HOXC11

gene
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Summary

HOXC11 (homeobox C11, HGNC:5123) is a protein-coding gene on chromosome 12q13.13, encoding Homeobox protein Hox-C11 (O43248). Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.

This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, which are located on different chromosomes and consist of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXC genes located in a cluster on chromosome 12. The product of this gene binds to a promoter element of the lactase-phlorizin hydrolase. It also may play a role in early intestinal development. An alternatively spliced variant encoding a shorter isoform has been described but its full-length nature has not been determined.

Source: NCBI Gene 3227 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 10 total
  • MANE Select transcript: NM_014212

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:5123
Approved symbolHOXC11
Namehomeobox C11
Location12q13.13
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000123388
Ensembl biotypeprotein_coding
OMIM605559
Entrez3227

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000243082, ENST00000546378

RefSeq mRNA: 1 — MANE Select: NM_014212 NM_014212

CCDS: CCDS8867

Canonical transcript exons

ENST00000546378 — 2 exons

ExonStartEnd
ENSE000023433065397312653973923
ENSE000023629195397518153977643

Expression profiles

Bgee: expression breadth broad, 63 present calls, max score 97.04.

FANTOM5 (CAGE): breadth broad, TPM avg 1.0850 / max 211.0531, expressed in 203 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
1258220.3865126
1258210.2632109
1258200.249765
1258230.114965
1258180.064623
1258190.00622

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047397.04gold quality
type B pancreatic cellCL:000016978.14gold quality
olfactory bulbUBERON:000226476.65gold quality
diaphragmUBERON:000110374.69gold quality
skin of legUBERON:000151173.34gold quality
popliteal arteryUBERON:000225073.18gold quality
tibial arteryUBERON:000761073.14gold quality
mucosa of paranasal sinusUBERON:000503072.48gold quality
endometrium epitheliumUBERON:000481172.43gold quality
vastus lateralisUBERON:000137970.20gold quality
epithelial cell of pancreasCL:000008370.00gold quality
zone of skinUBERON:000001469.97gold quality
quadriceps femorisUBERON:000137769.82gold quality
hair follicleUBERON:000207369.44gold quality
superficial temporal arteryUBERON:000161469.17gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451168.34gold quality
skin of abdomenUBERON:000141668.21gold quality
tibialis anteriorUBERON:000138566.70silver quality
pancreatic ductal cellCL:000207966.55silver quality
cerebellar vermisUBERON:000472065.71gold quality
deciduaUBERON:000245065.55gold quality
epithelium of nasopharynxUBERON:000195165.28gold quality
thymusUBERON:000237065.13gold quality
saphenous veinUBERON:000731865.13silver quality
cardia of stomachUBERON:000116264.88gold quality
layer of synovial tissueUBERON:000761664.81gold quality
dorsal plus ventral thalamusUBERON:000189764.30gold quality
subthalamic nucleusUBERON:000190664.20gold quality
inferior vagus X ganglionUBERON:000536363.99gold quality
ventral tegmental areaUBERON:000269163.75gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no1.14

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

4 targets.

TargetRegulation
CD24
LCTUnknown
PAWRRepression
S100BUnknown

JASPAR motifs

MotifNameFamily
MA0651.1HOXC11HOX
MA0651.2HOXC11HOX
MA0651.3HOXC11HOX

JASPAR matrix evidence (PMIDs): PMID:18585359

Upstream regulators (CollecTRI, top): KDM6A, PITX1

miRNA regulators (miRDB)

37 targeting HOXC11, 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-513A-5P100.0069.772465
HSA-MIR-3064-3P100.0070.091254
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-4776-3P100.0068.731340
HSA-MIR-6798-5P100.0065.77699
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-1212199.9966.64255
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-4715-3P99.9866.03670
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-314899.9775.066478
HSA-MIR-92A-2-5P99.7567.012164
HSA-MIR-4699-3P99.7170.153142
HSA-MIR-426199.5970.303415
HSA-MIR-3120-3P99.5470.282669
HSA-MIR-642A-5P99.5165.101152
HSA-MIR-217-5P99.4969.931419
HSA-MIR-147B-5P99.4570.622432
HSA-MIR-513A-3P99.3970.633620
HSA-MIR-513C-3P99.3970.633620
HSA-MIR-397899.2468.392201
HSA-MIR-122B-3P99.2168.901333
HSA-MIR-21-3P99.2168.951312

Literature-anchored findings (GeneRIF, showing 7)

