GCFC2

gene
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Also known as DNABFGCF

Summary

GCFC2 (GC-rich sequence DNA-binding factor 2, HGNC:1317) is a protein-coding gene on chromosome 2p12, encoding Intron Large complex component GCFC2 (P16383). Involved in pre-mRNA splicing through regulating spliceosome C complex formation.

The first mRNA transcript isolated for this gene was part of an artificial chimera derived from two distinct gene transcripts and a primer used in the cloning process (see Genbank accession M29204). A positively charged amino terminus present only in the chimera was determined to bind GC-rich DNA, thus mistakenly thought to identify a transcription factor gene.

Source: NCBI Gene 6936 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 123 total
  • MANE Select transcript: NM_003203

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1317
Approved symbolGCFC2
NameGC-rich sequence DNA-binding factor 2
Location2p12
Locus typegene with protein product
StatusApproved
AliasesDNABF, GCF
Ensembl geneENSG00000005436
Ensembl biotypeprotein_coding
OMIM189901
Entrez6936

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 15 protein_coding, 2 retained_intron, 2 nonsense_mediated_decay

ENST00000321027, ENST00000409857, ENST00000427862, ENST00000442309, ENST00000470197, ENST00000470285, ENST00000470503, ENST00000472230, ENST00000486016, ENST00000492826, ENST00000541687, ENST00000884726, ENST00000884727, ENST00000884728, ENST00000884729, ENST00000884730, ENST00000884731, ENST00000970645, ENST00000970646

RefSeq mRNA: 4 — MANE Select: NM_003203 NM_001201334, NM_001201335, NM_001410845, NM_003203

CCDS: CCDS1961, CCDS62943, CCDS92788

Canonical transcript exons

ENST00000321027 — 17 exons

ExonStartEnd
ENSE000012619007571059175710915
ENSE000034650787566270575664783
ENSE000034746207567344475673520
ENSE000034756057567195075672016
ENSE000034922427569620075696315
ENSE000035228657568019375680314
ENSE000035354547569197775692100
ENSE000035564207569063875690719
ENSE000035630517567013875670284
ENSE000035663597568782775687977
ENSE000035820237566592975666053
ENSE000035930817568996975690081
ENSE000036088787570219975702423
ENSE000036155197568902675689225
ENSE000036514647570652375706651
ENSE000036639337569424175694427
ENSE000036687487570119075701287

Expression profiles

Bgee: expression breadth ubiquitous, 268 present calls, max score 92.34.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.7927 / max 74.4960, expressed in 1782 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
2928511.49341780
292860.2993147

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ventricular zoneUBERON:000305392.34gold quality
gastrocnemiusUBERON:000138892.02gold quality
muscle of legUBERON:000138391.65gold quality
right lobe of liverUBERON:000111491.32gold quality
calcaneal tendonUBERON:000370190.75gold quality
adrenal tissueUBERON:001830390.21gold quality
endocervixUBERON:000045890.00gold quality
hindlimb stylopod muscleUBERON:000425290.00gold quality
right uterine tubeUBERON:000130289.77gold quality
body of pancreasUBERON:000115089.71gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099189.58gold quality
muscle organUBERON:000163089.38gold quality
ectocervixUBERON:001224989.34gold quality
left ovaryUBERON:000211989.06gold quality
ganglionic eminenceUBERON:000402388.96gold quality
metanephros cortexUBERON:001053388.86gold quality
olfactory segment of nasal mucosaUBERON:000538688.85gold quality
right ovaryUBERON:000211888.76gold quality
right lobe of thyroid glandUBERON:000111988.61gold quality
tibial nerveUBERON:000132388.46gold quality
left lobe of thyroid glandUBERON:000112088.28gold quality
body of uterusUBERON:000985388.21gold quality
left uterine tubeUBERON:000130388.18gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047388.01gold quality
thyroid glandUBERON:000204687.39gold quality
mucosa of stomachUBERON:000119987.35gold quality
C1 segment of cervical spinal cordUBERON:000646987.03gold quality
adenohypophysisUBERON:000219687.00gold quality
right coronary arteryUBERON:000162586.82gold quality
skin of abdomenUBERON:000141686.80gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.44
E-MTAB-4850no1178.85

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

7 targets.

TargetRegulation
EGF
EGFRRepression
GC
GCFC2
IGF1R
INSR
TGFA

Upstream regulators (CollecTRI, top): GCFC2

miRNA regulators (miRDB)

97 targeting GCFC2, 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-3613-3P100.0076.367965
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-186-5P99.9970.833707
HSA-MIR-548AW99.9972.573559
HSA-MIR-366299.9973.825684
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-428299.9975.366408
HSA-MIR-56899.9869.862084
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-60799.9773.625593
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-146A-5P99.9668.93988
HSA-MIR-146B-5P99.9669.13977
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-9-3P99.9670.882068
HSA-MIR-7153-5P99.9468.891006
HSA-MIR-314399.9371.963104
HSA-MIR-335-3P99.9373.364958
HSA-MIR-205-3P99.9269.923165
HSA-MIR-338-5P99.9272.342951
HSA-MIR-130599.9171.433443
HSA-MIR-367199.9073.043897
HSA-MIR-153-5P99.8973.866317
HSA-MIR-6780A-5P99.8866.692776
HSA-MIR-4728-5P99.8569.394718

Literature-anchored findings (GeneRIF, showing 3)

  • Study refined the 2p12 candidate region in two populations and report evidence supporting MRPL19 and C2ORF3 as candidate susceptibility genes for dyslexia. (PMID:17309879)
  • C2ORF3 protein is required for pre-mRNA splicing through its presumable role in efficient intron turnover (PMID:24304693)
  • Authors propose the GCF regulated transcriptional activity, at least in part, contributed to the upregulation of IER5 on radiation in HepG2 cells. The present findings provide insights into understanding the regulatory mechanisms of IER5. (PMID:26915404)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriogcfc2ENSDARG00000079020
mus_musculusGcfc2ENSMUSG00000035125
rattus_norvegicusGcfc2ENSRNOG00000006888
drosophila_melanogasterCG1965FBGN0037466
caenorhabditis_elegansmog-7WBGENE00009672

Paralogs (1): PAXBP1 (ENSG00000159086)

Protein

Protein identifiers

Intron Large complex component GCFC2P16383 (reviewed: P16383)

Alternative names: GC-rich sequence DNA-binding factor, GC-rich sequence DNA-binding factor 2, Transcription factor 9

All UniProt accessions (6): P16383, C9JII4, H7C335, S4R3C1, S4R461, S4R465

UniProt curated annotations — full annotation on UniProt →

Function. Involved in pre-mRNA splicing through regulating spliceosome C complex formation. May play a role during late-stage splicing events and turnover of excised introns.

Subunit / interactions. Found in the Intron Large (IL) complex, a post-mRNA release spliceosomal complex containing the excised intron, U2, U5 and U6 snRNPs, and splicing factors. Interacts with TFIP11 and DHX15.

Subcellular location. Nucleus. Nucleoplasm. Nucleolus.

Tissue specificity. Widely expressed in tissues and cell lines.

Similarity. Belongs to the GCF family.

Isoforms (4)

UniProt IDNamesCanonical?
P16383-11yes
P16383-22
P16383-33
P16383-44

RefSeq proteins (4): NP_001188263, NP_001188264, NP_001397774, NP_003194* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR012890GCFC2-likeFamily
IPR022783GCFC_domDomain

Pfam: PF07842

UniProt features (33 total): modified residue 12, compositionally biased region 8, splice variant 5, sequence variant 5, chain 1, region of interest 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P16383-F174.120.44

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 (12): 16, 17, 19, 40, 96, 97, 129, 174, 180, 213, 214, 217

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-72163mRNA Splicing - Major Pathway

