DMXL1

gene
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Summary

DMXL1 (Dmx like 1, HGNC:2937) is a protein-coding gene on chromosome 5q23.1, encoding DmX-like protein 1 (Q9Y485).

The protein encoded by this gene is a member of the WD repeat superfamily of proteins, which have regulatory functions. This gene is expressed in many tissue types including several types of eye tissue, and it has been associated with ocular phenotypes. In addition, it is upregulated in cultured cells that overexpress growth factor independence 1B, a transcription factor that is essential for hematopoietic cell development. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 1657 — RefSeq curated summary.

At a glance

  • GWAS associations: 8
  • Clinical variants (ClinVar): 590 total
  • MANE Select transcript: NM_001290321

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2937
Approved symbolDMXL1
NameDmx like 1
Location5q23.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000172869
Ensembl biotypeprotein_coding
OMIM605671
Entrez1657

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 9 protein_coding_CDS_not_defined, 4 protein_coding, 3 retained_intron

ENST00000311085, ENST00000502516, ENST00000503802, ENST00000504031, ENST00000504497, ENST00000505312, ENST00000507552, ENST00000509902, ENST00000510924, ENST00000511622, ENST00000512281, ENST00000514151, ENST00000514595, ENST00000515335, ENST00000539542, ENST00000939842

RefSeq mRNA: 8 — MANE Select: NM_001290321 NM_001290321, NM_001349239, NM_001349240, NM_001387933, NM_001387934, NM_001387937, NM_001387938, NM_005509

CCDS: CCDS4125, CCDS75289

Canonical transcript exons

ENST00000539542 — 44 exons

ExonStartEnd
ENSE00001083130119197755119197956
ENSE00001202207119133494119134178
ENSE00001202211119133132119133385
ENSE00001272322119196371119196456
ENSE00001272476119129211119129423
ENSE00001272492119118815119119004
ENSE00001272517119105180119105258
ENSE00001272572119246995119249127
ENSE00001367752119147249119147470
ENSE00001368091119134268119134389
ENSE00001377433119148739119150421
ENSE00001400702119167603119167864
ENSE00001404246119166616119166781
ENSE00001404744119193828119193970
ENSE00001409422119189708119189886
ENSE00001412462119177996119178244
ENSE00001417452119177357119177484
ENSE00001417604119165183119165280
ENSE00001423096119164507119164676
ENSE00001425422119175261119175337
ENSE00001426459119151929119152036
ENSE00001429600119171778119171969
ENSE00001434520119170190119171280
ENSE00002224323119206834119206896
ENSE00002279392119071087119071656
ENSE00003489787119101935119102006
ENSE00003489981119240419119240471
ENSE00003493530119220940119221081
ENSE00003495869119238989119239080
ENSE00003506049119220472119220593
ENSE00003509345119224709119224769
ENSE00003511570119146837119146956
ENSE00003572488119097979119098104
ENSE00003573913119244359119244576
ENSE00003602143119114475119114541
ENSE00003608671119143841119143930
ENSE00003616513119144536119144638
ENSE00003619105119120971119121139
ENSE00003641587119116158119116336
ENSE00003642078119203319119203436
ENSE00003648795119233340119233467
ENSE00003662943119237322119237414
ENSE00003684570119216901119216987
ENSE00003687950119110151119110283

Expression profiles

Bgee: expression breadth ubiquitous, 293 present calls, max score 96.92.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.9455 / max 685.2201, expressed in 1814 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
581079.58461708
581089.23021735
581063.37981348
581050.7509467

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
choroid plexus epitheliumUBERON:000391196.92gold quality
pigmented layer of retinaUBERON:000178296.85gold quality
retinaUBERON:000096696.83gold quality
endothelial cellCL:000011596.18gold quality
Brodmann (1909) area 23UBERON:001355495.88gold quality
calcaneal tendonUBERON:000370195.67gold quality
nephron tubuleUBERON:000123194.61gold quality
epithelium of nasopharynxUBERON:000195194.38gold quality
secondary oocyteCL:000065594.27gold quality
corpus callosumUBERON:000233694.23gold quality
oocyteCL:000002393.91gold quality
parietal pleuraUBERON:000240093.55gold quality
visceral pleuraUBERON:000240193.37gold quality
sural nerveUBERON:001548892.95gold quality
blood vessel layerUBERON:000479792.92gold quality
adrenal tissueUBERON:001830392.87gold quality
germinal epithelium of ovaryUBERON:000130492.85gold quality
pleuraUBERON:000097792.83gold quality
superficial temporal arteryUBERON:000161492.74gold quality
tibiaUBERON:000097992.63gold quality
oral cavityUBERON:000016792.26gold quality
tonsilUBERON:000237292.15gold quality
mucosa of paranasal sinusUBERON:000503092.14gold quality
jejunal mucosaUBERON:000039992.13gold quality
ponsUBERON:000098892.05gold quality
gingival epitheliumUBERON:000194991.98gold quality
skin of hipUBERON:000155491.92gold quality
subthalamic nucleusUBERON:000190691.77gold quality
upper leg skinUBERON:000426291.67gold quality
inferior olivary complexUBERON:000212791.62gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes7.32

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

163 targeting DMXL1, 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-3163100.0077.238605
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-8485100.0077.574731
HSA-MIR-656-3P100.0072.152788
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-126-5P100.0072.713180
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-3613-3P100.0076.367965
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-428299.9975.366408
HSA-MIR-548AW99.9972.573559
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-511-3P99.9968.851467
HSA-MIR-366299.9973.825684
HSA-MIR-477599.9875.006394
HSA-MIR-548N99.9871.944170
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-32-5P99.9875.211964
HSA-MIR-92A-3P99.9875.211960
HSA-MIR-92B-3P99.9875.251955
HSA-MIR-25-3P99.9874.601817
HSA-MIR-363-3P99.9874.721821
HSA-MIR-367-3P99.9874.831819
HSA-MIR-569699.9872.364487

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
ENSDARG00000098599
mus_musculusDmxl1ENSMUSG00000037416
rattus_norvegicusDmxl1ENSRNOG00000024671
drosophila_melanogasterRbcn-3AFBGN0023458
caenorhabditis_elegansWBGENE00004313

Paralogs (1): DMXL2 (ENSG00000104093)

Protein

Protein identifiers

DmX-like protein 1Q9Y485 (reviewed: Q9Y485)

All UniProt accessions (3): E7EMZ0, Q9Y485, F5H269

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed in bone, breast, eye, foreskin, heart, parathyroid, small intestine, testis, tonsils, placenta and uterus.

RefSeq proteins (8): NP_001277250, NP_001336168, NP_001336169, NP_001374862, NP_001374863, NP_001374866, NP_001374867, NP_005500 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001680WD40_rptRepeat
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR022033Rav1p_CDomain
IPR036322WD40_repeat_dom_sfHomologous_superfamily
IPR052208DmX-like/RAVE_componentFamily

Pfam: PF00400, PF12234

UniProt features (41 total): repeat 16, modified residue 11, region of interest 4, sequence variant 4, sequence conflict 3, compositionally biased region 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

No AlphaFold model available for Q9Y485 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (11): 324, 422, 425, 436, 574, 918, 924, 1830, 1896, 1908, 1970

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 217 (showing top): BROWNE_HCMV_INFECTION_30MIN_DN, GCANCTGNY_MYOD_Q6, AREB6_03, BROWNE_HCMV_INFECTION_48HR_DN, TCF4_Q5, ONKEN_UVEAL_MELANOMA_UP, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOBP_VACUOLAR_ACIDIFICATION, MYOD_Q6, SCHLOSSER_SERUM_RESPONSE_DN, GOBP_REGULATION_OF_PH, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP, GOBP_MONOATOMIC_ION_HOMEOSTASIS, FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN, BASAKI_YBX1_TARGETS_DN

GO Biological Process (1): vacuolar acidification (GO:0007035)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): RAVE complex (GO:0043291)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
intracellular pH reduction1
binding1
cytoplasm1
protein-containing complex1

Protein interactions and networks

STRING

1504 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
DMXL1RAB3GAP1Q15042682
DMXL1RAB3GAP2Q9H2M9649
DMXL1MADDQ8WXG6606
DMXL1WDR7Q9Y4E6545
DMXL1RPS6KA3P51812522
DMXL1SNX27Q96L92509
DMXL1TTLL2Q9BWV7506
DMXL1ROGDIQ9GZN7462
DMXL1COX7B2Q8TF08460
DMXL1ATP6V1AP38606453
DMXL1GPR153Q6NV75443
DMXL1RAB3AP20336441
DMXL1PLEKHG1Q9ULL1435
DMXL1ADPGKQ9BRR6428
DMXL1MSANTD2Q6P1R3419

IntAct

37 interactions, top by confidence:

ABTypeScore
ATP6V1C2ATP6V1G1psi-mi:“MI:0914”(association)0.640
STK4STRNpsi-mi:“MI:0914”(association)0.610
ATP6V1B2ATP6V1G1psi-mi:“MI:0914”(association)0.530
RPN1APBB1psi-mi:“MI:0914”(association)0.530
ZNRD2MYO9Apsi-mi:“MI:0914”(association)0.530
ATP6V1G2ATP6V1B1psi-mi:“MI:0914”(association)0.530
DMXL1PDIA6psi-mi:“MI:0915”(physical association)0.400
DMXL1H2AC14psi-mi:“MI:0915”(physical association)0.400
RNASEH2APHF20L1psi-mi:“MI:0914”(association)0.350
RAP1BKLC1psi-mi:“MI:0914”(association)0.350
ATP6V1C2POTEFpsi-mi:“MI:0914”(association)0.350
ROGDIpsi-mi:“MI:0914”(association)0.350
ATP6V1B1ATP6V1G1psi-mi:“MI:0914”(association)0.350
RYBPPIPSLpsi-mi:“MI:0914”(association)0.350
RYBPFAM186Apsi-mi:“MI:0914”(association)0.350
ITM2BILVBLpsi-mi:“MI:0914”(association)0.350
ATP6V1E1ATP6V1Dpsi-mi:“MI:0914”(association)0.350
ATP6V1FMID1psi-mi:“MI:0914”(association)0.350
ATP6V1G1MRPL3psi-mi:“MI:0914”(association)0.350
ATP6V1HATP6V1G1psi-mi:“MI:0914”(association)0.350
DDOSTATL3psi-mi:“MI:0914”(association)0.350
OST4ATL3psi-mi:“MI:0914”(association)0.350
RPN2APBB1psi-mi:“MI:0914”(association)0.350
STT3BAPBB1psi-mi:“MI:0914”(association)0.350
DMXL1LLGL1psi-mi:“MI:0914”(association)0.350
WDR7DMXL2psi-mi:“MI:0914”(association)0.350
atp6v1c_humanPOTEFpsi-mi:“MI:0914”(association)0.350
atp6v1g_humanHSPA8psi-mi:“MI:0914”(association)0.350
PPP4R1LIFT56psi-mi:“MI:0914”(association)0.350

BioGRID (78): DMXL1 (Affinity Capture-MS), DMXL1 (Affinity Capture-MS), DMXL1 (Affinity Capture-MS), DMXL1 (Affinity Capture-MS), DMXL1 (Affinity Capture-MS), DMXL1 (Affinity Capture-MS), DMXL1 (Affinity Capture-MS), DMXL1 (Affinity Capture-MS), DMXL1 (Affinity Capture-MS), DMXL1 (Affinity Capture-RNA), DMXL1 (Proximity Label-MS), DMXL1 (Proximity Label-MS), DMXL1 (Affinity Capture-RNA), DMXL1 (Two-hybrid), DMXL1 (Proximity Label-MS)