  • HOXC11 increases transcription of S100beta gene in BrdU-induced in vitro differentiation of GOTO neuroblastoma cells into Schwann cells. (PMID:17488478)
  • HOXC11 and SRC-1 cooperate to regulate expression of the calcium-binding protein S100beta in resistant breast cancer cells. (PMID:20145129)
  • Our data suggest that HOXC11 may contribute to RCC carcinogenesis by increasing tumor cell proliferation and imply that HOXC11 may be an important determinant of RCC patient prognosis (PMID:25476856)
  • MiR-1197 was upregulated in non-small cell lung cancer (NSCLC) and its downregulation has tumor-suppressing effects in NSCLC, very likely through inverse regulation on downstream target gene of HOXC11. (PMID:31181445)
  • HOXC11 was up-regulated and closely correlated with overall patient survival in colon adenocarcinoma and kidney renal clear cell carcinoma. (PMID:31923422)
  • HOXC11 Expression Is Associated with the Progression of Colon Adenocarcinoma and Is a Prognostic Biomarker. (PMID:34415792)
  • HOXC11 drives lung adenocarcinoma progression through transcriptional regulation of SPHK1. (PMID:36823149)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriohoxc11aENSDARG00000070351
mus_musculusHoxc11ENSMUSG00000001656
rattus_norvegicusHoxc11ENSRNOG00000016141

Paralogs (42): HOXA11 (ENSG00000005073), HOXC8 (ENSG00000037965), HOXA1 (ENSG00000105991), HOXA2 (ENSG00000105996), HOXA3 (ENSG00000105997), HOXA5 (ENSG00000106004), HOXA6 (ENSG00000106006), HOXA13 (ENSG00000106031), TLX1 (ENSG00000107807), HOXB6 (ENSG00000108511), TLX2 (ENSG00000115297), HOXB8 (ENSG00000120068), HOXB5 (ENSG00000120075), HOXB3 (ENSG00000120093), HOXB1 (ENSG00000120094), HOXA7 (ENSG00000122592), HOXC13 (ENSG00000123364), HOXC12 (ENSG00000123407), HOXD1 (ENSG00000128645), HOXD3 (ENSG00000128652), HOXD9 (ENSG00000128709), HOXD10 (ENSG00000128710), HOXD11 (ENSG00000128713), HOXD13 (ENSG00000128714), PDX1 (ENSG00000139515), HOXB13 (ENSG00000159184), TLX3 (ENSG00000164438), HOXD4 (ENSG00000170166), HOXD12 (ENSG00000170178), HOXB9 (ENSG00000170689), HOXC5 (ENSG00000172789), HOXB2 (ENSG00000173917), HOXD8 (ENSG00000175879), GSX2 (ENSG00000180613), HOXC9 (ENSG00000180806), HOXC10 (ENSG00000180818), HOXB4 (ENSG00000182742), HOXA4 (ENSG00000197576), HOXC6 (ENSG00000197757), HOXC4 (ENSG00000198353)

Protein

Protein identifiers

Homeobox protein Hox-C11O43248 (reviewed: O43248)

Alternative names: Homeobox protein Hox-3H

All UniProt accessions (2): O43248, J3KMZ0

UniProt curated annotations — full annotation on UniProt →

Function. Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Binds to a promoter element of the lactase-phlorizin hydrolase gene.

Subcellular location. Nucleus.

Similarity. Belongs to the Abd-B homeobox family.

RefSeq proteins (1): NP_055027* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001356HDDomain
IPR009057Homeodomain-like_sfHomologous_superfamily
IPR017970Homeobox_CSConserved_site
IPR020479HD_metazoaDomain
IPR021918DUF3528Domain

Pfam: PF00046, PF12045

UniProt features (9 total): cross-link 3, sequence variant 2, chain 1, DNA-binding region 1, region of interest 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O43248-F161.310.21

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): 82, 116, 178

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-9830674Formation of the ureteric bud

MSigDB gene sets: 180 (showing top): RNGTGGGC_UNKNOWN, MYAATNNNNNNNGGC_UNKNOWN, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, BENPORATH_ES_WITH_H3K27ME3, GOBP_METANEPHROS_DEVELOPMENT, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GOBP_EMBRYONIC_DIGIT_MORPHOGENESIS, GOBP_EMBRYONIC_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_EMBRYONIC_SKELETAL_SYSTEM_MORPHOGENESIS, GOBP_DEVELOPMENTAL_INDUCTION, GGGTGGRR_PAX4_03, USF_C, MORF_RAD51L3, TCF4_Q5

