HCFC2

gene
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Also known as HCF-2

Summary

HCFC2 (host cell factor C2, HGNC:24972) is a protein-coding gene on chromosome 12q23.3, encoding Host cell factor 2 (Q9Y5Z7).

This gene encodes one of two proteins which interact with VP16, a herpes simplex virus protein that initiates virus infection. Both the encoded protein and the original Herpes host cell factor interact with VP16 through a beta-propeller domain. The original Herpes host cell factor, however, is effective at initiating viral infection while the encoded protein is not. Transcripts of varying length due to alternative polyadenylation signals have been described.

Source: NCBI Gene 29915 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 68 total
  • MANE Select transcript: NM_013320

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24972
Approved symbolHCFC2
Namehost cell factor C2
Location12q23.3
Locus typegene with protein product
StatusApproved
AliasesHCF-2
Ensembl geneENSG00000111727
Ensembl biotypeprotein_coding
OMIM607926
Entrez29915

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000229330, ENST00000544223, ENST00000547194, ENST00000550335, ENST00000550444, ENST00000552343, ENST00000894561, ENST00000894562, ENST00000894563

RefSeq mRNA: 1 — MANE Select: NM_013320 NM_013320

CCDS: CCDS9097

Canonical transcript exons

ENST00000229330 — 15 exons

ExonStartEnd
ENSE00001104674104102959104106524
ENSE00001104675104080746104080830
ENSE00001104678104087986104088038
ENSE00001104682104086847104087014
ENSE00001104685104079445104079653
ENSE00001104687104082713104082901
ENSE00001104691104067947104068107
ENSE00001513397104064531104064723
ENSE00003463160104101968104102153
ENSE00003471401104066167104066315
ENSE00003527177104095360104095563
ENSE00003546291104098343104098480
ENSE00003551467104082500104082606
ENSE00003641940104093386104093563
ENSE00003645368104096360104096433

Expression profiles

Bgee: expression breadth ubiquitous, 264 present calls, max score 92.65.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.3295 / max 75.8534, expressed in 1411 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1277243.32951411

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370192.65gold quality
spermCL:000001992.10gold quality
left testisUBERON:000453391.42gold quality
right testisUBERON:000453490.71gold quality
testisUBERON:000047390.64gold quality
germinal epithelium of ovaryUBERON:000130490.25gold quality
male germ cellCL:000001589.60gold quality
cauda epididymisUBERON:000436088.79gold quality
tendonUBERON:000004388.28gold quality
mucosa of stomachUBERON:000119987.76gold quality
muscle layer of sigmoid colonUBERON:003580587.56gold quality
gastrocnemiusUBERON:000138887.14gold quality
biceps brachiiUBERON:000150787.13gold quality
adrenal tissueUBERON:001830386.99gold quality
islet of LangerhansUBERON:000000686.67gold quality
muscle of legUBERON:000138386.40gold quality
tibial arteryUBERON:000761086.34gold quality
popliteal arteryUBERON:000225086.33gold quality
oocyteCL:000002386.22gold quality
lower esophagus muscularis layerUBERON:003583386.07gold quality
lower esophagusUBERON:001347386.05gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451186.00gold quality
esophagogastric junction muscularis propriaUBERON:003584185.97gold quality
colonic epitheliumUBERON:000039785.46gold quality
Brodmann (1909) area 23UBERON:001355485.44gold quality
cortical plateUBERON:000534385.41gold quality
parietal pleuraUBERON:000240085.29gold quality
aortaUBERON:000094785.01gold quality
visceral pleuraUBERON:000240184.95gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450284.74gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.70

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

207 targeting HCFC2, 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-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-190A-3P100.0080.355520
HSA-MIR-5692A100.0074.406850
HSA-MIR-3163100.0077.238605
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-9-5P100.0072.282361
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-656-3P100.0072.152788
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-548AW99.9972.573559
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-366299.9973.825684
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-450099.9972.722367
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-477599.9875.006394
HSA-MIR-569699.9872.364487

