANCER_COPY_NUMBER_DN, ATGCAGT_MIR217, ATGTTAA_MIR302C, GOBP_ANTERIOR_POSTERIOR_PATTERN_SPECIFICATION, GOBP_SOMITOGENESIS, TCCCCAC_MIR491

GO Biological Process (8): regulation of transcription by RNA polymerase II (GO:0006357), sex differentiation (GO:0007548), regulation of somitogenesis (GO:0014807), embryonic skeletal system development (GO:0048706), myotome development (GO:0061055), positive regulation of myotome development (GO:2000287), regulation of DNA-templated transcription (GO:0006355), positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (9): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), identical protein binding (GO:0042802), metal ion binding (GO:0046872), RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA binding (GO:0003677), protein binding (GO:0005515), sequence-specific DNA binding (GO:0043565)

GO Cellular Component (3): chromatin (GO:0000785), nucleus (GO:0005634), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA polymerase II transcription regulatory region sequence-specific DNA binding3
transcription by RNA polymerase II2
regulation of transcription by RNA polymerase II2
cellular anatomical structure2
regulation of DNA-templated transcription1
developmental process involved in reproduction1
somitogenesis1
regulation of anatomical structure morphogenesis1
regulation of multicellular organismal process1
skeletal system development1
chordate embryonic development1
anatomical structure development1
somite development1
positive regulation of developmental process1
myotome development1
regulation of myotome development1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
positive regulation of DNA-templated transcription1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
DNA-binding transcription factor activity, RNA polymerase II-specific1
DNA-binding transcription activator activity1
positive regulation of transcription by RNA polymerase II1
protein binding1
cation binding1
transcription cis-regulatory region binding1
nucleic acid binding1
binding1
DNA binding1
chromosome1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

960 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
DMRT2SRYQ05066803
DMRT2DMRT3Q9NQL9534
DMRT2ZFYP08048505
DMRT2KANK1Q14678494
DMRT2FOXL2P58012483
DMRT2HNRNPUL2Q1KMD3477
DMRT2ASB18Q6ZVZ8452
DMRT2NR0B1P51843450
DMRT2FOXL3A0A1W2PRP0432
DMRT2AMHP03971415
DMRT2RPL7P18124413
DMRT2ACTBP02570409
DMRT2WNT4P56705408
DMRT2MYF5P13349405
DMRT2PDLIM7Q9NR12395
DMRT2SOX3P35714395

IntAct

6 interactions, top by confidence:

ABTypeScore
TLE5DMRT2psi-mi:“MI:0915”(physical association)0.560
DMRT2MAGED1psi-mi:“MI:0915”(physical association)0.560
DMRT2TLE5psi-mi:“MI:0915”(physical association)0.000
DMRT2MAGED1psi-mi:“MI:0915”(physical association)0.000

BioGRID (3): DMRT2 (Reconstituted Complex), DMRT2 (Two-hybrid), MAGED1 (Two-hybrid)

ESM2 similar proteins: A2A9I7, A7X8C7, A7X8C9, A7XW16, C7EMF5, F6W2R2, O15054, O43151, O43474, O55087, O62651, O94993, P08151, P0DPQ3, P10284, P17483, P31259, P31276, P47806, P52947, P86478, P86479, P86480, P86481, P86496, Q00175, Q08DG5, Q0P670, Q1KKY2, Q5NCY0, Q5ND04, Q5SSZ7, Q60793, Q63449, Q6NZN1, Q6XP49, Q801F8, Q80WT2, Q8BG36, Q8BG87

Diamond homologs: A2A9A2, A2A9I7, A4QNP7, A6QQ94, A8TSS9, B0I1G7, B7ZS42, C0LZJ1, D4A218, F6W2R2, G5EEJ1, J7FCF0, O18214, P23023, P57690, P83758, P85119, Q18248, Q19291, Q2I327, Q2MJB4, Q32LE6, Q3LH63, Q4AE28, Q5UU75, Q5VZB9, Q6YHU8, Q71MM5, Q76L87, Q801F8, Q80WT2, Q8BG36, Q8CFG4, Q8CGW9, Q8IXT2, Q8JIR6, Q90WM5, Q96MA1, Q96SC8, Q9DFI0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