GO Biological Process (11): metanephros development (GO:0001656), organ induction (GO:0001759), regulation of transcription by RNA polymerase II (GO:0006357), endoderm development (GO:0007492), anterior/posterior pattern specification (GO:0009952), proximal/distal pattern formation (GO:0009954), embryonic digit morphogenesis (GO:0042733), positive regulation of transcription by RNA polymerase II (GO:0045944), embryonic skeletal joint morphogenesis (GO:0060272), skeletal system development (GO:0001501), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (6): 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), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (4): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Kidney development1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA polymerase II transcription regulatory region sequence-specific DNA binding3
cellular anatomical structure3
transcription by RNA polymerase II2
regionalization2
regulation of transcription by RNA polymerase II2
kidney development1
regulation of animal organ formation1
specification of animal organ identity1
developmental induction1
positive regulation of animal organ morphogenesis1
regulation of DNA-templated transcription1
tissue development1
embryonic limb morphogenesis1
embryonic morphogenesis1
positive regulation of DNA-templated transcription1
embryonic skeletal system morphogenesis1
embryonic skeletal joint development1
system development1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
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
double-stranded DNA binding1
sequence-specific DNA binding1
nucleic acid binding1
binding1
chromosome1
intracellular membrane-bounded organelle1
nuclear lumen1
cytoplasm1

Protein interactions and networks

STRING

686 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
HOXC11TBX4P57082842
HOXC11TBX5Q99593724
HOXC11TBX3O15119580
HOXC11TBX6O95947580
HOXC11TBX2Q13207571
HOXC11SALL4Q9UJQ4567
HOXC11DUX4L2P0CJ85554
HOXC11EYA1Q99502545
HOXC11PAX2Q02962509
HOXC11HOXC5Q00444480
HOXC11TBR1Q16650470
HOXC11GAPDHP00354458
HOXC11SRCP12931453
HOXC11TBX1O43435450
HOXC11ATP2A2P16614411

IntAct

41 interactions, top by confidence:

ABTypeScore
HOXC11HTTpsi-mi:“MI:0915”(physical association)0.670
HOXC11TRIP10psi-mi:“MI:0915”(physical association)0.560
HOXC11PSMA1psi-mi:“MI:0915”(physical association)0.560
HOXC11psi-mi:“MI:0915”(physical association)0.560
HOXC11FGFR3psi-mi:“MI:0915”(physical association)0.560
HOXC11HRASpsi-mi:“MI:0915”(physical association)0.560
HOXC11PMP22psi-mi:“MI:0915”(physical association)0.560
HOXC11HDAC5psi-mi:“MI:0915”(physical association)0.370
HOXC11GTF2A1Lpsi-mi:“MI:0915”(physical association)0.370
HOXC11TBX21psi-mi:“MI:0915”(physical association)0.370
HOXC11SOX8psi-mi:“MI:0915”(physical association)0.370
GTF2H1HOXC11psi-mi:“MI:0915”(physical association)0.370
HOXC11IRF4psi-mi:“MI:0915”(physical association)0.370
HOXC11SMAD3psi-mi:“MI:0915”(physical association)0.370
HOXC11MEIS1psi-mi:“MI:0915”(physical association)0.370
HOXC11SP1psi-mi:“MI:0915”(physical association)0.370

BioGRID (23): HOXC11 (Reconstituted Complex), HOXC11 (Affinity Capture-MS), RCHY1 (PCA), TRIP10 (Two-hybrid), PSMA1 (Two-hybrid), HOXC11 (Affinity Capture-RNA), HOXC11 (Affinity Capture-MS), HOXC11 (Affinity Capture-MS), HOXC11 (Proximity Label-MS), HOXC11 (Proximity Label-MS), HOXC11 (Two-hybrid), IRF4 (Two-hybrid), SMAD3 (Two-hybrid), MEIS1 (Two-hybrid), SP1 (Two-hybrid)

ESM2 similar proteins: A1YEY5, A1YFA5, A1YFI3, A1YG57, A2T733, A2T764, A2T7P4, A6NJ46, O42115, O43248, O43711, O55144, O95096, P02830, P09023, P09024, P09629, P09633, P17509, P17919, P18864, P23410, P28362, P29454, P31259, P31311, P31313, P31315, P42586, P43120, P43345, P43697, P48031, P52951, P53544, P53545, P53546, P56915, P97334, Q02591

Diamond homologs: A1YFT7, A2D5V0, A2D635, A2T6F8, A2T7D1, A2T7H7, B5DFK3, O42502, O42503, O42506, O43248, P09013, P09014, P09023, P09025, P09067, P09079, P09087, P09631, P09632, P09633, P10179, P14838, P15861, P17481, P17482, P17509, P18863, P18866, P20615, P23459, P23813, P24340, P24341, P24342, P28356, P28357, P28358, P28359, P31257

SIGNOR signaling

3 interactions.

AEffectBMechanism
KDM6A“up-regulates quantity by expression”HOXC11“transcriptional regulation”
HOXC11“up-regulates quantity by expression”S100B“transcriptional regulation”
HOXC11up-regulatesHNF1A

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance9
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

283 predictions. Top by Δscore:

VariantEffectΔscore
12:53973924:G:GGdonor_gain1.0000
12:53973912:G:GTdonor_gain0.9900
12:53973921:CCAG:Cdonor_loss0.9900
12:53973923:AG:Adonor_loss0.9900
12:53973924:G:GAdonor_loss0.9900
12:53975157:ACTT:Aacceptor_gain0.9900
12:53975179:A:AGacceptor_gain0.9900
12:53975180:G:GAacceptor_gain0.9900
12:53975180:GAC:Gacceptor_gain0.9900
12:53973921:CCA:Cdonor_gain0.9800
12:53973922:CA:Cdonor_gain0.9800
12:53975157:A:AGacceptor_gain0.9800
12:53975158:C:Gacceptor_gain0.9800
12:53975176:TCCAG:Tacceptor_loss0.9800
12:53975177:CCAG:Cacceptor_loss0.9800
12:53975178:CAGA:Cacceptor_loss0.9800
12:53975179:A:Cacceptor_loss0.9800
12:53975179:AGAC:Aacceptor_gain0.9800
12:53975180:GA:Gacceptor_gain0.9800
12:53975180:GACG:Gacceptor_gain0.9800
12:53975180:GACGC:Gacceptor_gain0.9800
12:53973920:CCCA:Cdonor_gain0.9700
12:53975505:C:Aacceptor_gain0.9700
12:53973919:CCCCA:Cdonor_gain0.9600
12:53974277:G:GTdonor_gain0.9400
12:53973760:C:Tdonor_gain0.9300
12:53975160:T:TAacceptor_gain0.9200
12:53975154:C:Aacceptor_gain0.8800
12:53973911:G:GTdonor_gain0.8500
12:53973848:G:GTdonor_gain0.8300

AlphaMissense

1965 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:53975204:C:AR236S1.000
12:53975204:C:TR236C1.000
12:53975213:T:CY239H1.000
12:53975213:T:GY239D1.000
12:53975214:A:GY239C1.000
12:53975227:G:CQ243H1.000
12:53975227:G:TQ243H1.000
12:53975229:T:GI244S1.000
12:53975232:G:CR245P1.000
12:53975238:T:AL247Q1.000
12:53975238:T:CL247P1.000
12:53975238:T:GL247R1.000
12:53975240:G:AE248K1.000
12:53975241:A:TE248V1.000
12:53975242:G:CE248D1.000
12:53975242:G:TE248D1.000
12:53975244:G:CR249P1.000
12:53975246:G:AE250K1.000
12:53975249:T:AF251I1.000
12:53975249:T:CF251L1.000
12:53975249:T:GF251V1.000
12:53975250:T:CF251S1.000
12:53975250:T:GF251C1.000
12:53975251:T:AF251L1.000
12:53975251:T:GF251L1.000
12:53975264:T:CY256H1.000
12:53975264:T:GY256D1.000
12:53975265:A:GY256C1.000
12:53975268:T:AI257N1.000
12:53975268:T:CI257T1.000

dbSNP variants (sampled 300 via entrez): RS1000921625 (12:53973330 C>T), RS1001373646 (12:53973910 A>G), RS1001538915 (12:53975582 T>A), RS1001888327 (12:53974126 G>T), RS1002759828 (12:53972982 C>A,G,T), RS1002783761 (12:53972562 G>T), RS1002859654 (12:53976821 T>A,C), RS1003216059 (12:53977145 C>A,T), RS1003374468 (12:53971348 G>GA), RS1003896859 (12:53971601 G>A,T), RS1004791199 (12:53977334 A>G), RS1006063441 (12:53972422 G>A), RS1006120679 (12:53972746 A>T), RS1006738783 (12:53974933 C>A,G,T), RS1007789162 (12:53973991 G>A,C)

Disease associations

OMIM: gene MIM:605559 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST005956_70Waist-to-hip ratio adjusted for BMI4.000000e-13
GCST005957_6Waist-to-hip ratio adjusted for BMI (age <50)6.000000e-06
GCST005958_9Waist-to-hip ratio adjusted for BMI (age >50)1.000000e-08
GCST005962_20Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)7.000000e-13
GCST90014033_57Haemorrhoidal disease7.000000e-10

EFO canonical traits (3, from GWAS)

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

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

ChemicalActions (top 5)PubMed papers
Aflatoxin B1decreases methylation2
arseniteincreases methylation1
sodium arseniteaffects methylation1
Grape Seed Proanthocyanidinsaffects cotreatment, increases expression1
(+)-JQ1 compounddecreases expression1
Benzo(a)pyreneaffects methylation1
Catechinincreases expression, affects cotreatment1
Estradioldecreases expression1
Fluorouracilaffects expression, affects response to substance1
Methylcholanthreneaffects binding, increases reaction1
Nickeldecreases expression1
Asbestos, Serpentinedecreases methylation1
Asbestos, Crocidolitedecreases methylation1
Asbestos, Amositedecreases methylation1
Lactic Acidincreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): hemorrhoid