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RMC1

gene
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Also known as MIC1HsT2591

Summary

RMC1 (regulator of MON1-CCZ1, HGNC:24326) is a protein-coding gene on chromosome 18q11.2, encoding Regulator of MON1-CCZ1 complex (Q96DM3). Component of the CCZ1-MON1 RAB7A guanine exchange factor (GEF).

This gene encodes a colon cancer associated protein.

Source: NCBI Gene 29919 — RefSeq curated summary.

At a glance

  • GWAS associations: 24
  • Clinical variants (ClinVar): 8 total
  • MANE Select transcript: NM_013326

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24326
Approved symbolRMC1
Nameregulator of MON1-CCZ1
Location18q11.2
Locus typegene with protein product
StatusApproved
AliasesMIC1, HsT2591
Ensembl geneENSG00000141452
Ensembl biotypeprotein_coding
OMIM620267
Entrez29919

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 16 protein_coding, 5 retained_intron, 4 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000269221, ENST00000587153, ENST00000587690, ENST00000589215, ENST00000589409, ENST00000589860, ENST00000590387, ENST00000590868, ENST00000590870, ENST00000591367, ENST00000592119, ENST00000592682, ENST00000593081, ENST00000615148, ENST00000897720, ENST00000897721, ENST00000897722, ENST00000897723, ENST00000897724, ENST00000897725, ENST00000897726, ENST00000926737, ENST00000949335, ENST00000949336, ENST00000949337, ENST00000949338, ENST00000949339

RefSeq mRNA: 5 — MANE Select: NM_013326 NM_001276342, NM_001318707, NM_001318708, NM_001318709, NM_013326

CCDS: CCDS32803, CCDS82243

Canonical transcript exons

ENST00000269221 — 20 exons

ExonStartEnd
ENSE000011372282350697023507054
ENSE000011372332350437123504447
ENSE000028105432350351123503720
ENSE000034624102352020223520313
ENSE000034712912351632023516423
ENSE000035100272353022923530297
ENSE000035124382351906923519174
ENSE000035293502351889023518979
ENSE000035293682353038723530612
ENSE000035394562351585623515996
ENSE000035642502352413023524174
ENSE000035876522352779523527901
ENSE000035941242353002823530132
ENSE000036233002353162523531822
ENSE000036419812352442923524482
ENSE000036426582352963523529712
ENSE000036734212352917923529298
ENSE000036941802352663723526765
ENSE000040137722350798523508041
ENSE000040137732350919323509279

Expression profiles

Bgee: expression breadth ubiquitous, 270 present calls, max score 98.36.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 21.5635 / max 178.4977, expressed in 1817 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
16967221.17391817
1696730.3896182

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065598.36gold quality
oocyteCL:000002397.98gold quality
granulocyteCL:000009496.15gold quality
adrenal tissueUBERON:001830395.98gold quality
adenohypophysisUBERON:000219695.43gold quality
pituitary glandUBERON:000000794.65gold quality
lower esophagus mucosaUBERON:003583494.28gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099193.30gold quality
upper lobe of left lungUBERON:000895293.17gold quality
spleenUBERON:000210693.08gold quality
right lobe of liverUBERON:000111492.99gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047392.88gold quality
monocyteCL:000057692.78gold quality
mucosa of transverse colonUBERON:000499192.72gold quality
leukocyteCL:000073892.71gold quality
mononuclear cellCL:000084292.61gold quality
right lungUBERON:000216792.53gold quality
small intestine Peyer’s patchUBERON:000345492.43gold quality
metanephros cortexUBERON:001053392.35gold quality
C1 segment of cervical spinal cordUBERON:000646992.34gold quality
body of stomachUBERON:000116192.25gold quality
upper lobe of lungUBERON:000894892.10gold quality
right adrenal gland cortexUBERON:003582791.98gold quality
mucosa of stomachUBERON:000119991.84gold quality
bloodUBERON:000017891.83gold quality
lymph nodeUBERON:000002991.75gold quality
lower esophagusUBERON:001347391.58gold quality
lower esophagus muscularis layerUBERON:003583391.58gold quality
cortical plateUBERON:000534391.53gold quality
right coronary arteryUBERON:000162591.36gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes13.74