MSigDB gene sets: 143 (showing top): MORF_ATRX, PUJANA_CHEK2_PCC_NETWORK, OSWALD_HEMATOPOIETIC_STEM_CELL_IN_COLLAGEN_GEL_UP, BLALOCK_ALZHEIMERS_DISEASE_UP, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_RNA_SPLICING, REACTOME_MRNA_SPLICING, DODD_NASOPHARYNGEAL_CARCINOMA_UP, chr2p12, DANG_BOUND_BY_MYC, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, REACTOME_METABOLISM_OF_RNA, GOCC_U2_TYPE_SPLICEOSOMAL_COMPLEX, GOCC_SPLICEOSOMAL_COMPLEX

GO Biological Process (4): spliceosomal complex assembly (GO:0000245), mRNA splicing, via spliceosome (GO:0000398), mRNA processing (GO:0006397), RNA splicing (GO:0008380)

GO Molecular Function (2): DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (5): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytosol (GO:0005829), U2-type post-mRNA release spliceosomal complex (GO:0071008)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
mRNA Splicing1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA processing2
nuclear lumen2
cellular anatomical structure2
mRNA splicing, via spliceosome1
protein-RNA complex assembly1
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile1
mRNA processing1
mRNA metabolic process1
nucleic acid binding1
binding1
intracellular membrane-bounded organelle1
intracellular membraneless organelle1
cytoplasm1
U2-type spliceosomal complex1
U6 snRNP1
post-mRNA release spliceosomal complex1

Protein interactions and networks

STRING

906 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GCFC2LRRFIP1Q32MZ4845
GCFC2KIAA0319Q5VV43780
GCFC2MRPL19P49406773
GCFC2DNAAF4Q8WXU2773
GCFC2DCDC2Q9UHG0766
GCFC2FLIIQ13045763
GCFC2KNL1Q8NG31689
GCFC2TFIP11Q9UBB9650
GCFC2RBM8AQ9Y5S9640
GCFC2ROBO1Q9Y6N7582
GCFC2KIAA0319LQ8IZA0580
GCFC2ATP2C2O75185577
GCFC2CMIPQ8IY22573
GCFC2SRYQ05066571
GCFC2DHX15O43143567

IntAct

62 interactions, top by confidence:

ABTypeScore
PPIEAQRpsi-mi:“MI:0914”(association)0.810
GCFC2TFIP11psi-mi:“MI:0915”(physical association)0.670
SNRPBPRMT5psi-mi:“MI:0914”(association)0.670
SNRPA1HTATSF1psi-mi:“MI:0914”(association)0.640
HDAC11CLUHpsi-mi:“MI:0914”(association)0.640
GCFC2SNRNP200psi-mi:“MI:0914”(association)0.640
SNRPA1U2SURPpsi-mi:“MI:0914”(association)0.640
TFIP11DHX15psi-mi:“MI:0914”(association)0.600
SNRPEPRMT5psi-mi:“MI:0914”(association)0.530
SNRPESNRPGP15psi-mi:“MI:0914”(association)0.530
ELAVL2IGF2BP3psi-mi:“MI:0914”(association)0.530
YJU2BRCCD1psi-mi:“MI:0914”(association)0.530
LPAR1TMEM223psi-mi:“MI:0914”(association)0.530
GCFC2DHX15psi-mi:“MI:0914”(association)0.530
CRKGCFC2psi-mi:“MI:0915”(physical association)0.400
GCFC2FYNpsi-mi:“MI:0915”(physical association)0.400
GCFC2VIMpsi-mi:“MI:0915”(physical association)0.400
CREB3L2GCFC2psi-mi:“MI:0915”(physical association)0.370
SLF2GCFC2psi-mi:“MI:0914”(association)0.350
CDK8CCNCpsi-mi:“MI:0914”(association)0.350
HNRNPDARHGAP32psi-mi:“MI:0914”(association)0.350
SYNCRIPARHGAP32psi-mi:“MI:0914”(association)0.350
DHX15BBXpsi-mi:“MI:0914”(association)0.350
BSGMETTL15psi-mi:“MI:0914”(association)0.350
ELAVL2IGF2BP3psi-mi:“MI:0914”(association)0.350