Literature-anchored findings (GeneRIF, showing 1)

  • HCF-2 is broadly present in human and mouse cells, and possesses activities distinct from HCF-1 (PMID:31049581)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
mus_musculusHcfc2ENSMUSG00000020246
rattus_norvegicusHcfc2ENSRNOG00000053510
drosophila_melanogasterHcfFBGN0039904
caenorhabditis_elegansWBGENE00001827

Paralogs (10): FBXO42 (ENSG00000037637), LZTR1 (ENSG00000099949), KLHDC4 (ENSG00000104731), KLHDC3 (ENSG00000124702), KLHDC10 (ENSG00000128607), RABEPK (ENSG00000136933), KLHDC9 (ENSG00000162755), KLHDC2 (ENSG00000165516), HCFC1 (ENSG00000172534), KLHDC1 (ENSG00000197776)

Protein

Protein identifiers

Host cell factor 2Q9Y5Z7 (reviewed: Q9Y5Z7)

Alternative names: C2 factor

All UniProt accessions (2): Q9Y5Z7, F8VU09

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Binds KMT2A/MLL1. Component of the MLL1/MLL complex, at least composed of KMT2A/MLL1, ASH2L, RBBP5, DPY30, WDR5, MEN1, HCFC1 and HCFC2. Interacts with TASOR.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Highly expressed in testis. Detected at lower levels in spleen, thymus, prostate, ovary, small intestine and colon.

Isoforms (2)

UniProt IDNamesCanonical?
Q9Y5Z7-11yes
Q9Y5Z7-22

RefSeq proteins (1): NP_037452* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003961FN3_domDomain
IPR011043Gal_Oxase/kelch_b-propellerHomologous_superfamily
IPR013783Ig-like_foldHomologous_superfamily
IPR015915Kelch-typ_b-propellerHomologous_superfamily
IPR036116FN3_sfHomologous_superfamily
IPR043536HCF1/2Family
IPR059124Kelch_HCFDomain

Pfam: PF13854

UniProt features (15 total): repeat 4, domain 3, splice variant 2, sequence variant 2, chain 1, cross-link 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y5Z7-F173.780.51

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): 553

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-9772755Formation of WDR5-containing histone-modifying complexes

MSigDB gene sets: 189 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_DN, GOBP_RESPONSE_TO_NITROGEN_COMPOUND, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, CAGCTG_AP4_Q5, GOBP_POSITIVE_REGULATION_OF_RESPONSE_TO_EXTERNAL_STIMULUS, GOBP_REGULATION_OF_IMMUNE_RESPONSE, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, TGIF_01, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, GOBP_DEFENSE_RESPONSE_TO_VIRUS, GOBP_POSITIVE_REGULATION_OF_RESPONSE_TO_BIOTIC_STIMULUS, GOBP_REGULATION_OF_RESPONSE_TO_EXTERNAL_STIMULUS, GOBP_INTRACELLULAR_RECEPTOR_SIGNALING_PATHWAY, GOBP_REGULATION_OF_RESPONSE_TO_BIOTIC_STIMULUS, GOBP_CYTOPLASMIC_PATTERN_RECOGNITION_RECEPTOR_SIGNALING_PATHWAY

GO Biological Process (9): negative regulation of transcription by RNA polymerase II (GO:0000122), chromatin remodeling (GO:0006338), regulation of DNA-templated transcription (GO:0006355), regulation of transcription by RNA polymerase II (GO:0006357), viral process (GO:0016032), regulation of toll-like receptor 3 signaling pathway (GO:0034139), antiviral innate immune response (GO:0140374), immune response involved in response to exogenous dsRNA (GO:1902615), positive regulation of DNA-templated transcription (GO:0045893)

GO Molecular Function (3): transcription coactivator activity (GO:0003713), transcription coregulator activity (GO:0003712), protein binding (GO:0005515)