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting RMC1, 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-190A-3P100.0080.355520
HSA-MIR-493-5P99.9672.472382
HSA-LET-7C-3P99.9573.422862
HSA-MIR-314399.9371.963104
HSA-MIR-153-5P99.8973.866317
HSA-LET-7A-2-3P99.8770.531921
HSA-LET-7G-3P99.8570.431929
HSA-MIR-46699.6770.852863
HSA-MIR-570099.6469.882280
HSA-MIR-127699.3668.181642
HSA-MIR-155-5P99.3570.161509
HSA-MIR-393596.3366.79797

Literature-anchored findings (GeneRIF, showing 1)

  • Authors identified C18orf8/RMC1 as a new subunit of the CCZ1-MON1 RAB7 guanine exchange factor (GEF) that positively regulates RAB7 recruitment to LE/autophagosomes. (PMID:29038162)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriormc1ENSDARG00000029307
mus_musculusRmc1ENSMUSG00000024410
rattus_norvegicusRmc1ENSRNOG00000012597
drosophila_melanogasterBulliFBGN0035703
caenorhabditis_elegansWBGENE00021738

Protein

Protein identifiers

Regulator of MON1-CCZ1 complex — Q96DM3 (reviewed: Q96DM3)

Alternative names: Colon cancer-associated protein Mic1, WD repeat-containing protein 98

All UniProt accessions (7): A0A087WZD4, Q96DM3, K7EIS6, K7EL80, K7ENL9, K7EQ65, K7EQJ3

UniProt curated annotations — full annotation on UniProt →

Function. Component of the CCZ1-MON1 RAB7A guanine exchange factor (GEF). Acts as a positive regulator of CCZ1-MON1A/B function necessary for endosomal/autophagic flux and efficient RAB7A localization.

Subunit / interactions. Found in a complex with RMC1, CCZ1 MON1A and MON1B.

Subcellular location. Lysosome membrane. Late endosome membrane.

Similarity. Belongs to the RMC1 family.

RefSeq proteins (5): NP_001263271, NP_001305636, NP_001305637, NP_001305638, NP_037458* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR009755RMC1_CDomain
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR036322WD40_repeat_dom_sfHomologous_superfamily
IPR040371RMC1Family
IPR049040RMC1_NDomain

Pfam: PF07035, PF21029

UniProt features (5 total): sequence conflict 3, chain 1, domain 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
9L0DELECTRON MICROSCOPY3.41

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96DM3-F189.060.68

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 124 (showing top): GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_UP, ELVIDGE_HYPOXIA_DN, GOBP_REGULATION_OF_AUTOPHAGY, GOCC_VACUOLAR_MEMBRANE, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, IVANOVA_HEMATOPOIESIS_MATURE_CELL, GOBP_REGULATION_OF_CATABOLIC_PROCESS, BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_TRANS, MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_UP, BURTON_ADIPOGENESIS_5, NERF_Q2, chr18q11, GOCC_LATE_ENDOSOME_MEMBRANE, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, GOMF_GUANYL_NUCLEOTIDE_EXCHANGE_FACTOR_ACTIVITY

GO Biological Process (2): autophagy (GO:0006914), regulation of autophagy (GO:0010506)

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

GO Cellular Component (6): lysosomal membrane (GO:0005765), late endosome membrane (GO:0031902), Mon1-Ccz1 complex (GO:0035658), lysosome (GO:0005764), endosome (GO:0005768), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
late endosome2
catabolic process1
transmembrane transport1
process utilizing autophagic mechanism1
autophagy1
regulation of catabolic process1
binding1
lysosome1
lytic vacuole membrane1
endosome membrane1
guanyl-nucleotide exchange factor complex1
lytic vacuole1
endomembrane system1
cytoplasmic vesicle1
cellular anatomical structure1

