TMCC1

gene
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Also known as KIAA0779

Summary

TMCC1 (transmembrane and coiled-coil domain family 1, HGNC:29116) is a protein-coding gene on chromosome 3q22.1, encoding Transmembrane and coiled-coil domains protein 1 (O94876). Endoplasmic reticulum membrane protein that promotes endoplasmic reticulum-associated endosome fission.

Enables identical protein binding activity. Involved in several processes, including endosome fission; endosome membrane tubulation; and membrane fission. Located in cytosol; endoplasmic reticulum-endosome membrane contact site; and rough endoplasmic reticulum.

Source: NCBI Gene 23023 — RefSeq curated summary.

At a glance

  • GWAS associations: 31
  • Clinical variants (ClinVar): 52 total
  • MANE Select transcript: NM_001017395

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29116
Approved symbolTMCC1
Nametransmembrane and coiled-coil domain family 1
Location3q22.1
Locus typegene with protein product
StatusApproved
AliasesKIAA0779
Ensembl geneENSG00000172765
Ensembl biotypeprotein_coding
OMIM616242
Entrez23023

Gene structure

Transcript identifiers

Ensembl transcripts: 46 — 38 protein_coding, 6 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000393238, ENST00000426664, ENST00000432054, ENST00000503256, ENST00000505616, ENST00000505924, ENST00000508729, ENST00000508869, ENST00000509440, ENST00000510323, ENST00000510521, ENST00000512902, ENST00000513411, ENST00000515024, ENST00000648771, ENST00000698214, ENST00000698215, ENST00000858270, ENST00000858271, ENST00000858272, ENST00000858273, ENST00000858274, ENST00000858275, ENST00000858276, ENST00000915954, ENST00000915955, ENST00000915956, ENST00000915957, ENST00000915958, ENST00000915959, ENST00000915960, ENST00000955168, ENST00000955169, ENST00000955170, ENST00000955171, ENST00000955172, ENST00000955173, ENST00000955174, ENST00000955175, ENST00000955176, ENST00000955177, ENST00000955178, ENST00000955179, ENST00000955180, ENST00000955181, ENST00000955182

RefSeq mRNA: 16 — MANE Select: NM_001017395 NM_001017395, NM_001128224, NM_001349263, NM_001349264, NM_001349265, NM_001349266, NM_001349268, NM_001349269, NM_001349270, NM_001349271, NM_001349272, NM_001349273, NM_001349274, NM_001349275, NM_001349276, NM_015008

CCDS: CCDS33855, CCDS93382, CCDS93383

Canonical transcript exons

ENST00000393238 — 7 exons

ExonStartEnd
ENSE00001194452129654968129655103
ENSE00001322029129647792129651795
ENSE00001404015129832774129832826
ENSE00001428379129880309129880559
ENSE00002216878129827803129828508
ENSE00003617457129670330129671264
ENSE00003920315129893494129893711

Expression profiles

Bgee: expression breadth ubiquitous, 292 present calls, max score 98.17.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.7358 / max 498.3795, expressed in 1756 samples.

FANTOM5 promoters (21 alternative TSS)

Promoter IDTPM avgSamples expressed
445698.07381719
445700.6079293
445530.5500159
445660.3172113
445600.2792126
445580.219992
445500.191538
445670.182873
445540.176798
445570.175976

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065598.17gold quality
oocyteCL:000002397.49gold quality
dorsal motor nucleus of vagus nerveUBERON:000287095.56gold quality
colonic epitheliumUBERON:000039794.42gold quality
spermCL:000001994.22gold quality
biceps brachiiUBERON:000150793.98gold quality
Brodmann (1909) area 23UBERON:001355493.90gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450293.58gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451193.25gold quality
cortical plateUBERON:000534393.24gold quality
sural nerveUBERON:001548893.21gold quality
male germ cellCL:000001592.59gold quality
lateral nuclear group of thalamusUBERON:000273692.40gold quality
middle temporal gyrusUBERON:000277192.31gold quality
deltoidUBERON:000147692.09silver quality
skeletal muscle tissueUBERON:000113492.08gold quality
vastus lateralisUBERON:000137991.77gold quality
corpus callosumUBERON:000233691.63gold quality
substantia nigra pars reticulataUBERON:000196691.55gold quality
quadriceps femorisUBERON:000137791.37gold quality
palpebral conjunctivaUBERON:000181291.36gold quality
ponsUBERON:000098891.27gold quality
germinal epithelium of ovaryUBERON:000130490.86gold quality
lateral globus pallidusUBERON:000247690.78gold quality
substantia nigra pars compactaUBERON:000196590.67gold quality
muscle tissueUBERON:000238590.52gold quality
muscle organUBERON:000163090.36gold quality
gall bladderUBERON:000211090.25gold quality
entorhinal cortexUBERON:000272890.18gold quality
gluteal muscleUBERON:000200090.15gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes6.13