GO Cellular Component (9): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), plasma membrane (GO:0005886), histone methyltransferase complex (GO:0035097), MLL1/2 complex (GO:0044665), Set1C/COMPASS complex (GO:0048188), MLL1 complex (GO:0071339)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Epigenetic regulation by WDR5-containing histone modifying complexes1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
transcription by RNA polymerase II2
DNA-templated transcription2
regulation of DNA-templated transcription2
histone methyltransferase complex2
regulation of transcription by RNA polymerase II1
negative regulation of DNA-templated transcription1
chromatin organization1
regulation of gene expression1
regulation of RNA biosynthetic process1
biological_process1
toll-like receptor 3 signaling pathway1
regulation of cytoplasmic pattern recognition receptor signaling pathway1
innate immune response1
defense response to virus1
immune response1
response to exogenous dsRNA1
positive regulation of RNA biosynthetic process1
transcription coregulator activity1
positive regulation of DNA-templated transcription1
transcription regulator activity1
binding1
intracellular membrane-bounded organelle1
nuclear lumen1
intracellular anatomical structure1
cytoplasm1
membrane1
cell periphery1
nucleoplasm1
methyltransferase complex1
nuclear protein-containing complex1
MLL1/2 complex1

Protein interactions and networks

STRING

774 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
HCFC2CREBZFQ9NS37971
HCFC2CREB3O43889868
HCFC2POU2F1P14859836
HCFC2CREB3L4Q8TEY5832
HCFC2POU2F2P09086764
HCFC2WDR5P61964560
HCFC2RBBP5Q15291556
HCFC2IRF2P14316506
HCFC2TET1Q8NFU7469
HCFC2NPC1O15118451
HCFC2TMPRSS2O15393448
HCFC2PPARGC1AQ9UBK2441
HCFC2TET2Q6N021439
HCFC2CTSBP07858433
HCFC2RNF2Q99496433

IntAct

64 interactions, top by confidence:

ABTypeScore
WDR5KMT2Dpsi-mi:“MI:0914”(association)0.910
ASH2LKMT2Dpsi-mi:“MI:0914”(association)0.890
RBBP5KMT2Dpsi-mi:“MI:0914”(association)0.840
RAMACRNMTpsi-mi:“MI:0914”(association)0.810
NFE2L3MAFGpsi-mi:“MI:0914”(association)0.780
BAP1OGTpsi-mi:“MI:0914”(association)0.730
WDR5MEN1psi-mi:“MI:0914”(association)0.710
HCFC2NUDCD3psi-mi:“MI:0915”(physical association)0.670
CSNK2BRPS6KA4psi-mi:“MI:0914”(association)0.640
PPP2R2BMYO9Apsi-mi:“MI:0914”(association)0.640
KMT2AMEN1psi-mi:“MI:0914”(association)0.640
HCFC2SETD1Apsi-mi:“MI:0914”(association)0.530
THAP2OGTpsi-mi:“MI:0914”(association)0.530
IRF2CTSSpsi-mi:“MI:0914”(association)0.530
CREB3MYO9Apsi-mi:“MI:0914”(association)0.530
GLMNMGST3psi-mi:“MI:0914”(association)0.530
ZNF597HCFC1psi-mi:“MI:0914”(association)0.530
BAP1HAT1psi-mi:“MI:0914”(association)0.530
PPP2R2BDDX3Xpsi-mi:“MI:0914”(association)0.460
FOXO3HCFC2psi-mi:“MI:0915”(physical association)0.400
HCFC2SIRT1psi-mi:“MI:0915”(physical association)0.400
HCFC2MEN1psi-mi:“MI:0915”(physical association)0.400
NUDCHCFC2psi-mi:“MI:0915”(physical association)0.400
SetZKSCAN1psi-mi:“MI:0914”(association)0.350
IRF2VWA8psi-mi:“MI:0914”(association)0.350