Protein interactions and networks

STRING

512 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RMC1SLC20A2Q08357825
RMC1LAMC1P11047749
RMC1CCZ1BP86790742
RMC1XPR1Q9UBH6716
RMC1WDR91A4D1P6447
RMC1NPIPB6E9PJ23430
RMC1RIMOC1A6NDU8397
RMC1RMI1Q9H9A7389
RMC1ZKSCAN5Q9Y2L8380
RMC1DLG4P78352375
RMC1TBC1D15Q8TC07374
RMC1SPACA9Q96E40359
RMC1FERRY3Q9NQ89349
RMC1NPC1O15118349
RMC1ANKRD29Q8N6D5335

IntAct

33 interactions, top by confidence:

ABTypeScore
RMC1CCZ1psi-mi:“MI:0914”(association)0.600
RAB7ACCZ1psi-mi:“MI:0914”(association)0.590
RMC1C11orf52psi-mi:“MI:0915”(physical association)0.560
C11orf52RMC1psi-mi:“MI:0915”(physical association)0.560
SP6CCZ1Bpsi-mi:“MI:0914”(association)0.530
NEFLRABEP1psi-mi:“MI:0914”(association)0.530
NFKB1NFKB1psi-mi:“MI:0914”(association)0.350
NOTCH1CNOT1psi-mi:“MI:0914”(association)0.350
PCMT1YDJCpsi-mi:“MI:0914”(association)0.350
NEFLSEC16Apsi-mi:“MI:0914”(association)0.350
SP6GNB2psi-mi:“MI:0914”(association)0.350
FYCO1SEC24Bpsi-mi:“MI:0914”(association)0.350
RMC1ANXA2P2psi-mi:“MI:0914”(association)0.350
RMC1ARID1Apsi-mi:“MI:0914”(association)0.350
MON1BCCZ1psi-mi:“MI:0914”(association)0.350
CCZ1MON1Bpsi-mi:“MI:0914”(association)0.350
CCZ1BPRPF40Apsi-mi:“MI:0914”(association)0.350
CCZ1CCZ1Bpsi-mi:“MI:0914”(association)0.350
CSNK2A2VWA8psi-mi:“MI:0914”(association)0.350
PLAAT4PLEKHG3psi-mi:“MI:0914”(association)0.350
CCL3KRBA1psi-mi:“MI:0914”(association)0.350
RNF181CHEK1psi-mi:“MI:0914”(association)0.350
TNFSF10CCZ1Bpsi-mi:“MI:0914”(association)0.350
SP6GPX1psi-mi:“MI:0914”(association)0.350

BioGRID (155): C18orf8 (Affinity Capture-MS), C18orf8 (Affinity Capture-MS), C18orf8 (Affinity Capture-MS), C18orf8 (Affinity Capture-MS), C18orf8 (Affinity Capture-MS), C18orf8 (Affinity Capture-MS), C18orf8 (Affinity Capture-MS), C18orf8 (Proximity Label-MS), C18orf8 (Affinity Capture-MS), C11orf52 (Two-hybrid), C18orf8 (Affinity Capture-MS), AARS (Affinity Capture-MS), ACLY (Affinity Capture-MS), ADSS (Affinity Capture-MS), ANXA2P2 (Affinity Capture-MS)

ESM2 similar proteins: A0JN27, A0PJN4, A1L167, C1C3R6, O88761, O94973, P17427, P18484, P22234, P38024, P48444, P51583, P97834, Q08211, Q0VCK5, Q13042, Q13098, Q28141, Q28F89, Q2YDL1, Q3MHJ2, Q3TXS7, Q4R9A8, Q4VC33, Q5F398, Q5F418, Q5R532, Q5R5S4, Q5R874, Q5RA77, Q5RB59, Q5RBN9, Q5RDU4, Q5RKJ1, Q6GR10, Q6NRB5, Q6NRT5, Q76EZ2, Q7L5Y9, Q7SXR3

Diamond homologs: Q54LC7, Q8VC42, Q96DM3, Q9VRX1

SIGNOR signaling

4 interactions.