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

  • roles of TMCC1 in ER organization (PMID:24454821)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriotmcc1bENSDARG00000060954
danio_rerioTMCC1ENSDARG00000076747
mus_musculusTmcc1ENSMUSG00000030126
rattus_norvegicusTmcc1ENSRNOG00000011614
drosophila_melanogasterDmtnFBGN0037443
caenorhabditis_elegansWBGENE00015800

Paralogs (3): TMCC3 (ENSG00000057704), TMCC2 (ENSG00000133069), TEX28 (ENSG00000278057)

Protein

Protein identifiers

Transmembrane and coiled-coil domains protein 1O94876 (reviewed: O94876)

All UniProt accessions (6): O94876, A0A8V8TLJ9, D6RBT7, D6RH19, E9PC87, Q6N039

UniProt curated annotations — full annotation on UniProt →

Function. Endoplasmic reticulum membrane protein that promotes endoplasmic reticulum-associated endosome fission. Localizes to contact sites between the endoplasmic reticulum and endosomes and acts by promoting recruitment of the endoplasmic reticulum to endosome tubules for fission. Endosome membrane fission of early and late endosomes is essential to separate regions destined for lysosomal degradation from carriers to be recycled to the plasma membrane.

Subunit / interactions. May form homodimers and heterodimers with TMCC2 or TMCC3 via the coiled-coil domains. Interacts with ribosomal proteins RPL4 and RPS6.

Subcellular location. Endoplasmic reticulum membrane.

Similarity. Belongs to the TEX28 family.

Isoforms (2)

UniProt IDNamesCanonical?
O94876-11yes
O94876-22

RefSeq proteins (16): NP_001017395, NP_001121696, NP_001336192, NP_001336193, NP_001336194, NP_001336195, NP_001336197, NP_001336198, NP_001336199, NP_001336200, NP_001336201, NP_001336202, NP_001336203, NP_001336204, NP_001336205, NP_055823 (=MANE)

Domains & families (InterPro)

IDNameType
IPR019394TEX28/TMCCFamily

Pfam: PF10267

UniProt features (27 total): compositionally biased region 7, region of interest 5, modified residue 3, topological domain 2, coiled-coil region 2, transmembrane region 2, splice variant 2, sequence conflict 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O94876-F163.550.27

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 (3): 1, 382, 414

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 286 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_UP, GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_DN, RNGTGGGC_UNKNOWN, AP1_01, GOBP_ENDOSOME_ORGANIZATION, DACOSTA_UV_RESPONSE_VIA_ERCC3_XPCS_DN, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, FISCHER_G1_S_CELL_CYCLE, GOBP_VESICLE_ORGANIZATION, MORF_ATRX, IVANOVA_HEMATOPOIESIS_MATURE_CELL, TGACCTY_ERR1_Q2, GOBP_VESICLE_MEDIATED_TRANSPORT, BILD_SRC_ONCOGENIC_SIGNATURE, TTGGGAG_MIR150

GO Biological Process (5): endoplasmic reticulum organization (GO:0007029), endosomal transport (GO:0016197), membrane fission (GO:0090148), endosome membrane tubulation (GO:0097750), endosome fission (GO:0140285)

