RMND5A

gene
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Also known as FLJ13910RMD5GID2GID2Ap44CTLH

Summary

RMND5A (required for meiotic nuclear division 5 homolog A, HGNC:25850) is a protein-coding gene on chromosome 2p11.2, encoding E3 ubiquitin-protein transferase RMND5A (Q9H871). Core component of the CTLH E3 ubiquitin-protein ligase complex that selectively accepts ubiquitin from UBE2H and mediates ubiquitination and subsequent proteasomal degradation of the transcription factor HBP1. It is a selective cancer dependency (DepMap: 31.7% of cell lines).

Predicted to enable ubiquitin protein ligase activity and zinc ion binding activity. Predicted to contribute to ubiquitin-protein transferase activity. Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process and protein polyubiquitination. Located in cytoplasm and nucleoplasm. Part of ubiquitin ligase complex.

Source: NCBI Gene 64795 — RefSeq curated summary.

At a glance

  • GWAS associations: 14
  • Clinical variants (ClinVar): 34 total
  • Cancer dependency (DepMap): dependent in 31.7% of screened cell lines
  • MANE Select transcript: NM_022780

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25850
Approved symbolRMND5A
Namerequired for meiotic nuclear division 5 homolog A
Location2p11.2
Locus typegene with protein product
StatusApproved
AliasesFLJ13910, RMD5, GID2, GID2A, p44CTLH
Ensembl geneENSG00000153561
Ensembl biotypeprotein_coding
OMIM618964
Entrez64795

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 3 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000283632, ENST00000466417, ENST00000471113, ENST00000472843, ENST00000882508, ENST00000932494

RefSeq mRNA: 1 — MANE Select: NM_022780 NM_022780

CCDS: CCDS1991

Canonical transcript exons

ENST00000283632 — 9 exons

ExonStartEnd
ENSE000010114388675345886753558
ENSE000010114408676502786765193
ENSE000012216318677334886778041
ENSE000016537948672029186720809
ENSE000025317308674092786741069
ENSE000035011558677002386770125
ENSE000035158448675189686752030
ENSE000035532438677155886771712
ENSE000036079358676585986766024

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 99.38.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.7331 / max 162.8225, expressed in 1729 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
213049.35491724
2022680.3538155
213060.01312
213070.00824
213050.00302

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065599.38gold quality
oocyteCL:000002398.35gold quality
buccal mucosa cellCL:000233697.78gold quality
esophagus squamous epitheliumUBERON:000692096.88gold quality
epithelium of esophagusUBERON:000197696.33gold quality
amniotic fluidUBERON:000017395.82gold quality
paraflocculusUBERON:000535195.68gold quality
lower esophagus mucosaUBERON:003583495.37gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450295.35gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451195.30gold quality
gluteal muscleUBERON:000200095.29gold quality
biceps brachiiUBERON:000150795.12gold quality
left ventricle myocardiumUBERON:000656695.01gold quality
skeletal muscle tissueUBERON:000113494.96gold quality
deltoidUBERON:000147694.69gold quality
tibialis anteriorUBERON:000138594.56gold quality
cerebellumUBERON:000203794.33gold quality
cerebellar cortexUBERON:000212993.99gold quality
quadriceps femorisUBERON:000137793.92gold quality
cerebellar hemisphereUBERON:000224593.91gold quality
vastus lateralisUBERON:000137993.89gold quality
muscle tissueUBERON:000238593.88gold quality
hindlimb stylopod muscleUBERON:000425293.59gold quality
muscle organUBERON:000163093.53gold quality
skeletal muscle organUBERON:001489293.53gold quality
triceps brachiiUBERON:000150993.37gold quality
muscle of legUBERON:000138393.18gold quality
gastrocnemiusUBERON:000138893.14gold quality
heart right ventricleUBERON:000208093.13gold quality
corpus callosumUBERON:000233692.87gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes8.72
E-MTAB-6058no506.33

