GCFC2
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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
| Field | Value |
|---|---|
| HGNC ID | HGNC:1317 |
| Approved symbol | GCFC2 |
| Name | GC-rich sequence DNA-binding factor 2 |
| Location | 2p12 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | DNABF, GCF |
| Ensembl gene | ENSG00000005436 |
| Ensembl biotype | protein_coding |
| OMIM | 189901 |
| Entrez | 6936 |
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
| Exon | Start | End |
|---|---|---|
| ENSE00001261900 | 75710591 | 75710915 |
| ENSE00003465078 | 75662705 | 75664783 |
| ENSE00003474620 | 75673444 | 75673520 |
| ENSE00003475605 | 75671950 | 75672016 |
| ENSE00003492242 | 75696200 | 75696315 |
| ENSE00003522865 | 75680193 | 75680314 |
| ENSE00003535454 | 75691977 | 75692100 |
| ENSE00003556420 | 75690638 | 75690719 |
| ENSE00003563051 | 75670138 | 75670284 |
| ENSE00003566359 | 75687827 | 75687977 |
| ENSE00003582023 | 75665929 | 75666053 |
| ENSE00003593081 | 75689969 | 75690081 |
| ENSE00003608878 | 75702199 | 75702423 |
| ENSE00003615519 | 75689026 | 75689225 |
| ENSE00003651464 | 75706523 | 75706651 |
| ENSE00003663933 | 75694241 | 75694427 |
| ENSE00003668748 | 75701190 | 75701287 |
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 ID | TPM avg | Samples expressed |
|---|---|---|
| 29285 | 11.4934 | 1780 |
| 29286 | 0.2993 | 147 |
Top tissues by expression
289 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| ventricular zone | UBERON:0003053 | 92.34 | gold quality |
| gastrocnemius | UBERON:0001388 | 92.02 | gold quality |
| muscle of leg | UBERON:0001383 | 91.65 | gold quality |
| right lobe of liver | UBERON:0001114 | 91.32 | gold quality |
| calcaneal tendon | UBERON:0003701 | 90.75 | gold quality |
| adrenal tissue | UBERON:0018303 | 90.21 | gold quality |
| endocervix | UBERON:0000458 | 90.00 | gold quality |
| hindlimb stylopod muscle | UBERON:0004252 | 90.00 | gold quality |
| right uterine tube | UBERON:0001302 | 89.77 | gold quality |
| body of pancreas | UBERON:0001150 | 89.71 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 89.58 | gold quality |
| muscle organ | UBERON:0001630 | 89.38 | gold quality |
| ectocervix | UBERON:0012249 | 89.34 | gold quality |
| left ovary | UBERON:0002119 | 89.06 | gold quality |
| ganglionic eminence | UBERON:0004023 | 88.96 | gold quality |
| metanephros cortex | UBERON:0010533 | 88.86 | gold quality |
| olfactory segment of nasal mucosa | UBERON:0005386 | 88.85 | gold quality |
| right ovary | UBERON:0002118 | 88.76 | gold quality |
| right lobe of thyroid gland | UBERON:0001119 | 88.61 | gold quality |
| tibial nerve | UBERON:0001323 | 88.46 | gold quality |
| left lobe of thyroid gland | UBERON:0001120 | 88.28 | gold quality |
| body of uterus | UBERON:0009853 | 88.21 | gold quality |
| left uterine tube | UBERON:0001303 | 88.18 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 88.01 | gold quality |
| thyroid gland | UBERON:0002046 | 87.39 | gold quality |
| mucosa of stomach | UBERON:0001199 | 87.35 | gold quality |
| C1 segment of cervical spinal cord | UBERON:0006469 | 87.03 | gold quality |
| adenohypophysis | UBERON:0002196 | 87.00 | gold quality |
| right coronary artery | UBERON:0001625 | 86.82 | gold quality |
| skin of abdomen | UBERON:0001416 | 86.80 | gold quality |
Single-cell (SCXA)
Detected in 2 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 5.44 |
| E-MTAB-4850 | no | 1178.85 |
Regulation
Is transcription factor: yes
Downstream targets (CollecTRI)
7 targets.