GO Molecular Function (2): identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (7): endoplasmic reticulum membrane (GO:0005789), rough endoplasmic reticulum (GO:0005791), cytosol (GO:0005829), endomembrane system (GO:0012505), endoplasmic reticulum-endosome membrane contact site (GO:0140284), endoplasmic reticulum (GO:0005783), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
cytoplasm2
organelle organization1
endomembrane system organization1
vesicle-mediated transport1
intracellular transport1
membrane organization1
endosome organization1
membrane tubulation1
organelle fission1
protein binding1
binding1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
endoplasmic reticulum1
vacuole1
plasma membrane1
organelle membrane contact site1
endomembrane system1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

484 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TMCC1CFAP100Q494V2879
TMCC1PODXL2Q9NZ53875
TMCC1KLF15Q9UIH9847
TMCC1PLXND1Q9Y4D7845
TMCC1PLXNA1Q9UIW2688
TMCC1CORO1CQ9ULV4639
TMCC1GATA2P23769492
TMCC1VSTM2BA6NLU5448
TMCC1IST1P53990414
TMCC1TMCO1Q9UM00377
TMCC1ZFYVE27Q5T4F4355
TMCC1RSRP1Q9BUV0327
TMCC1SNX2P82862323
TMCC1EFCAB8A8MWE9314
TMCC1SPASTQ9UBP0313

IntAct

44 interactions, top by confidence:

ABTypeScore
YWHAGBLTP3Bpsi-mi:“MI:2364”(proximity)0.640
TEX28TMCC2psi-mi:“MI:0914”(association)0.640
YWHABBLTP3Bpsi-mi:“MI:2364”(proximity)0.610
YWHAHBLTP3Bpsi-mi:“MI:2364”(proximity)0.570
SLC30A2ESYT2psi-mi:“MI:0914”(association)0.530
ARHGEF4TMCC1psi-mi:“MI:0915”(physical association)0.400
TMCC1CBX5psi-mi:“MI:0915”(physical association)0.400
TMCC1rstBpsi-mi:“MI:0915”(physical association)0.370
TMCC1ZDHHC17psi-mi:“MI:0915”(physical association)0.370
ESR1ESYT2psi-mi:“MI:0914”(association)0.350
TEX28NBASpsi-mi:“MI:0914”(association)0.350
HCN1USP27Xpsi-mi:“MI:0914”(association)0.350
HCN1POTEFpsi-mi:“MI:0914”(association)0.350
MAPRE1SCAMP1psi-mi:“MI:0914”(association)0.350
CXCR4ESYT2psi-mi:“MI:0914”(association)0.350
SAAL1TMEM223psi-mi:“MI:0914”(association)0.350
SLC39A4GPR39psi-mi:“MI:0914”(association)0.350
TEX28PRAF2psi-mi:“MI:0914”(association)0.350
TMCC1TMCC2psi-mi:“MI:0914”(association)0.350
SLC19A2TMEM223psi-mi:“MI:0914”(association)0.350
SLC30A5NBASpsi-mi:“MI:0914”(association)0.350
SLC30A7ESYT2psi-mi:“MI:0914”(association)0.350
SLC39A4ESYT2psi-mi:“MI:0914”(association)0.350
SFNBLTP3Bpsi-mi:“MI:2364”(proximity)0.270
YWHABE2F8psi-mi:“MI:2364”(proximity)0.270

BioGRID (38): TMCC1 (Two-hybrid), TMCC1 (Reconstituted Complex), TMCC1 (Affinity Capture-MS), TMCC1 (Affinity Capture-RNA), TMCC1 (Affinity Capture-MS), TMCC1 (Affinity Capture-RNA), TMCC1 (Affinity Capture-RNA), TMCC1 (Proximity Label-MS), CBX5 (Proximity Label-MS), TMCC1 (Proximity Label-MS), TMCC1 (Proximity Label-MS), TMCC1 (Proximity Label-MS), TMCC1 (Proximity Label-MS), TMCC1 (Affinity Capture-MS), TMCC1 (Proximity Label-MS)