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

313 targeting RMND5A, 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-3924100.0072.092394
HSA-MIR-9-5P100.0072.282361
HSA-MIR-8485100.0077.574731
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-3646100.0073.565283
HSA-MIR-188-3P100.0068.761240
HSA-MIR-4692100.0067.322066
HSA-MIR-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-4262100.0073.263931
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-340-5P100.0072.504437
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-548AW99.9972.573559
HSA-MIR-451499.9967.101870
HSA-MIR-366299.9973.825684
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-181A-5P99.9972.962995

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 31.7% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 5)

  • RanBPM, ARMC8alpha, ARMC8beta, Muskelin, p48EMLP, and p44CTLH form complexes in cells. (PMID:17467196)
  • Duplications of this region involving RMND5A, whose product contains a C-terminal to lis homology (LisH) domain, have not previously been associated with a defined phenotype but may present insight into encephalocele formation. (PMID:22681319)
  • The study identifies a miR-138-RMND5A-Exportin-5 as a previously unknown miRNA processing regulatory pathway in HeLa cells. (PMID:24057215)
  • GID2 Interacts With CDKN3 and Regulates Pancreatic Cancer Growth and Apoptosis. (PMID:36828188)
  • Non-canonical substrate recognition by the human WDR26-CTLH E3 ligase regulates prodrug metabolism. (PMID:38759627)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
mus_musculusRmnd5aENSMUSG00000002222
rattus_norvegicusRmnd5aENSRNOG00000065409
drosophila_melanogasterSouFBGN0034573
caenorhabditis_elegansWBGENE00020301

Paralogs (2): MAEA (ENSG00000090316), RMND5B (ENSG00000145916)

Protein

Protein identifiers

E3 ubiquitin-protein transferase RMND5AQ9H871 (reviewed: Q9H871)

Alternative names: P44CTLH, Protein RMD5 homolog A

All UniProt accessions (1): Q9H871

UniProt curated annotations — full annotation on UniProt →

Function. Core component of the CTLH E3 ubiquitin-protein ligase complex that selectively accepts ubiquitin from UBE2H and mediates ubiquitination and subsequent proteasomal degradation of the transcription factor HBP1. MAEA and RMND5A are both required for catalytic activity of the CTLH E3 ubiquitin-protein ligase complex. Catalytic activity of the complex is required for normal cell proliferation. The CTLH E3 ubiquitin-protein ligase complex is not required for the degradation of enzymes involved in gluconeogenesis, such as FBP1.

Subunit / interactions. Identified in the CTLH complex that contains GID4, RANBP9 and/or RANBP10, MKLN1, MAEA, RMND5A (or alternatively its paralog RMND5B), GID8, ARMC8, WDR26 and YPEL5. Within this complex, MAEA, RMND5A (or alternatively its paralog RMND5B), GID8, WDR26, and RANBP9 and/or RANBP10 form the catalytic core, while GID4, MKLN1, ARMC8 and YPEL5 have ancillary roles.

Subcellular location. Nucleus. Nucleoplasm. Cytoplasm.

Isoforms (2)

UniProt IDNamesCanonical?
Q9H871-11yes
Q9H871-22

RefSeq proteins (1): NP_073617* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006594LisHConserved_site
IPR006595CTLH_CDomain
IPR013144CRA_domDomain
IPR024964CTLH/CRADomain
IPR027370Znf-RING_eukDomain
IPR037680RMD5A_dRINGDomain
IPR044063ZF_RING_GIDDomain
IPR045098Fyv10_famFamily

Pfam: PF10607, PF13445

UniProt features (26 total): helix 10, strand 6, domain 2, splice variant 2, sequence conflict 2, chain 1, turn 1, zinc finger region 1, modified residue 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
8PJNELECTRON MICROSCOPY3.4

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H871-F189.970.65

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 (1): 1

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-9861718Regulation of pyruvate metabolism
R-HSA-1428517Aerobic respiration and respiratory electron transport
R-HSA-1430728Metabolism
R-HSA-70268Pyruvate metabolism