| Target | Regulation |
|---|---|
| EGF | |
| EGFR | Repression |
| 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):
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-3613-3P | 100.00 | 76.36 | 7965 |
| HSA-MIR-1277-5P | 100.00 | 73.95 | 5056 |
| HSA-MIR-4668-3P | 100.00 | 68.74 | 2635 |
| HSA-MIR-548C-3P | 99.99 | 74.01 | 7587 |
| HSA-MIR-186-5P | 99.99 | 70.83 | 3707 |
| HSA-MIR-548AW | 99.99 | 72.57 | 3559 |
| HSA-MIR-3662 | 99.99 | 73.82 | 5684 |
| HSA-MIR-371B-5P | 99.99 | 75.34 | 4759 |
| HSA-MIR-4282 | 99.99 | 75.36 | 6408 |
| HSA-MIR-568 | 99.98 | 69.86 | 2084 |
| HSA-MIR-373-5P | 99.98 | 75.36 | 4753 |
| HSA-MIR-616-5P | 99.98 | 75.58 | 4775 |
| HSA-MIR-3065-5P | 99.97 | 71.56 | 3281 |
| HSA-MIR-607 | 99.97 | 73.62 | 5593 |
| HSA-MIR-1468-3P | 99.96 | 72.74 | 3797 |
| HSA-MIR-146A-5P | 99.96 | 68.93 | 988 |
| HSA-MIR-146B-5P | 99.96 | 69.13 | 977 |
| HSA-MIR-1250-3P | 99.96 | 70.04 | 4038 |
| HSA-MIR-4666A-3P | 99.96 | 71.71 | 3434 |
| HSA-MIR-9-3P | 99.96 | 70.88 | 2068 |
| HSA-MIR-7153-5P | 99.94 | 68.89 | 1006 |
| HSA-MIR-3143 | 99.93 | 71.96 | 3104 |
| HSA-MIR-335-3P | 99.93 | 73.36 | 4958 |
| HSA-MIR-205-3P | 99.92 | 69.92 | 3165 |
| HSA-MIR-338-5P | 99.92 | 72.34 | 2951 |
| HSA-MIR-1305 | 99.91 | 71.43 | 3443 |
| HSA-MIR-3671 | 99.90 | 73.04 | 3897 |
| HSA-MIR-153-5P | 99.89 | 73.86 | 6317 |
| HSA-MIR-6780A-5P | 99.88 | 66.69 | 2776 |
| HSA-MIR-4728-5P | 99.85 | 69.39 | 4718 |
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
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | gcfc2 | ENSDARG00000079020 |
| mus_musculus | Gcfc2 | ENSMUSG00000035125 |
| rattus_norvegicus | Gcfc2 | ENSRNOG00000006888 |
| drosophila_melanogaster | CG1965 | FBGN0037466 |
| caenorhabditis_elegans | mog-7 | WBGENE00009672 |
Paralogs (1): PAXBP1 (ENSG00000159086)
Protein
Protein identifiers
Intron Large complex component GCFC2 — P16383 (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 ID | Names | Canonical? |
|---|---|---|
| P16383-1 | 1 | yes |
| P16383-2 | 2 | |
| P16383-3 | 3 | |
| P16383-4 | 4 |
RefSeq proteins (4): NP_001188263, NP_001188264, NP_001397774, NP_003194* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR012890 | GCFC2-like | Family |
| IPR022783 | GCFC_dom | Domain |
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)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-P16383-F1 | 74.12 | 0.44 |
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
| ID | Pathway |
|---|---|
| R-HSA-72163 | mRNA 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:
| Category | Pathways |
|---|---|
| mRNA Splicing | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| RNA processing | 2 |
| nuclear lumen | 2 |
| cellular anatomical structure | 2 |
| mRNA splicing, via spliceosome | 1 |
| protein-RNA complex assembly | 1 |
| RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 1 |
| mRNA processing | 1 |
| mRNA metabolic process | 1 |