BioGRID (92): PRPF6 (Affinity Capture-MS), SNRNP200 (Affinity Capture-MS), PRPF8 (Affinity Capture-MS), DDX23 (Affinity Capture-MS), CSNK2A2 (Affinity Capture-MS), UBR2 (Affinity Capture-MS), CSNK2A1 (Affinity Capture-MS), ECD (Affinity Capture-MS), GCFC2 (Affinity Capture-MS), GCFC2 (Affinity Capture-MS), GCFC2 (Affinity Capture-MS), GCFC2 (Affinity Capture-MS), GCFC2 (Affinity Capture-MS), GCFC2 (Affinity Capture-MS), GCFC2 (Affinity Capture-MS)

ESM2 similar proteins: A2BDB7, A6PVY3, F6RRD7, F7BHS0, O14990, O55036, O60566, P16383, P54274, P58501, Q08B36, Q0VFF9, Q28C41, Q28GJ0, Q28GL6, Q2T9X8, Q2TBG9, Q2WG79, Q3ZCI6, Q4R6Q9, Q5BJ78, Q5M8L3, Q5NVK0, Q5R6R3, Q5R789, Q5R939, Q5RA37, Q5RBY6, Q5TID7, Q5XIG5, Q640L3, Q68G75, Q6AYN9, Q6GNQ4, Q6NTW1, Q6NZY4, Q6PCG6, Q80VH0, Q80ZU5, Q8AVX1

Diamond homologs: P16383, P58501, Q8BKT3, Q9Y5B6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 74 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
mRNA Splicing1021.5×2e-09
mRNA Splicing - Major Pathway1718.2×4e-15
Processing of Capped Intron-Containing Pre-mRNA1117.7×2e-09
Dengue Virus-Host Interactions1513.4×2e-11
mRNA Polyadenylation712.1×7e-05
CHD1 and CHD2 subfamily510.7×3e-03
Metabolism of RNA129.8×1e-07

GO biological processes:

GO termPartnersFoldFDR
mRNA splicing, via spliceosome1723.6×1e-16
RNA processing723.2×4e-06
RNA splicing810.7×1e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance90
Likely benign12
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

3954 predictions. Top by Δscore:

VariantEffectΔscore
2:75652213:A:Gdonor_gain1.0000
2:75652261:GTCA:Gdonor_gain1.0000
2:75652265:G:GGdonor_gain1.0000
2:75652269:GAGCT:Gdonor_gain1.0000
2:75652271:GCT:Gdonor_gain1.0000
2:75652512:T:TAacceptor_gain1.0000
2:75652515:A:AGacceptor_gain1.0000
2:75652516:T:Gacceptor_gain1.0000
2:75652518:T:TAacceptor_gain1.0000
2:75652518:TGTA:Tacceptor_loss1.0000
2:75652520:TA:Tacceptor_loss1.0000
2:75652521:A:Gacceptor_loss1.0000
2:75652521:AG:Aacceptor_gain1.0000
2:75652522:GG:Gacceptor_gain1.0000
2:75652522:GGAA:Gacceptor_gain1.0000
2:75652653:ACAAG:Adonor_gain1.0000
2:75652654:CAAG:Cdonor_gain1.0000
2:75652654:CAAGG:Cdonor_loss1.0000
2:75652655:AAGG:Adonor_loss1.0000
2:75652656:AG:Adonor_gain1.0000
2:75652657:GG:Gdonor_gain1.0000
2:75652657:GGTA:Gdonor_loss1.0000
2:75652658:G:GGdonor_gain1.0000
2:75652658:GTAA:Gdonor_loss1.0000
2:75664779:CATCC:Cacceptor_gain1.0000
2:75664781:TCC:Tacceptor_gain1.0000
2:75664781:TCCCT:Tacceptor_loss1.0000
2:75664782:CC:Cacceptor_gain1.0000
2:75664782:CCC:Cacceptor_gain1.0000
2:75664782:CCCT:Cacceptor_loss1.0000