BioGRID (158): HCFC2 (Affinity Capture-MS), HCFC2 (Affinity Capture-MS), HCFC2 (Affinity Capture-MS), HCFC2 (Affinity Capture-MS), HCFC2 (Affinity Capture-MS), KMT2B (Affinity Capture-MS), KMT2A (Affinity Capture-MS), CXXC1 (Affinity Capture-MS), SETD1A (Affinity Capture-MS), DIDO1 (Affinity Capture-MS), BOD1L1 (Affinity Capture-MS), ASH2L (Affinity Capture-MS), CCT2 (Affinity Capture-MS), HCFC2 (Affinity Capture-MS), CCT6B (Affinity Capture-MS)

ESM2 similar proteins: A1Z7A6, A8Y3R9, B0WAU8, B3NKK1, B4IMC3, B4IT27, B4NSS9, G5EC23, G5EEW9, G5EFD2, H2KZW3, O43150, O45487, O61460, O73630, P24583, P36582, Q09441, Q09589, Q10149, Q12469, Q13972, Q19857, Q20500, Q45FX5, Q4P3S3, Q5ACW8, Q5DX34, Q5RDX4, Q5RKG2, Q6BU95, Q6DTM3, Q6NRL1, Q754R5, Q7PLI7, Q7S9B6, Q7SIG6, Q8BXK8, Q8K3E5, Q8TBZ3

Diamond homologs: A8JAM0, D3ZN95, P38853, P51610, P51611, Q2R2W1, Q39610, Q4V516, Q5E9A7, Q5RKG2, Q61191, Q6PDJ6, Q7M3S9, Q86L99, Q8N7A1, Q8RWD9, Q9D968, Q9MA55, Q9V4C8, Q9Y5Z7, G5EC23, Q10AZ7, Q4V8F4, Q53EP0, Q5RDA9, Q6AYI2, Q6NWW9, Q6P3S6, Q8H4D4, Q8VEM9, Q93XW5, Q9BQ90, A1XLE2, G1FNI6, O04316, O04318, O49326, Q5EA50, Q5ZJ37, Q6AXB2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 78 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
Formation of WDR5-containing histone-modifying complexes1258.0×2e-16
Deactivation of the beta-catenin transactivating complex625.4×7e-06
Epigenetic regulation by WDR5-containing histone modifying complexes822.4×3e-07
Epigenetic regulation of gene expression by MLL3 and MLL4 complexes621.5×2e-05
Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells)718.6×7e-06
PKMTs methylate histone lysines617.6×4e-05
Formation of the beta-catenin:TCF transactivating complex817.5×1e-06
RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function715.3×2e-05

GO biological processes:

GO termPartnersFoldFDR
transcription initiation-coupled chromatin remodeling526.6×2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance52
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2238 predictions. Top by Δscore:

VariantEffectΔscore
12:104064722:GG:Gdonor_gain1.0000
12:104064723:GG:Gdonor_gain1.0000
12:104064723:GGT:Gdonor_loss1.0000
12:104064724:GTAG:Gdonor_loss1.0000
12:104064725:T:Gdonor_loss1.0000
12:104066157:T:TAacceptor_gain1.0000
12:104066158:G:Aacceptor_gain1.0000
12:104066161:A:AGacceptor_gain1.0000
12:104066162:A:Gacceptor_gain1.0000
12:104066316:G:GGdonor_gain1.0000
12:104067942:TTTA:Tacceptor_loss1.0000
12:104067945:A:AGacceptor_gain1.0000
12:104067946:G:Aacceptor_loss1.0000
12:104067946:G:GGacceptor_gain1.0000
12:104067946:GGCAA:Gacceptor_gain1.0000
12:104068104:CCAGG:Cdonor_loss1.0000
12:104068105:CAGGT:Cdonor_loss1.0000
12:104068106:AGGTA:Adonor_loss1.0000
12:104068108:G:Tdonor_loss1.0000
12:104068109:T:Adonor_loss1.0000
12:104080744:A:AGacceptor_gain1.0000
12:104080745:G:GGacceptor_gain1.0000
12:104080831:G:GGdonor_gain1.0000
12:104082711:A:AGacceptor_gain1.0000
12:104082712:G:GAacceptor_gain1.0000
12:104082712:GA:Gacceptor_gain1.0000
12:104082712:GAT:Gacceptor_gain1.0000
12:104082712:GATA:Gacceptor_gain1.0000
12:104082712:GATAC:Gacceptor_gain1.0000
12:104082902:GTAG:Gdonor_gain1.0000