| nucleic acid binding | 1 |
| binding | 1 |
| intracellular membrane-bounded organelle | 1 |
| intracellular membraneless organelle | 1 |
| cytoplasm | 1 |
| U2-type spliceosomal complex | 1 |
| U6 snRNP | 1 |
| post-mRNA release spliceosomal complex | 1 |
Protein interactions and networks
STRING
906 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| GCFC2 | LRRFIP1 | Q32MZ4 | 845 |
| GCFC2 | KIAA0319 | Q5VV43 | 780 |
| GCFC2 | MRPL19 | P49406 | 773 |
| GCFC2 | DNAAF4 | Q8WXU2 | 773 |
| GCFC2 | DCDC2 | Q9UHG0 | 766 |
| GCFC2 | FLII | Q13045 | 763 |
| GCFC2 | KNL1 | Q8NG31 | 689 |
| GCFC2 | TFIP11 | Q9UBB9 | 650 |
| GCFC2 | RBM8A | Q9Y5S9 | 640 |
| GCFC2 | ROBO1 | Q9Y6N7 | 582 |
| GCFC2 | KIAA0319L | Q8IZA0 | 580 |
| GCFC2 | ATP2C2 | O75185 | 577 |
| GCFC2 | CMIP | Q8IY22 | 573 |
| GCFC2 | SRY | Q05066 | 571 |
| GCFC2 | DHX15 | O43143 | 567 |
IntAct
62 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| PPIE | AQR | psi-mi:“MI:0914”(association) | 0.810 |
| GCFC2 | TFIP11 | psi-mi:“MI:0915”(physical association) | 0.670 |
| SNRPB | PRMT5 | psi-mi:“MI:0914”(association) | 0.670 |
| SNRPA1 | HTATSF1 | psi-mi:“MI:0914”(association) | 0.640 |
| HDAC11 | CLUH | psi-mi:“MI:0914”(association) | 0.640 |
| GCFC2 | SNRNP200 | psi-mi:“MI:0914”(association) | 0.640 |
| SNRPA1 | U2SURP | psi-mi:“MI:0914”(association) | 0.640 |
| TFIP11 | DHX15 | psi-mi:“MI:0914”(association) | 0.600 |
| SNRPE | PRMT5 | psi-mi:“MI:0914”(association) | 0.530 |
| SNRPE | SNRPGP15 | psi-mi:“MI:0914”(association) | 0.530 |
| ELAVL2 | IGF2BP3 | psi-mi:“MI:0914”(association) | 0.530 |
| YJU2B | RCCD1 | psi-mi:“MI:0914”(association) | 0.530 |
| LPAR1 | TMEM223 | psi-mi:“MI:0914”(association) | 0.530 |
| GCFC2 | DHX15 | psi-mi:“MI:0914”(association) | 0.530 |
| CRK | GCFC2 | psi-mi:“MI:0915”(physical association) | 0.400 |
| GCFC2 | FYN | psi-mi:“MI:0915”(physical association) | 0.400 |
| GCFC2 | VIM | psi-mi:“MI:0915”(physical association) | 0.400 |
| CREB3L2 | GCFC2 | psi-mi:“MI:0915”(physical association) | 0.370 |
| SLF2 | GCFC2 | psi-mi:“MI:0914”(association) | 0.350 |
| CDK8 | CCNC | psi-mi:“MI:0914”(association) | 0.350 |
| HNRNPD | ARHGAP32 | psi-mi:“MI:0914”(association) | 0.350 |
| SYNCRIP | ARHGAP32 | psi-mi:“MI:0914”(association) | 0.350 |
| DHX15 | BBX | psi-mi:“MI:0914”(association) | 0.350 |
| BSG | METTL15 | psi-mi:“MI:0914”(association) | 0.350 |
| ELAVL2 | IGF2BP3 | psi-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:
| Pathway | Partners | Fold | FDR |
|---|---|---|---|
| mRNA Splicing | 10 | 21.5× | 2e-09 |
| mRNA Splicing - Major Pathway | 17 | 18.2× | 4e-15 |
| Processing of Capped Intron-Containing Pre-mRNA | 11 | 17.7× | 2e-09 |
| Dengue Virus-Host Interactions | 15 | 13.4× | 2e-11 |
| mRNA Polyadenylation | 7 | 12.1× | 7e-05 |
| CHD1 and CHD2 subfamily | 5 | 10.7× | 3e-03 |
| Metabolism of RNA | 12 | 9.8× | 1e-07 |
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| mRNA splicing, via spliceosome | 17 | 23.6× | 1e-16 |
| RNA processing | 7 | 23.2× | 4e-06 |
| RNA splicing | 8 | 10.7× | 1e-04 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
123 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 90 |
| Likely benign | 12 |
| Benign | 1 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
3954 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 2:75652213:A:G | donor_gain | 1.0000 |
| 2:75652261:GTCA:G | donor_gain | 1.0000 |
| 2:75652265:G:GG | donor_gain | 1.0000 |
| 2:75652269:GAGCT:G | donor_gain | 1.0000 |
| 2:75652271:GCT:G | donor_gain | 1.0000 |
| 2:75652512:T:TA | acceptor_gain | 1.0000 |
| 2:75652515:A:AG | acceptor_gain | 1.0000 |
| 2:75652516:T:G | acceptor_gain | 1.0000 |
| 2:75652518:T:TA | acceptor_gain | 1.0000 |
| 2:75652518:TGTA:T | acceptor_loss | 1.0000 |
| 2:75652520:TA:T | acceptor_loss | 1.0000 |
| 2:75652521:A:G | acceptor_loss | 1.0000 |
| 2:75652521:AG:A | acceptor_gain | 1.0000 |
| 2:75652522:GG:G | acceptor_gain | 1.0000 |
| 2:75652522:GGAA:G | acceptor_gain | 1.0000 |
| 2:75652653:ACAAG:A | donor_gain | 1.0000 |
| 2:75652654:CAAG:C | donor_gain | 1.0000 |
| 2:75652654:CAAGG:C | donor_loss | 1.0000 |
| 2:75652655:AAGG:A | donor_loss | 1.0000 |
| 2:75652656:AG:A | donor_gain | 1.0000 |
| 2:75652657:GG:G | donor_gain | 1.0000 |
| 2:75652657:GGTA:G | donor_loss | 1.0000 |
| 2:75652658:G:GG | donor_gain | 1.0000 |
| 2:75652658:GTAA:G | donor_loss | 1.0000 |
| 2:75664779:CATCC:C | acceptor_gain | 1.0000 |
| 2:75664781:TCC:T | acceptor_gain | 1.0000 |
| 2:75664781:TCCCT:T | acceptor_loss | 1.0000 |
| 2:75664782:CC:C | acceptor_gain | 1.0000 |
| 2:75664782:CCC:C | acceptor_gain | 1.0000 |
| 2:75664782:CCCT:C | acceptor_loss | 1.0000 |
AlphaMissense
5174 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 2:75680297:A:G | W570R | 0.994 |
| 2:75680297:A:T | W570R | 0.994 |
| 2:75687947:A:G | W524R | 0.990 |
| 2:75687947:A:T | W524R | 0.990 |
| 2:75689136:A:G | W477R | 0.989 |
| 2:75689136:A:T | W477R | 0.989 |
| 2:75689132:C:G | R478P | 0.988 |
| 2:75670263:A:G | W660R | 0.987 |
| 2:75670263:A:T | W660R | 0.987 |
| 2:75673464:A:C | F623L | 0.973 |
| 2:75673464:A:T | F623L | 0.973 |
| 2:75673466:A:G | F623L | 0.973 |
| 2:75689040:A:G | W509R | 0.971 |
| 2:75689040:A:T | W509R | 0.971 |
| 2:75680295:C:A | W570C | 0.970 |
| 2:75680295:C:G | W570C | 0.970 |
| 2:75694251:A:G | L337P | 0.969 |
| 2:75689134:C:A | W477C | 0.968 |
| 2:75689134:C:G | W477C | 0.968 |
| 2:75689135:C:G | W477S | 0.966 |
| 2:75701229:C:A | W226C | 0.965 |
| 2:75701229:C:G | W226C | 0.965 |
| 2:75689057:C:G | R503P | 0.963 |
| 2:75689112:A:C | Y485D | 0.963 |
| 2:75666029:A:G | W710R | 0.962 |
| 2:75666029:A:T | W710R | 0.962 |
| 2:75680285:A:G | S574P | 0.961 |
| 2:75690018:A:C | S430R | 0.961 |
| 2:75690018:A:T | S430R | 0.961 |
| 2:75690020:T:G | S430R | 0.961 |
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):
| Study | Trait | p-value |
|---|---|---|
| GCST001530_7 | Hippocampal atrophy | 5.000000e-08 |
| GCST002449_1 | Plasma omega-6 polyunsaturated fatty acid levels (arachidonic acid) | 4.000000e-06 |
| GCST002701_36 | Verbal declarative memory | 5.000000e-06 |
| GCST003901_12 | Cognitive decline (age-related) | 3.000000e-06 |
| GCST007576_269 | Chronotype | 2.000000e-10 |
| GCST009391_647 | Metabolite levels | 5.000000e-07 |
| GCST011678_1 | Depression in multiple sclerosis (post-diagnosis) | 3.000000e-06 |
EFO canonical traits (6, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0005039 | hippocampal atrophy |
| EFO:0005680 | omega-6 polyunsaturated fatty acid measurement |
| EFO:0004874 | memory performance |
| EFO:0006805 | word list delayed recall measurement |
| EFO:0008328 | chronotype measurement |
| EFO:0010505 | isocitrate 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.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| sodium arsenite | decreases expression, affects cotreatment, increases abundance, increases expression | 2 |
| manganese chloride | decreases expression, affects cotreatment, increases abundance, increases expression | 2 |
| Air Pollutants | decreases expression, increases abundance, increases expression | 2 |
| Arsenic | affects methylation, affects cotreatment, increases abundance, increases expression | 2 |
| Manganese | increases abundance, increases expression, decreases expression, affects cotreatment | 2 |
| Particulate Matter | decreases expression, increases abundance, increases expression | 2 |
| FR900359 | affects phosphorylation | 1 |
| triphenyl phosphate | affects expression | 1 |
| ochratoxin A | decreases expression | 1 |
| aflatoxin B2 | decreases methylation | 1 |
| tanespimycin | increases expression | 1 |
| nutlin 3 | affects cotreatment, increases secretion | 1 |
| abrine | increases expression | 1 |
| 5-(2,4-dihydroxy-5-isopropylphenyl)-4-(4-morpholin-4-ylmethylphenyl)isoxazole-3-carboxylic acid ethylamide | increases expression | 1 |
| STA 9090 | increases expression | 1 |
| bisphenol S | affects cotreatment, decreases methylation | 1 |
| jinfukang | decreases expression | 1 |
| Resveratrol | affects cotreatment, increases expression | 1 |
| Sunitinib | increases expression | 1 |
| Fulvestrant | affects cotreatment, decreases methylation | 1 |
| Vorinostat | increases expression | 1 |
| Benzo(a)pyrene | increases methylation | 1 |
| Cadmium | increases abundance, increases expression | 1 |
| Caffeine | increases phosphorylation | 1 |
| Dactinomycin | affects cotreatment, increases secretion | 1 |
| Dichlorodiphenyl Dichloroethylene | increases expression | 1 |
| Diazinon | increases methylation | 1 |
| Enzyme Inhibitors | increases O-linked glycosylation, decreases activity | 1 |
| Ivermectin | decreases expression | 1 |
| Methyl Methanesulfonate | increases expression | 1 |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): multiple sclerosis