MSigDB gene sets: 290 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP, FREAC2_01, GCM_ZNF198, MORF_RRM1, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, BROWNE_HCMV_INFECTION_16HR_UP, CACCAGC_MIR138, PUJANA_CHEK2_PCC_NETWORK, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOBP_PROTEIN_POLYUBIQUITINATION, TANAKA_METHYLATED_IN_ESOPHAGEAL_CARCINOMA, AACTTT_UNKNOWN, PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP

GO Biological Process (2): protein polyubiquitination (GO:0000209), proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)

GO Molecular Function (6): ubiquitin-protein transferase activity (GO:0004842), zinc ion binding (GO:0008270), ubiquitin protein ligase activity (GO:0061630), protein binding (GO:0005515), transferase activity (GO:0016740), metal ion binding (GO:0046872)

GO Cellular Component (6): ubiquitin ligase complex (GO:0000151), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), GID complex (GO:0034657)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Pyruvate metabolism1
Metabolism1
Aerobic respiration and respiratory electron transport1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
protein ubiquitination1
ubiquitin-dependent protein catabolic process1
proteasomal protein catabolic process1
ubiquitin-like protein transferase activity1
transition metal ion binding1
ubiquitin-protein transferase activity1
ubiquitin-like protein ligase activity1
binding1
catalytic activity1
cation binding1
intracellular protein-containing complex1
transferase complex1
intracellular membrane-bounded organelle1
nuclear lumen1
intracellular anatomical structure1
cytoplasm1
ubiquitin ligase complex1

Protein interactions and networks

STRING

886 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RMND5AGID8Q9NWU2993
RMND5ARANBP9Q96S59960
RMND5AARMC8Q8IUR7948
RMND5AWDR26Q9H7D7947
RMND5AMKLN1Q9UL63945
RMND5AGID4Q8IVV7942
RMND5APAFAH1B1P43034764
RMND5ARANBP10Q6VN20731
RMND5AYPEL5P62699608
RMND5AUBE2HP37286607
RMND5AMAEAQ7L5Y9582
RMND5ASWSAP1Q6NVH7556
RMND5AZNHIT3Q15649546
RMND5AZMYND19Q96E35509
RMND5ASCFD1Q8WVM8464

IntAct

155 interactions, top by confidence:

ABTypeScore
RMND5AGID8psi-mi:“MI:0915”(physical association)0.880
ARMC8HTRA2psi-mi:“MI:0914”(association)0.750
GID8MAEApsi-mi:“MI:0914”(association)0.730
GID8PGRMC2psi-mi:“MI:0914”(association)0.640
CCDC120AIPpsi-mi:“MI:0914”(association)0.640
CRIPTOAIPpsi-mi:“MI:0914”(association)0.640
NDUFS6NDUFS8psi-mi:“MI:0914”(association)0.640
RANBP10MAEApsi-mi:“MI:0914”(association)0.640
RANBP9YPEL5psi-mi:“MI:0914”(association)0.640
PRG2YPEL5psi-mi:“MI:0914”(association)0.640
CAMKVAP3B1psi-mi:“MI:0914”(association)0.640
GID8HTRA2psi-mi:“MI:0914”(association)0.610
RMND5AMEOX2psi-mi:“MI:0915”(physical association)0.560
MEOX2RMND5Apsi-mi:“MI:0915”(physical association)0.560
RMND5ANDUFV1psi-mi:“MI:0915”(physical association)0.560
RMND5AWFS1psi-mi:“MI:0915”(physical association)0.560
ATXN1RMND5Apsi-mi:“MI:0915”(physical association)0.560
TARDBPRMND5Apsi-mi:“MI:0915”(physical association)0.560

BioGRID (283): RMND5A (Two-hybrid), RMND5A (Affinity Capture-MS), RMND5A (Affinity Capture-MS), RMND5A (Affinity Capture-MS), RMND5A (Affinity Capture-MS), RMND5A (Affinity Capture-MS), RMND5A (Affinity Capture-MS), RMND5A (Affinity Capture-MS), RMND5A (Affinity Capture-MS), RMND5A (Affinity Capture-MS), RMND5A (Affinity Capture-MS), RMND5A (Affinity Capture-MS), RANBP10 (Affinity Capture-MS), RANBP9 (Affinity Capture-MS), WDR26 (Affinity Capture-MS)

ESM2 similar proteins: A0MT11, A1Z3X3, A2VD00, A4GWN3, A4II09, A4QNE0, A4VCH4, B5KFI0, O35841, P48553, P49754, Q09161, Q0P5I8, Q15386, Q3TLI0, Q3UYV9, Q56A27, Q5E9L7, Q5KU39, Q5R644, Q5XI83, Q5ZJZ6, Q5ZKG8, Q5ZMW3, Q640V2, Q6GLK9, Q6GLP4, Q6N069, Q6NRL4, Q6TGY8, Q6WKZ8, Q7L5D6, Q7ZY79, Q80U95, Q80UM3, Q80YQ8, Q8BWQ6, Q8IWV8, Q8VZM1, Q91W86

Diamond homologs: O59668, Q640V2, Q6GLP4, Q80YQ8, Q9H871, Q9T075, Q91YQ7, Q96G75, Q11072

SIGNOR signaling

1 interactions.

AEffectBMechanism
Ub:E2“up-regulates activity”RMND5Aubiquitination

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 130 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 pyruvate metabolism853.1×3e-10
Aerobic respiration and respiratory electron transport77.2×7e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance20
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1380 predictions. Top by Δscore:

VariantEffectΔscore
2:86740922:TATA:Tacceptor_loss1.0000
2:86740924:TA:Tacceptor_loss1.0000
2:86740925:A:AGacceptor_gain1.0000
2:86740925:A:Tacceptor_loss1.0000
2:86740926:G:GAacceptor_gain1.0000
2:86741067:AAGG:Adonor_loss1.0000
2:86741068:AGGT:Adonor_loss1.0000
2:86741070:G:GCdonor_loss1.0000
2:86741070:G:GGdonor_gain1.0000
2:86741071:T:Adonor_loss1.0000
2:86751891:CCCAG:Cacceptor_loss1.0000
2:86751894:A:AGacceptor_gain1.0000
2:86751895:G:GGacceptor_gain1.0000
2:86751895:GA:Gacceptor_gain1.0000
2:86751895:GAA:Gacceptor_gain1.0000
2:86751895:GAAT:Gacceptor_gain1.0000
2:86751895:GAATT:Gacceptor_gain1.0000
2:86752027:TCAG:Tdonor_loss1.0000
2:86752028:CAG:Cdonor_loss1.0000
2:86752031:GT:Gdonor_loss1.0000
2:86752032:T:Gdonor_loss1.0000
2:86753454:CCA:Cacceptor_loss1.0000
2:86753456:A:AGacceptor_gain1.0000
2:86753457:G:GGacceptor_gain1.0000
2:86753457:GGA:Gacceptor_gain1.0000
2:86753457:GGAAT:Gacceptor_gain1.0000
2:86753556:GGA:Gdonor_gain1.0000
2:86753557:GA:Gdonor_gain1.0000
2:86753557:GAG:Gdonor_gain1.0000
2:86753559:G:GGdonor_gain1.0000

AlphaMissense

2589 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:86741023:A:TK80I1.000
2:86741024:A:CK80N1.000
2:86741024:A:TK80N1.000
2:86741031:C:GH83D1.000
2:86741041:T:AV86D1.000
2:86741053:G:AG90E1.000
2:86741055:A:GK91E1.000
2:86741057:A:CK91N1.000
2:86741057:A:TK91N1.000
2:86753552:C:AA172D1.000
2:86765028:T:AW175R1.000
2:86765028:T:CW175R1.000
2:86765030:G:CW175C1.000
2:86765030:G:TW175C1.000
2:86765031:G:CA176P1.000
2:86765086:T:CL194P1.000
2:86765095:T:CL197P1.000
2:86765155:C:AA217D1.000
2:86765967:T:CF266S1.000
2:86765978:G:CA270P1.000
2:86770033:G:CG289R1.000
2:86770034:G:AG289D1.000
2:86770121:T:CL318S1.000
2:86771600:T:CF334L1.000
2:86771601:T:CF334S1.000
2:86771602:T:AF334L1.000
2:86771602:T:GF334L1.000
2:86771604:C:AA335D1.000
2:86771606:T:AC336S1.000
2:86771606:T:CC336R1.000

dbSNP variants (sampled 300 via entrez): RS1000106432 (2:86719805 G>A,C), RS1000193952 (2:86772484 CAAAAA>C,CA,CAAAA,CAAAAAA), RS1000222729 (2:86765430 A>G), RS1000290826 (2:86745864 A>T), RS1000294570 (2:86764844 T>C), RS1000434612 (2:86772097 G>A,C), RS1000524793 (2:86759280 T>A), RS1000689517 (2:86760170 G>C), RS1000779085 (2:86772317 T>C), RS1000866255 (2:86760420 G>T), RS1000946323 (2:86754708 G>A), RS1000975687 (2:86754446 A>T), RS1001001520 (2:86747482 A>G), RS1001087980 (2:86767381 G>A), RS1001131549 (2:86760403 G>A)

Disease associations

OMIM: gene MIM:618964 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

14 associations (top):

StudyTraitp-value
GCST004602_89Mean corpuscular volume9.000000e-15
GCST004611_14High light scatter reticulocyte count9.000000e-15
GCST004612_170High light scatter reticulocyte percentage of red cells5.000000e-15
GCST004619_56Reticulocyte fraction of red cells3.000000e-12
GCST004622_152Reticulocyte count3.000000e-11
GCST004628_147Immature fraction of reticulocytes1.000000e-09
GCST004630_29Mean corpuscular hemoglobin4.000000e-10
GCST90002385_134High light scatter reticulocyte count6.000000e-28
GCST90002386_250High light scatter reticulocyte percentage of red cells1.000000e-29
GCST90002387_260Immature fraction of reticulocytes2.000000e-14
GCST90002390_365Mean corpuscular hemoglobin2.000000e-21
GCST90002392_207Mean corpuscular volume9.000000e-25
GCST90002405_130Reticulocyte count2.000000e-25
GCST90002406_23Reticulocyte fraction of red cells7.000000e-29

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0007986reticulocyte count
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

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

ChemicalActions (top 5)PubMed papers
Tobacco Smoke Pollutionincreases expression, increases methylation3
Cadmium Chlorideincreases abundance, increases expression2
triphenyl phosphateaffects expression1
terbufosincreases methylation1
tetrahydropalmatineincreases expression1
cobaltous chlorideincreases expression1
butyraldehydedecreases expression1
potassium chromate(VI)affects cotreatment, increases expression1
epigallocatechin gallateaffects cotreatment, increases expression1
pentanaldecreases expression1
tamibarotenedecreases expression1
K 7174increases expression1
abrineincreases expression1
jinfukangdecreases expression1
PCI 5002affects cotreatment, increases expression1
Acetaminophenincreases expression1
Air Pollutants, Occupationalaffects expression1
Amphotericin Bdecreases expression1
Benzo(a)pyrenedecreases methylation1
Cadmiumincreases abundance, increases expression1
Fonofosincreases methylation1
Estradiolaffects cotreatment, decreases expression1
Hydrogen Peroxideaffects cotreatment, increases expression1
Ivermectindecreases expression1
Parathionincreases methylation1
Plant Oilsincreases expression1
Silverincreases expression1
Theophyllineaffects cotreatment, increases expression1
Tretinoindecreases expression1
Urethaneincreases expression1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

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

CellosaurusNameCategorySex
CVCL_E2JFHAP1 RMND5A (-) 1Cancer cell lineMale
CVCL_E2JGHAP1 RMND5A (-) 2Cancer cell lineMale
CVCL_E2JHHAP1 RMND5A (-) 3Cancer cell lineMale

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.