AlphaMissense

5159 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:104064619:C:AP20H1.000
12:104064630:C:GH24D1.000
12:104064631:A:GH24R1.000
12:104064632:C:AH24Q1.000
12:104064632:C:GH24Q1.000
12:104064633:G:AG25R1.000
12:104064633:G:CG25R1.000
12:104064634:G:AG25E1.000
12:104064634:G:TG25V1.000
12:104064661:T:CL34P1.000
12:104064675:G:AG39R1.000
12:104064675:G:CG39R1.000
12:104064676:G:AG39E1.000
12:104064676:G:TG39V1.000
12:104064678:G:AG40R1.000
12:104064678:G:CG40R1.000
12:104064678:G:TG40W1.000
12:104064679:G:AG40E1.000
12:104064679:G:TG40V1.000
12:104064681:G:AG41R1.000
12:104064681:G:CG41R1.000
12:104064682:G:AG41E1.000
12:104064686:T:AN42K1.000
12:104064686:T:GN42K1.000
12:104064690:G:CG44R1.000
12:104064712:T:AV51D1.000
12:104064714:T:GY52D1.000
12:104066178:T:AW59R1.000
12:104066178:T:CW59R1.000
12:104066180:G:CW59C1.000

dbSNP variants (sampled 300 via entrez): RS1000125776 (12:104082066 TAA>T), RS1000143897 (12:104076761 G>A,C,T), RS1000206894 (12:104065731 G>A), RS1000538136 (12:104080275 C>A), RS1000575728 (12:104066073 T>C,G), RS1000635585 (12:104071305 C>A), RS1000643527 (12:104101252 C>T), RS1000669227 (12:104093932 C>G), RS1000715069 (12:104101633 A>T), RS1000837904 (12:104092193 T>A,G), RS1000851925 (12:104078000 G>A), RS1000905194 (12:104072596 G>A), RS1000948881 (12:104086054 G>C), RS1000980267 (12:104086483 C>A,G), RS1001118234 (12:104093676 A>C,G,T)

Disease associations

OMIM: gene MIM:607926 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST010320_5PR interval3.000000e-11
GCST010321_76PR interval2.000000e-12

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004462PR interval

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, decreases expression3
Acetaminophendecreases expression, increases expression2
Cadmium Chlorideincreases abundance, increases expression2
bisphenol Faffects cotreatment, increases expression1
TAK-243decreases sumoylation1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
pirinixic acidaffects binding, decreases expression, increases activity1
bisphenol Aaffects cotreatment, increases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
butyraldehydedecreases expression1
perfluorooctane sulfonic aciddecreases expression1
CGP 52608increases reaction, affects binding1
monomethylarsonous acidincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
ICG 001decreases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, increases expression1
jinfukangdecreases expression, affects cotreatment1
Resveratrolaffects cotreatment, increases expression1
Sunitinibincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Cadmiumincreases abundance, increases expression1
Cisplatinaffects cotreatment, decreases expression1
Dexamethasoneincreases expression, affects cotreatment1
Diazinonincreases methylation1
Doxorubicindecreases expression1
Endosulfanincreases expression1
Ethyl Methanesulfonateincreases expression1
Indomethacinaffects cotreatment, increases 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.