ESM2 similar proteins: A0JNJ3, A0M8T5, A4IG66, F1Q930, F7AEX0, O00750, O15327, O48832, O94876, P35612, P97578, Q00PJ1, Q05764, Q07E15, Q07E28, Q09YG9, Q0P4J3, Q155Q3, Q1JPG0, Q2QLA2, Q2T9N1, Q2TBG9, Q2VUH7, Q3ZC62, Q4R4D7, Q4V8E4, Q5BJ78, Q5BLE2, Q5JTW2, Q5R5V7, Q5RA60, Q5T1M5, Q69ZZ6, Q6GR21, Q6INU2, Q6IP02, Q6NTW1, Q8BG50, Q8C5W4, Q8C6E0

Diamond homologs: O75069, O94876, Q69ZZ6, Q80W04, Q8R310, Q9ULS5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 35 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
Activation of BAD and translocation to mitochondria7213.2×6e-14
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex7188.1×9e-14
SARS-CoV-1 targets host intracellular signalling and regulatory pathways7188.1×9e-14
Activation of BH3-only proteins7139.0×9e-13
RHO GTPases activate PKNs788.8×3e-11
Intrinsic Pathway for Apoptosis782.0×4e-11
FOXO-mediated transcription567.2×8e-08
SARS-CoV-1-host interactions749.2×1e-09

GO biological processes:

GO termPartnersFoldFDR
protein targeting557.2×3e-06
intracellular protein localization826.2×1e-07

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance44
Likely benign0
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2702 predictions. Top by Δscore:

VariantEffectΔscore
3:129651582:T:TAdonor_gain1.0000
3:129654122:ATTT:Adonor_gain1.0000
3:129654122:ATTTC:Adonor_gain1.0000
3:129654965:AAC:Adonor_loss1.0000
3:129654966:A:ACdonor_gain1.0000
3:129654966:A:ATdonor_loss1.0000
3:129654967:C:CCdonor_gain1.0000
3:129655099:CACAT:Cacceptor_gain1.0000
3:129655100:ACAT:Aacceptor_gain1.0000
3:129655101:CAT:Cacceptor_gain1.0000
3:129655101:CATC:Cacceptor_gain1.0000
3:129655102:AT:Aacceptor_gain1.0000
3:129655103:TCT:Tacceptor_loss1.0000
3:129655104:C:CAacceptor_loss1.0000
3:129655104:C:CCacceptor_gain1.0000
3:129655105:T:Cacceptor_loss1.0000
3:129671260:TCGAT:Tacceptor_gain1.0000
3:129671261:CGAT:Cacceptor_gain1.0000
3:129671261:CGATC:Cacceptor_gain1.0000
3:129671263:AT:Aacceptor_gain1.0000
3:129671264:TC:Tacceptor_loss1.0000
3:129671265:C:CCacceptor_gain1.0000
3:129671265:CTAGT:Cacceptor_loss1.0000
3:129671268:G:Cacceptor_gain1.0000
3:129671268:G:GCacceptor_gain1.0000
3:129671270:G:GCacceptor_gain1.0000
3:129822569:T:Adonor_gain1.0000
3:129822586:ATTT:Adonor_gain1.0000
3:129651578:AACGT:Adonor_gain0.9900
3:129651793:CTC:Cacceptor_gain0.9900

AlphaMissense

4297 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:129651641:A:GL601S1.000
3:129651662:A:GL594P1.000
3:129651662:A:TL594Q1.000
3:129651752:A:GL564P1.000
3:129651770:C:GR558P1.000
3:129651788:A:GL552P1.000
3:129651792:C:GA551P1.000
3:129654978:C:GR546P1.000
3:129654984:C:GR544P1.000
3:129654994:A:GS541P1.000
3:129655000:A:CY539D1.000
3:129655000:A:GY539H1.000
3:129655026:A:GL530P1.000
3:129655038:A:GL526S1.000
3:129655056:T:GQ520P1.000
3:129655060:G:CH519D1.000
3:129655062:A:GL518P1.000
3:129655071:A:GL515P1.000
3:129655080:A:GL512P1.000
3:129655083:T:GQ511P1.000
3:129670998:A:CF281L1.000
3:129670998:A:TF281L1.000
3:129671000:A:GF281L1.000
3:129671053:A:GL263S1.000
3:129671057:A:GY262H1.000
3:129651630:A:GS605P0.999
3:129651632:A:TV604D0.999
3:129651641:A:CL601W0.999
3:129651647:A:TV599D0.999
3:129651651:C:GA598P0.999