ESM2 similar proteins: A1L3L1, A2RT67, A3KPW7, A4IIA7, A8C750, A8C752, D2HNY3, E1BGQ2, E1C3P4, Q08CL8, Q08DZ8, Q0IHB3, Q149N8, Q1RMU2, Q1RMZ1, Q3MJ13, Q3T1H6, Q5F3F2, Q5RED8, Q5VVJ2, Q5ZJ87, Q66J91, Q69Z66, Q6AYF5, Q6DE97, Q6GR37, Q6P1E7, Q6PNC0, Q6YHU6, Q7TPQ3, Q8BKW4, Q8BXK4, Q8IWR0, Q8IYF3, Q8IZE3, Q8K2I9, Q8NA31, Q8NEN0, Q8NFZ0, Q96EW2

Diamond homologs: P87314, Q6PNC0, Q8BPN8, Q8TDJ6, Q9Y485

SIGNOR signaling

1 interactions.

AEffectBMechanism
DMXL1“form complex”“RAVE complex, DMXL1 variant”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 52 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy6106.1×5e-10
Insulin receptor recycling990.2×5e-14
Transferrin endocytosis and recycling987.2×5e-14
ROS and RNS production in phagocytes979.5×8e-14
PD-L1(CD274) glycosylation and translocation to plasma membrane568.3×3e-07
Amino acids regulate mTORC1947.5×1e-11
Maturation of spike protein534.9×9e-06
Maturation of DENV proteins527.8×3e-05

GO biological processes:

GO termPartnersFoldFDR
synaptic vesicle lumen acidification7145.6×5e-12
vacuolar acidification697.7×2e-09
regulation of macroautophagy852.6×2e-10
proton transmembrane transport641.6×4e-07
protein N-linked glycosylation529.3×3e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance437
Likely benign39
Benign54

Top pathogenic / likely-pathogenic (0)

SpliceAI

7158 predictions. Top by Δscore:

VariantEffectΔscore
5:119071653:CACGG:Cdonor_loss1.0000
5:119071656:GGT:Gdonor_loss1.0000
5:119071657:G:GCdonor_loss1.0000
5:119071657:G:GGdonor_gain1.0000
5:119071658:T:Adonor_loss1.0000
5:119071659:GAGT:Gdonor_loss1.0000
5:119097973:TTTTA:Tacceptor_loss1.0000
5:119097974:TTTAG:Tacceptor_loss1.0000
5:119097975:TTAG:Tacceptor_loss1.0000
5:119097976:TAGG:Tacceptor_loss1.0000
5:119097977:A:AGacceptor_gain1.0000
5:119097977:AG:Aacceptor_gain1.0000
5:119097978:G:GGacceptor_gain1.0000
5:119097978:GG:Gacceptor_gain1.0000
5:119097978:GGCTT:Gacceptor_gain1.0000
5:119098101:CAAG:Cdonor_loss1.0000
5:119098102:AAGGT:Adonor_loss1.0000
5:119110284:G:GGdonor_gain1.0000
5:119114470:TACA:Tacceptor_loss1.0000
5:119114471:ACAGA:Aacceptor_loss1.0000
5:119114472:CAG:Cacceptor_loss1.0000
5:119114473:A:AGacceptor_gain1.0000
5:119114473:A:ATacceptor_loss1.0000
5:119114474:G:GGacceptor_gain1.0000
5:119114474:GA:Gacceptor_gain1.0000
5:119114474:GAACT:Gacceptor_gain1.0000
5:119116153:CTTA:Cacceptor_loss1.0000
5:119116154:TTA:Tacceptor_loss1.0000
5:119116155:TAG:Tacceptor_loss1.0000
5:119116156:A:AGacceptor_gain1.0000