AEffectBMechanism
RMC1“form complex”“MON1-CCZ1 guanyl-nucleotide exchange factor complex, MON1B variant”binding
RMC1“form complex”“MON1-CCZ1 guanyl-nucleotide exchange factor complex, MON1A variant”binding
RMC1“form complex”“MON1-CCZ1B guanyl-nucleotide exchange factor complex, MON1A variant”binding
RMC1“form complex”“MON1-CCZ1B guanyl-nucleotide exchange factor complex, MON1B variant”binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance0
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3582 predictions. Top by Δscore:

VariantEffectΔscore
18:23503716:AGCAG:Adonor_loss1.0000
18:23503717:GCAG:Gdonor_gain1.0000
18:23503718:CAGGT:Cdonor_loss1.0000
18:23503719:AGGTC:Adonor_loss1.0000
18:23503720:GG:Gdonor_loss1.0000
18:23503721:G:GAdonor_loss1.0000
18:23506966:A:AGacceptor_gain1.0000
18:23506967:A:Gacceptor_gain1.0000
18:23506968:A:Gacceptor_gain1.0000
18:23506968:AGAAT:Aacceptor_gain1.0000
18:23506969:G:GTacceptor_gain1.0000
18:23506969:GA:Gacceptor_gain1.0000
18:23506969:GAAT:Gacceptor_gain1.0000
18:23506969:GAATG:Gacceptor_gain1.0000
18:23507051:TGTGG:Tdonor_loss1.0000
18:23507052:GTG:Gdonor_gain1.0000
18:23507053:TGGTA:Tdonor_loss1.0000
18:23507055:G:GGdonor_gain1.0000
18:23507056:T:TCdonor_loss1.0000
18:23509191:A:AGacceptor_gain1.0000
18:23509192:G:GGacceptor_gain1.0000
18:23515851:TTCA:Tacceptor_loss1.0000
18:23515852:TCA:Tacceptor_loss1.0000
18:23515853:CAG:Cacceptor_loss1.0000
18:23515855:GGT:Gacceptor_gain1.0000
18:23515992:TTAGG:Tdonor_gain1.0000
18:23515993:TAGG:Tdonor_gain1.0000
18:23515994:AGGGT:Adonor_loss1.0000
18:23515995:GG:Gdonor_gain1.0000
18:23515996:GG:Gdonor_gain1.0000

AlphaMissense

4332 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
18:23507029:C:AA80D1.000
18:23509223:T:AW118R1.000
18:23509223:T:CW118R1.000
18:23519146:T:CL274P1.000
18:23524440:T:AW340R1.000
18:23524440:T:CW340R1.000
18:23526725:A:CR383S1.000
18:23526725:A:TR383S1.000
18:23530239:T:CL537P1.000
18:23530278:T:CL550P1.000
18:23530293:T:CL555P1.000
18:23530424:T:CL569P1.000
18:23530427:T:CL570P1.000
18:23503667:T:CF17L0.999
18:23503669:C:AF17L0.999
18:23503669:C:GF17L0.999
18:23503697:T:CF27L0.999
18:23503699:C:AF27L0.999
18:23503699:C:GF27L0.999
18:23504381:T:AV38D0.999
18:23504411:T:AV48D0.999
18:23507028:G:CA80P0.999
18:23509225:G:CW118C0.999
18:23509225:G:TW118C0.999
18:23519152:T:AV276D0.999
18:23524449:T:CF343L0.999
18:23524451:T:AF343L0.999
18:23524451:T:GF343L0.999
18:23526643:T:CL356P0.999
18:23526645:T:AW357R0.999