256 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic2
Likely pathogenic1
Uncertain significance185
Likely benign53
Benign8

Top pathogenic / likely-pathogenic (3)

Variant IDHGVSClassification
253670GRCh37/hg19 9p24.3-22.1(chr9:213161-19450250)x3Pathogenic
638656NM_181872.6(DMRT2):c.1A>T (p.Met1Leu)Pathogenic
3900977NM_181872.6(DMRT2):c.129del (p.Asp43fs)Likely pathogenic

SpliceAI

803 predictions. Top by Δscore:

VariantEffectΔscore
9:1053717:TACAG:Tacceptor_loss1.0000
9:1053719:CAGG:Cacceptor_loss1.0000
9:1053720:A:AGacceptor_gain1.0000
9:1053721:G:GGacceptor_gain1.0000
9:1053721:G:GTacceptor_loss1.0000
9:1052137:AGG:Adonor_loss0.9900
9:1052138:GGT:Gdonor_loss0.9900
9:1052140:T:Gdonor_loss0.9900
9:1053720:AG:Aacceptor_gain0.9900
9:1053721:GG:Gacceptor_gain0.9900
9:1053823:AGGT:Adonor_loss0.9900
9:1053824:GGTAA:Gdonor_loss0.9900
9:1053825:G:Adonor_loss0.9900
9:1053826:T:Gdonor_loss0.9900
9:1055217:A:AGacceptor_gain0.9900
9:1055217:AAAT:Aacceptor_gain0.9900
9:1055218:A:Gacceptor_gain0.9900
9:1056045:G:GTdonor_gain0.9900
9:1056046:A:Tdonor_gain0.9900
9:1050479:CAAG:Cdonor_loss0.9800
9:1050480:AAGGT:Adonor_loss0.9800
9:1050481:AG:Adonor_loss0.9800
9:1050482:GG:Gdonor_loss0.9800
9:1050483:GTG:Gdonor_loss0.9800
9:1050484:T:Gdonor_loss0.9800
9:1050543:GC:Gdonor_gain0.9800
9:1051569:GA:Gacceptor_gain0.9800
9:1052136:GAG:Gdonor_gain0.9800
9:1052139:G:GGdonor_gain0.9800
9:1053782:C:Tdonor_gain0.9800

AlphaMissense

3654 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:1051980:T:AC123S1.000
9:1051980:T:CC123R1.000
9:1051981:G:CC123S1.000
9:1051982:C:GC123W1.000
9:1051986:C:AR125S1.000
9:1051989:T:AC126S1.000
9:1051989:T:CC126R1.000
9:1051990:G:AC126Y1.000
9:1051990:G:CC126S1.000
9:1051991:C:GC126W1.000
9:1051992:C:AR127S1.000
9:1051995:A:GN128D1.000
9:1051997:C:AN128K1.000
9:1051997:C:GN128K1.000
9:1051998:C:AH129N1.000
9:1051998:C:GH129D1.000
9:1052000:C:AH129Q1.000
9:1052000:C:GH129Q1.000
9:1052002:G:AG130D1.000
9:1052021:G:CK136N1.000
9:1052021:G:TK136N1.000
9:1052025:C:GH138D1.000
9:1052027:C:AH138Q1.000
9:1052027:C:GH138Q1.000
9:1052028:A:GK139E1.000
9:1052029:A:TK139M1.000
9:1052030:G:CK139N1.000
9:1052030:G:TK139N1.000
9:1052037:T:AC142S1.000
9:1052037:T:CC142R1.000

dbSNP variants (sampled 300 via entrez): RS1000029198 (9:1052153 G>A,C,T), RS1000232486 (9:1054648 A>G), RS1000277493 (9:1054487 T>C), RS1000395121 (9:1050531 G>C), RS1000556180 (9:1055878 T>A), RS1000628015 (9:1054674 C>A,T), RS1000703162 (9:1050362 C>A,G), RS1001018184 (9:1051642 C>A,T), RS1001623190 (9:1050073 C>G), RS1001671357 (9:1055276 C>G), RS1002011041 (9:1054087 A>T), RS1002054081 (9:1056155 T>C,G), RS1002253152 (9:1051934 C>A,G,T), RS1002824345 (9:1048429 C>A,G,T), RS1002858603 (9:1049447 C>A)

Disease associations

OMIM: gene MIM:604935 | disease phenotypes: MIM:600171, MIM:621523

GenCC curated gene-disease

DiseaseClassificationInheritance
spondylocostal dysostosisLimitedAutosomal recessive

Mondo (3): gonadal agenesis (MONDO:0010838), spondylocostal dysostosis 7, autosomal recessive (MONDO:0981023), spondylocostal dysostosis (MONDO:0000359)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

20 associations (top):

StudyTraitp-value
GCST000278_8Hyperactive-impulsive symptoms5.000000e-06
GCST001144_7Dupuytren’s disease6.000000e-09
GCST003059_15Parkinson’s disease1.000000e-06
GCST003542_195Night sleep phenotypes4.000000e-06
GCST003542_8Night sleep phenotypes3.000000e-08
GCST003996_2Monobrow4.000000e-62
GCST003999_7Nose size1.000000e-09
GCST004858_13Dupuytren’s disease4.000000e-26
GCST006152_2Language impairment in frontotemporal lobe dementia6.000000e-06
GCST006481_17Lung function (FEV1)5.000000e-08
GCST006481_41Lung function (FEV1)5.000000e-06
GCST006483_64Lung function (FVC)3.000000e-08
GCST006483_65Lung function (FVC)1.000000e-07
GCST006483_68Lung function (FVC)7.000000e-09
GCST010118_170Type 2 diabetes2.000000e-08
GCST010173_135Triglyceride levels9.000000e-09
GCST010242_185HDL cholesterol levels5.000000e-08
GCST010244_299Triglyceride levels3.000000e-12
GCST90002385_375High light scatter reticulocyte count3.000000e-10
GCST90002386_420High light scatter reticulocyte percentage of red cells2.000000e-09

EFO canonical traits (7, from GWAS)

EFO IDTrait name
EFO:0004229Dupuytren Contracture
EFO:0007906synophrys measurement
EFO:0004314forced expiratory volume
EFO:0004312vital capacity
EFO:0004530triglyceride measurement
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0007986reticulocyte count

MeSH disease descriptors (1)

DescriptorNameTree numbers
C537565Jarcho-Levin syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases expression3
tungsten carbideaffects binding, decreases expression1
terbufosincreases methylation1
arseniteincreases methylation1
cobaltous chloridedecreases expression1
butyraldehydeincreases expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression, affects cotreatment, decreases expression1
15-acetyldeoxynivalenolincreases expression1
monomethylarsonous aciddecreases expression1
(+)-JQ1 compounddecreases expression1
Cobaltaffects binding, decreases expression1
Fonofosincreases methylation1
Lipopolysaccharidesincreases expression, affects cotreatment, decreases expression, affects response to substance1
Parathionincreases methylation1
Tobacco Smoke Pollutiondecreases expression1
Aflatoxin B1decreases methylation1
Antirheumatic Agentsincreases expression1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_A0Z8SEES3-1V human DMRT2, clone1Embryonic stem cellMale
CVCL_A0Z9SEES3-1V human DMRT2, clone2Embryonic stem cellMale
CVCL_A1A0SEES3-1V human DMRT2, clone3Embryonic stem cellMale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.