AlphaMissense

20100 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:119116308:T:AW239R1.000
5:119116308:T:CW239R1.000
5:119118870:T:AW267R1.000
5:119118870:T:CW267R1.000
5:119129288:T:AW394R1.000
5:119129288:T:CW394R1.000
5:119133332:T:AW506R1.000
5:119133332:T:CW506R1.000
5:119133747:T:CL608P1.000
5:119133755:T:AW611R1.000
5:119133755:T:CW611R1.000
5:119133836:T:CF638L1.000
5:119133837:T:CF638S1.000
5:119133838:T:AF638L1.000
5:119133838:T:GF638L1.000
5:119134038:T:CL705P1.000
5:119134046:T:AW708R1.000
5:119134046:T:CW708R1.000
5:119177478:T:AW2294R1.000
5:119177478:T:CW2294R1.000
5:119216970:G:CA2645P1.000
5:119233343:T:CL2760P1.000
5:119233367:T:AV2768D1.000
5:119233381:T:AW2773R1.000
5:119233381:T:CW2773R1.000
5:119071589:T:CL7P0.999
5:119071605:C:AN12K0.999
5:119071605:C:GN12K0.999
5:119097980:C:AA30D0.999
5:119098010:T:CL40P0.999

dbSNP variants (sampled 300 via entrez): RS1000006788 (5:119082854 C>A,G), RS1000016499 (5:119190375 C>T), RS1000028711 (5:119225666 A>G), RS1000035757 (5:119235164 A>G), RS1000042801 (5:119170552 G>T), RS1000061990 (5:119198017 C>T), RS1000066002 (5:119116528 C>T), RS1000074682 (5:119185071 T>A,C), RS1000087663 (5:119147642 C>G,T), RS1000089122 (5:119074006 C>T), RS1000110621 (5:119083317 G>C), RS1000113691 (5:119139247 A>C,T), RS1000122198 (5:119213729 C>G,T), RS1000130611 (5:119159384 G>A), RS1000145945 (5:119108858 A>G)

Disease associations

OMIM: gene MIM:605671 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

8 associations (top):

StudyTraitp-value
GCST001915_11Alzheimer’s disease (cognitive decline)9.000000e-07
GCST005956_40Waist-to-hip ratio adjusted for BMI2.000000e-06
GCST005958_18Waist-to-hip ratio adjusted for BMI (age >50)9.000000e-07
GCST005962_27Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)9.000000e-09
GCST009391_1634Metabolite levels1.000000e-06
GCST009798_70Asthma3.000000e-11
GCST011068_1Cognitive impairment in depression5.000000e-06
GCST90002390_139Mean corpuscular hemoglobin4.000000e-10

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0008007age at assessment
EFO:0008343sex interaction measurement
EFO:0007787plasma betaine measurement
EFO:0004527mean corpuscular hemoglobin

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

54 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
entinostatincreases expression, affects cotreatment2
Benzo(a)pyrenedecreases expression2
Quercetindecreases expression, affects expression2
Cadmium Chloridedecreases expression, increases abundance, increases expression2
aristolochic acid Idecreases expression1
FR900359affects phosphorylation1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
bisphenol Adecreases expression, increases expression1
kojic aciddecreases expression1
trichostatin Aaffects expression1
beta-lapachonedecreases expression1
sodium arseniteincreases expression1
cobaltous chlorideincreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, decreases expression1
aflatoxin B2increases methylation1
epigallocatechin gallateaffects cotreatment, decreases expression1
3-deazaneplanocindecreases expression1
di-n-butylphosphoric acidaffects expression1
oxamflatinincreases expression1
apicidinincreases expression1
acylineincreases expression1
scriptaidincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinaffects cotreatment, increases expression1
suberoyl bis-hydroxamic acidincreases expression1
jinfukangdecreases expression1
Resveratrolaffects cotreatment, increases expression1
Arsenic Trioxidedecreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.