AlphaMissense

5174 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:75680297:A:GW570R0.994
2:75680297:A:TW570R0.994
2:75687947:A:GW524R0.990
2:75687947:A:TW524R0.990
2:75689136:A:GW477R0.989
2:75689136:A:TW477R0.989
2:75689132:C:GR478P0.988
2:75670263:A:GW660R0.987
2:75670263:A:TW660R0.987
2:75673464:A:CF623L0.973
2:75673464:A:TF623L0.973
2:75673466:A:GF623L0.973
2:75689040:A:GW509R0.971
2:75689040:A:TW509R0.971
2:75680295:C:AW570C0.970
2:75680295:C:GW570C0.970
2:75694251:A:GL337P0.969
2:75689134:C:AW477C0.968
2:75689134:C:GW477C0.968
2:75689135:C:GW477S0.966
2:75701229:C:AW226C0.965
2:75701229:C:GW226C0.965
2:75689057:C:GR503P0.963
2:75689112:A:CY485D0.963
2:75666029:A:GW710R0.962
2:75666029:A:TW710R0.962
2:75680285:A:GS574P0.961
2:75690018:A:CS430R0.961
2:75690018:A:TS430R0.961
2:75690020:T:GS430R0.961

dbSNP variants (sampled 300 via entrez): RS1000042858 (2:75680714 A>C), RS1000136704 (2:75663392 G>A), RS1000278429 (2:75680399 C>G), RS1000300017 (2:75692321 T>G), RS1000325280 (2:75710264 T>C), RS1000411013 (2:75714418 T>A), RS1000577582 (2:75700087 G>A), RS1000616626 (2:75686545 T>C), RS1000688879 (2:75690949 T>A), RS1000753859 (2:75687424 A>C), RS1000893498 (2:75675174 T>C,G), RS1000954087 (2:75697211 T>C), RS1000954524 (2:75705266 T>A,C), RS1000977013 (2:75670851 T>G), RS1001077221 (2:75663922 G>A)

Disease associations

OMIM: gene MIM:189901 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

StudyTraitp-value
GCST001530_7Hippocampal atrophy5.000000e-08
GCST002449_1Plasma omega-6 polyunsaturated fatty acid levels (arachidonic acid)4.000000e-06
GCST002701_36Verbal declarative memory5.000000e-06
GCST003901_12Cognitive decline (age-related)3.000000e-06
GCST007576_269Chronotype2.000000e-10
GCST009391_647Metabolite levels5.000000e-07
GCST011678_1Depression in multiple sclerosis (post-diagnosis)3.000000e-06

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0005039hippocampal atrophy
EFO:0005680omega-6 polyunsaturated fatty acid measurement
EFO:0004874memory performance
EFO:0006805word list delayed recall measurement
EFO:0008328chronotype measurement
EFO:0010505isocitrate measurement

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
sodium arsenitedecreases expression, affects cotreatment, increases abundance, increases expression2
manganese chloridedecreases expression, affects cotreatment, increases abundance, increases expression2
Air Pollutantsdecreases expression, increases abundance, increases expression2
Arsenicaffects methylation, affects cotreatment, increases abundance, increases expression2
Manganeseincreases abundance, increases expression, decreases expression, affects cotreatment2
Particulate Matterdecreases expression, increases abundance, increases expression2
FR900359affects phosphorylation1
triphenyl phosphateaffects expression1
ochratoxin Adecreases expression1
aflatoxin B2decreases methylation1
tanespimycinincreases expression1
nutlin 3affects cotreatment, increases secretion1
abrineincreases expression1
5-(2,4-dihydroxy-5-isopropylphenyl)-4-(4-morpholin-4-ylmethylphenyl)isoxazole-3-carboxylic acid ethylamideincreases expression1
STA 9090increases expression1
bisphenol Saffects cotreatment, decreases methylation1
jinfukangdecreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibincreases expression1
Fulvestrantaffects cotreatment, decreases methylation1
Vorinostatincreases expression1
Benzo(a)pyreneincreases methylation1
Cadmiumincreases abundance, increases expression1
Caffeineincreases phosphorylation1
Dactinomycinaffects cotreatment, increases secretion1
Dichlorodiphenyl Dichloroethyleneincreases expression1
Diazinonincreases methylation1
Enzyme Inhibitorsincreases O-linked glycosylation, decreases activity1
Ivermectindecreases expression1
Methyl Methanesulfonateincreases 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): multiple sclerosis