dbSNP variants (sampled 300 via entrez): RS1000003865 (3:129754511 C>T), RS1000010079 (3:129708526 A>G), RS1000018136 (3:129795093 A>T), RS1000022178 (3:129707271 C>A,T), RS1000034064 (3:129692188 T>A,C), RS1000049429 (3:129744837 T>C), RS1000051139 (3:129806497 T>C), RS1000070869 (3:129705604 A>C,T), RS1000071541 (3:129707029 T>C,G), RS1000073087 (3:129877244 T>C), RS1000095699 (3:129700265 C>A,T), RS1000101892 (3:129845422 A>G), RS1000102338 (3:129888269 C>A,T), RS1000110711 (3:129761440 G>A), RS1000113029 (3:129701748 C>T)

Disease associations

OMIM: gene MIM:616242 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

31 associations (top):

StudyTraitp-value
GCST001585_20Breast size5.000000e-07
GCST005956_82Waist-to-hip ratio adjusted for BMI2.000000e-07
GCST005958_5Waist-to-hip ratio adjusted for BMI (age >50)4.000000e-10
GCST005962_16Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)2.000000e-11
GCST008163_451Height4.000000e-07
GCST009379_134Type 2 diabetes4.000000e-08
GCST009379_135Type 2 diabetes7.000000e-06
GCST012227_1259Hip circumference adjusted for BMI4.000000e-12
GCST012229_48Hip index2.000000e-08
GCST90020024_1265A body shape index2.000000e-14
GCST90020024_1267A body shape index8.000000e-10
GCST90020025_461Waist-to-hip ratio adjusted for BMI5.000000e-15
GCST90020025_463Waist-to-hip ratio adjusted for BMI9.000000e-09
GCST90020025_465Waist-to-hip ratio adjusted for BMI2.000000e-22
GCST90020025_466Waist-to-hip ratio adjusted for BMI9.000000e-24
GCST90020026_113Hip index3.000000e-09
GCST90020026_114Hip index3.000000e-28
GCST90020026_115Hip index1.000000e-20
GCST90020026_116Hip index1.000000e-15
GCST90020026_117Hip index3.000000e-08
GCST90020027_302Waist-hip index9.000000e-09
GCST90020027_304Waist-hip index5.000000e-22
GCST90020027_305Waist-hip index5.000000e-23
GCST90020027_311Waist-hip index2.000000e-14
GCST90020028_1709Hip circumference adjusted for BMI6.000000e-29
GCST90020028_1710Hip circumference adjusted for BMI2.000000e-19
GCST90020028_1711Hip circumference adjusted for BMI8.000000e-12
GCST90020028_1856Hip circumference adjusted for BMI2.000000e-11
GCST90020028_1857Hip circumference adjusted for BMI1.000000e-08
GCST90020028_1858Hip circumference adjusted for BMI1.000000e-31

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0008007age at assessment
EFO:0008343sex interaction measurement
EFO:0008039BMI-adjusted hip circumference
EFO:0007789BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs2811332TMCC10.000

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, affects expression, decreases methylation7
Tetrachlorodibenzodioxinaffects expression, increases expression4
Benzo(a)pyreneaffects methylation, decreases expression, increases expression, increases methylation3
Cyclosporinedecreases expression, increases expression3
bisphenol Aaffects expression, affects cotreatment, decreases methylation2
Estradiolaffects cotreatment, increases expression2
Formaldehydedecreases expression2
Aflatoxin B1decreases expression, decreases methylation2
Cadmium Chlorideincreases expression2
aristolochic acid Idecreases expression1
FR900359increases phosphorylation1
triphenyl phosphateaffects expression1
trichostatin Adecreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
butyraldehydedecreases expression1
9,10-dihydro-9,10-dihydroxybenzo(a)pyreneincreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, decreases expression1
resorcinolincreases expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
monomethylarsonous acidincreases expression1
K 7174decreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrinedecreases expression1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
dorsomorphinaffects cotreatment, decreases expression1
eprenetapoptaffects expression, affects reaction1
Zoledronic Aciddecreases 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.