dbSNP variants (sampled 300 via entrez): RS1000096150 (18:23512137 C>T), RS1000189135 (18:23522885 C>A,T), RS1000197680 (18:23519473 G>A), RS1000230978 (18:23528626 C>T), RS1000298366 (18:23516886 C>T), RS1000475914 (18:23523997 C>T), RS1000569329 (18:23519361 T>C), RS1000644424 (18:23523136 C>T), RS1000865602 (18:23516656 T>A), RS1000954028 (18:23511973 A>G), RS1001004176 (18:23505569 G>A), RS1001023600 (18:23519535 T>C,G), RS1001088228 (18:23518288 C>T), RS1001269257 (18:23524600 G>A), RS1001460407 (18:23518539 A>G)

Disease associations

OMIM: gene MIM:620267 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

24 associations (top):

StudyTraitp-value
GCST002783_303Body mass index4.000000e-08
GCST002783_32Body mass index1.000000e-08
GCST002783_559Body mass index4.000000e-08
GCST004066_133Hip circumference2.000000e-10
GCST004066_20Hip circumference1.000000e-10
GCST004495_5BMI (adjusted for smoking behaviour)1.000000e-06
GCST004495_6BMI (adjusted for smoking behaviour)8.000000e-06
GCST004904_194Body mass index1.000000e-09
GCST005316_219Intelligence (MTAG)3.000000e-08
GCST005830_28Hand grip strength2.000000e-08
GCST006802_33Body mass index2.000000e-07
GCST007328_54Alcohol consumption (drinks per week)4.000000e-08
GCST007429_136Lung function (FVC)7.000000e-12
GCST007432_96FEV11.000000e-10
GCST008151_107Waist circumference2.000000e-06
GCST008152_6Weight1.000000e-11
GCST008158_58Body mass index2.000000e-09
GCST008160_109Waist circumference2.000000e-06
GCST008162_57Hip circumference4.000000e-08
GCST008522_39Bitter alcoholic beverage consumption2.000000e-10
GCST010139_1Poultry consumption1.000000e-09
GCST010196_57Protein levels in obesity4.000000e-06
GCST011122_9Walking pace3.000000e-11
GCST90002394_420Monocyte percentage of white cells1.000000e-11

EFO canonical traits (11, from GWAS)

EFO IDTrait name
EFO:0004340body mass index
EFO:0004318smoking behavior
EFO:0004337intelligence
EFO:0006941grip strength measurement
EFO:0004312vital capacity
EFO:0004314forced expiratory volume
EFO:0004338body weight
EFO:0010092bitter alcoholic beverage consumption measurement
EFO:0008111diet measurement
EFO:0004747protein measurement
EFO:0007989monocyte percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases expression, affects cotreatment, decreases expression, affects expression7
trichostatin Aaffects expression, decreases expression2
cobaltous chlorideincreases expression2
Cyclosporineincreases expression2
methylmercuric chlorideincreases expression1
beta-lapachoneincreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
sodium arseniteincreases expression1
K 7174increases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
Acetaminophenincreases expression1
Air Pollutantsincreases abundance, increases expression1
Benzo(a)pyreneincreases expression1
Caffeinedecreases phosphorylation1
Doxorubicindecreases expression1
Dihydrotestosteroneincreases expression1
Tobacco Smoke Pollutionincreases expression1
Urethaneincreases expression1
Metriboloneincreases expression1
Antirheumatic Agentsdecreases expression1
Okadaic Acidincreases expression1
Copper Sulfateincreases expression1
Particulate Matterincreases abundance, increases expression1

Cellosaurus cell lines

2 cell lines: 1 transformed cell line, 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_D9QMUbigene HEK293 RMC1 KOTransformed cell lineFemale
CVCL_E0MTUbigene HeLa RMC1 KOCancer cell lineFemale

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.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot