HCFC2
gene geneOn this page
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
| Field | Value |
|---|---|
| HGNC ID | HGNC:24972 |
| Approved symbol | HCFC2 |
| Name | host cell factor C2 |
| Location | 12q23.3 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | HCF-2 |
| Ensembl gene | ENSG00000111727 |
| Ensembl biotype | protein_coding |
| OMIM | 607926 |
| Entrez | 29915 |
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
| Exon | Start | End |
|---|---|---|
| ENSE00001104674 | 104102959 | 104106524 |
| ENSE00001104675 | 104080746 | 104080830 |
| ENSE00001104678 | 104087986 | 104088038 |
| ENSE00001104682 | 104086847 | 104087014 |
| ENSE00001104685 | 104079445 | 104079653 |
| ENSE00001104687 | 104082713 | 104082901 |
| ENSE00001104691 | 104067947 | 104068107 |
| ENSE00001513397 | 104064531 | 104064723 |
| ENSE00003463160 | 104101968 | 104102153 |
| ENSE00003471401 | 104066167 | 104066315 |
| ENSE00003527177 | 104095360 | 104095563 |
| ENSE00003546291 | 104098343 | 104098480 |
| ENSE00003551467 | 104082500 | 104082606 |
| ENSE00003641940 | 104093386 | 104093563 |
| ENSE00003645368 | 104096360 | 104096433 |
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 ID | TPM avg | Samples expressed |
|---|---|---|
| 127724 | 3.3295 | 1411 |
Top tissues by expression
282 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| calcaneal tendon | UBERON:0003701 | 92.65 | gold quality |
| sperm | CL:0000019 | 92.10 | gold quality |
| left testis | UBERON:0004533 | 91.42 | gold quality |
| right testis | UBERON:0004534 | 90.71 | gold quality |
| testis | UBERON:0000473 | 90.64 | gold quality |
| germinal epithelium of ovary | UBERON:0001304 | 90.25 | gold quality |
| male germ cell | CL:0000015 | 89.60 | gold quality |
| cauda epididymis | UBERON:0004360 | 88.79 | gold quality |
| tendon | UBERON:0000043 | 88.28 | gold quality |
| mucosa of stomach | UBERON:0001199 | 87.76 | gold quality |
| muscle layer of sigmoid colon | UBERON:0035805 | 87.56 | gold quality |
| gastrocnemius | UBERON:0001388 | 87.14 | gold quality |
| biceps brachii | UBERON:0001507 | 87.13 | gold quality |
| adrenal tissue | UBERON:0018303 | 86.99 | gold quality |
| islet of Langerhans | UBERON:0000006 | 86.67 | gold quality |
| muscle of leg | UBERON:0001383 | 86.40 | gold quality |
| tibial artery | UBERON:0007610 | 86.34 | gold quality |
| popliteal artery | UBERON:0002250 | 86.33 | gold quality |
| oocyte | CL:0000023 | 86.22 | gold quality |
| lower esophagus muscularis layer | UBERON:0035833 | 86.07 | gold quality |
| lower esophagus | UBERON:0013473 | 86.05 | gold quality |
| skeletal muscle tissue of rectus abdominis | UBERON:0004511 | 86.00 | gold quality |
| esophagogastric junction muscularis propria | UBERON:0035841 | 85.97 | gold quality |
| colonic epithelium | UBERON:0000397 | 85.46 | gold quality |
| Brodmann (1909) area 23 | UBERON:0013554 | 85.44 | gold quality |
| cortical plate | UBERON:0005343 | 85.41 | gold quality |
| parietal pleura | UBERON:0002400 | 85.29 | gold quality |
| aorta | UBERON:0000947 | 85.01 | gold quality |
| visceral pleura | UBERON:0002401 | 84.95 | gold quality |
| skeletal muscle tissue of biceps brachii | UBERON:0004502 | 84.74 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 5.70 |
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):
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-30A-5P | 100.00 | 76.31 | 3233 |
| HSA-MIR-30B-5P | 100.00 | 76.29 | 3248 |
| HSA-MIR-30C-5P | 100.00 | 76.29 | 3248 |
| HSA-MIR-30D-5P | 100.00 | 76.32 | 3233 |
| HSA-MIR-30E-5P | 100.00 | 76.32 | 3242 |
| HSA-MIR-190A-3P | 100.00 | 80.35 | 5520 |
| HSA-MIR-5692A | 100.00 | 74.40 | 6850 |
| HSA-MIR-3163 | 100.00 | 77.23 | 8605 |
| HSA-MIR-5011-5P | 100.00 | 83.46 | 5820 |
| HSA-MIR-9-5P | 100.00 | 72.28 | 2361 |
| HSA-LET-7A-3P | 100.00 | 74.03 | 3932 |
| HSA-LET-7B-3P | 100.00 | 74.08 | 3913 |
| HSA-LET-7F-1-3P | 100.00 | 74.02 | 3928 |
| HSA-MIR-98-3P | 100.00 | 74.08 | 3907 |
| HSA-MIR-656-3P | 100.00 | 72.15 | 2788 |
| HSA-MIR-4668-3P | 100.00 | 68.74 | 2635 |
| HSA-MIR-3613-3P | 100.00 | 76.36 | 7965 |
| HSA-MIR-548AW | 99.99 | 72.57 | 3559 |
| HSA-MIR-548C-3P | 99.99 | 74.01 | 7587 |
| HSA-MIR-3667-3P | 99.99 | 67.17 | 1636 |
| HSA-MIR-3662 | 99.99 | 73.82 | 5684 |
| HSA-MIR-196A-1-3P | 99.99 | 72.15 | 2772 |
| HSA-MIR-4789-3P | 99.99 | 70.75 | 2484 |
| HSA-MIR-4500 | 99.99 | 72.72 | 2367 |
| HSA-MIR-19A-3P | 99.98 | 75.33 | 2762 |
| HSA-MIR-19B-3P | 99.98 | 75.44 | 2754 |
| HSA-MIR-520D-5P | 99.98 | 73.34 | 4883 |
| HSA-MIR-524-5P | 99.98 | 73.43 | 4882 |
| HSA-MIR-4775 | 99.98 | 75.00 | 6394 |
| HSA-MIR-5696 | 99.98 | 72.36 | 4487 |
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
| Organism | Symbol | Gene ID |
|---|---|---|
| mus_musculus | Hcfc2 | ENSMUSG00000020246 |
| rattus_norvegicus | Hcfc2 | ENSRNOG00000053510 |
| drosophila_melanogaster | Hcf | FBGN0039904 |
| caenorhabditis_elegans | WBGENE00001827 |
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 2 — Q9Y5Z7 (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 ID | Names | Canonical? |
|---|---|---|
| Q9Y5Z7-1 | 1 | yes |
| Q9Y5Z7-2 | 2 |
RefSeq proteins (1): NP_037452* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR003961 | FN3_dom | Domain |
| IPR011043 | Gal_Oxase/kelch_b-propeller | Homologous_superfamily |
| IPR013783 | Ig-like_fold | Homologous_superfamily |
| IPR015915 | Kelch-typ_b-propeller | Homologous_superfamily |
| IPR036116 | FN3_sf | Homologous_superfamily |
| IPR043536 | HCF1/2 | Family |
| IPR059124 | Kelch_HCF | Domain |
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)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9Y5Z7-F1 | 73.78 | 0.51 |
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
| ID | Pathway |
|---|---|
| R-HSA-9772755 | Formation 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:
| Category | Pathways |
|---|---|
| Epigenetic regulation by WDR5-containing histone modifying complexes | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cellular anatomical structure | 3 |
| transcription by RNA polymerase II | 2 |
| DNA-templated transcription | 2 |
| regulation of DNA-templated transcription | 2 |
| histone methyltransferase complex | 2 |
| regulation of transcription by RNA polymerase II | 1 |
| negative regulation of DNA-templated transcription | 1 |
| chromatin organization | 1 |
| regulation of gene expression | 1 |
| regulation of RNA biosynthetic process | 1 |
| biological_process | 1 |
| toll-like receptor 3 signaling pathway | 1 |
| regulation of cytoplasmic pattern recognition receptor signaling pathway | 1 |
| innate immune response | 1 |
| defense response to virus | 1 |
| immune response | 1 |
| response to exogenous dsRNA | 1 |
| positive regulation of RNA biosynthetic process | 1 |
| transcription coregulator activity | 1 |
| positive regulation of DNA-templated transcription | 1 |
| transcription regulator activity | 1 |
| binding | 1 |
| intracellular membrane-bounded organelle | 1 |
| nuclear lumen | 1 |
| intracellular anatomical structure | 1 |
| cytoplasm | 1 |
| membrane | 1 |
| cell periphery | 1 |
| nucleoplasm | 1 |
| methyltransferase complex | 1 |
| nuclear protein-containing complex | 1 |
| MLL1/2 complex | 1 |
Protein interactions and networks
STRING
774 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| HCFC2 | CREBZF | Q9NS37 | 971 |
| HCFC2 | CREB3 | O43889 | 868 |
| HCFC2 | POU2F1 | P14859 | 836 |
| HCFC2 | CREB3L4 | Q8TEY5 | 832 |
| HCFC2 | POU2F2 | P09086 | 764 |
| HCFC2 | WDR5 | P61964 | 560 |
| HCFC2 | RBBP5 | Q15291 | 556 |
| HCFC2 | IRF2 | P14316 | 506 |
| HCFC2 | TET1 | Q8NFU7 | 469 |
| HCFC2 | NPC1 | O15118 | 451 |
| HCFC2 | TMPRSS2 | O15393 | 448 |
| HCFC2 | PPARGC1A | Q9UBK2 | 441 |
| HCFC2 | TET2 | Q6N021 | 439 |
| HCFC2 | CTSB | P07858 | 433 |
| HCFC2 | RNF2 | Q99496 | 433 |
IntAct
64 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| WDR5 | KMT2D | psi-mi:“MI:0914”(association) | 0.910 |
| ASH2L | KMT2D | psi-mi:“MI:0914”(association) | 0.890 |
| RBBP5 | KMT2D | psi-mi:“MI:0914”(association) | 0.840 |
| RAMAC | RNMT | psi-mi:“MI:0914”(association) | 0.810 |
| NFE2L3 | MAFG | psi-mi:“MI:0914”(association) | 0.780 |
| BAP1 | OGT | psi-mi:“MI:0914”(association) | 0.730 |
| WDR5 | MEN1 | psi-mi:“MI:0914”(association) | 0.710 |
| HCFC2 | NUDCD3 | psi-mi:“MI:0915”(physical association) | 0.670 |
| CSNK2B | RPS6KA4 | psi-mi:“MI:0914”(association) | 0.640 |
| PPP2R2B | MYO9A | psi-mi:“MI:0914”(association) | 0.640 |
| KMT2A | MEN1 | psi-mi:“MI:0914”(association) | 0.640 |
| HCFC2 | SETD1A | psi-mi:“MI:0914”(association) | 0.530 |
| THAP2 | OGT | psi-mi:“MI:0914”(association) | 0.530 |
| IRF2 | CTSS | psi-mi:“MI:0914”(association) | 0.530 |
| CREB3 | MYO9A | psi-mi:“MI:0914”(association) | 0.530 |
| GLMN | MGST3 | psi-mi:“MI:0914”(association) | 0.530 |
| ZNF597 | HCFC1 | psi-mi:“MI:0914”(association) | 0.530 |
| BAP1 | HAT1 | psi-mi:“MI:0914”(association) | 0.530 |
| PPP2R2B | DDX3X | psi-mi:“MI:0914”(association) | 0.460 |
| FOXO3 | HCFC2 | psi-mi:“MI:0915”(physical association) | 0.400 |
| HCFC2 | SIRT1 | psi-mi:“MI:0915”(physical association) | 0.400 |
| HCFC2 | MEN1 | psi-mi:“MI:0915”(physical association) | 0.400 |
| NUDC | HCFC2 | psi-mi:“MI:0915”(physical association) | 0.400 |
| Set | ZKSCAN1 | psi-mi:“MI:0914”(association) | 0.350 |
| IRF2 | VWA8 | psi-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:
| Pathway | Partners | Fold | FDR |
|---|---|---|---|
| Formation of WDR5-containing histone-modifying complexes | 12 | 58.0× | 2e-16 |
| Deactivation of the beta-catenin transactivating complex | 6 | 25.4× | 7e-06 |
| Epigenetic regulation by WDR5-containing histone modifying complexes | 8 | 22.4× | 3e-07 |
| Epigenetic regulation of gene expression by MLL3 and MLL4 complexes | 6 | 21.5× | 2e-05 |
| Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells) | 7 | 18.6× | 7e-06 |
| PKMTs methylate histone lysines | 6 | 17.6× | 4e-05 |
| Formation of the beta-catenin:TCF transactivating complex | 8 | 17.5× | 1e-06 |
| RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function | 7 | 15.3× | 2e-05 |
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| transcription initiation-coupled chromatin remodeling | 5 | 26.6× | 2e-04 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
68 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 52 |
| Likely benign | 3 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
2238 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 12:104064722:GG:G | donor_gain | 1.0000 |
| 12:104064723:GG:G | donor_gain | 1.0000 |
| 12:104064723:GGT:G | donor_loss | 1.0000 |
| 12:104064724:GTAG:G | donor_loss | 1.0000 |
| 12:104064725:T:G | donor_loss | 1.0000 |
| 12:104066157:T:TA | acceptor_gain | 1.0000 |
| 12:104066158:G:A | acceptor_gain | 1.0000 |
| 12:104066161:A:AG | acceptor_gain | 1.0000 |
| 12:104066162:A:G | acceptor_gain | 1.0000 |
| 12:104066316:G:GG | donor_gain | 1.0000 |
| 12:104067942:TTTA:T | acceptor_loss | 1.0000 |
| 12:104067945:A:AG | acceptor_gain | 1.0000 |
| 12:104067946:G:A | acceptor_loss | 1.0000 |
| 12:104067946:G:GG | acceptor_gain | 1.0000 |
| 12:104067946:GGCAA:G | acceptor_gain | 1.0000 |
| 12:104068104:CCAGG:C | donor_loss | 1.0000 |
| 12:104068105:CAGGT:C | donor_loss | 1.0000 |
| 12:104068106:AGGTA:A | donor_loss | 1.0000 |
| 12:104068108:G:T | donor_loss | 1.0000 |
| 12:104068109:T:A | donor_loss | 1.0000 |
| 12:104080744:A:AG | acceptor_gain | 1.0000 |
| 12:104080745:G:GG | acceptor_gain | 1.0000 |
| 12:104080831:G:GG | donor_gain | 1.0000 |
| 12:104082711:A:AG | acceptor_gain | 1.0000 |
| 12:104082712:G:GA | acceptor_gain | 1.0000 |
| 12:104082712:GA:G | acceptor_gain | 1.0000 |
| 12:104082712:GAT:G | acceptor_gain | 1.0000 |
| 12:104082712:GATA:G | acceptor_gain | 1.0000 |
| 12:104082712:GATAC:G | acceptor_gain | 1.0000 |
| 12:104082902:GTAG:G | donor_gain | 1.0000 |
AlphaMissense
5159 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 12:104064619:C:A | P20H | 1.000 |
| 12:104064630:C:G | H24D | 1.000 |
| 12:104064631:A:G | H24R | 1.000 |
| 12:104064632:C:A | H24Q | 1.000 |
| 12:104064632:C:G | H24Q | 1.000 |
| 12:104064633:G:A | G25R | 1.000 |
| 12:104064633:G:C | G25R | 1.000 |
| 12:104064634:G:A | G25E | 1.000 |
| 12:104064634:G:T | G25V | 1.000 |
| 12:104064661:T:C | L34P | 1.000 |
| 12:104064675:G:A | G39R | 1.000 |
| 12:104064675:G:C | G39R | 1.000 |
| 12:104064676:G:A | G39E | 1.000 |
| 12:104064676:G:T | G39V | 1.000 |
| 12:104064678:G:A | G40R | 1.000 |
| 12:104064678:G:C | G40R | 1.000 |
| 12:104064678:G:T | G40W | 1.000 |
| 12:104064679:G:A | G40E | 1.000 |
| 12:104064679:G:T | G40V | 1.000 |
| 12:104064681:G:A | G41R | 1.000 |
| 12:104064681:G:C | G41R | 1.000 |
| 12:104064682:G:A | G41E | 1.000 |
| 12:104064686:T:A | N42K | 1.000 |
| 12:104064686:T:G | N42K | 1.000 |
| 12:104064690:G:C | G44R | 1.000 |
| 12:104064712:T:A | V51D | 1.000 |
| 12:104064714:T:G | Y52D | 1.000 |
| 12:104066178:T:A | W59R | 1.000 |
| 12:104066178:T:C | W59R | 1.000 |
| 12:104066180:G:C | W59C | 1.000 |
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):
| Study | Trait | p-value |
|---|---|---|
| GCST010320_5 | PR interval | 3.000000e-11 |
| GCST010321_76 | PR interval | 2.000000e-12 |
EFO canonical traits (1, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0004462 | PR 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.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | affects cotreatment, increases expression, decreases expression | 3 |
| Acetaminophen | decreases expression, increases expression | 2 |
| Cadmium Chloride | increases abundance, increases expression | 2 |
| bisphenol F | affects cotreatment, increases expression | 1 |
| TAK-243 | decreases sumoylation | 1 |
| methylmercuric chloride | decreases expression | 1 |
| triphenyl phosphate | affects expression | 1 |
| pirinixic acid | affects binding, decreases expression, increases activity | 1 |
| bisphenol A | affects cotreatment, increases expression | 1 |
| tris(1,3-dichloro-2-propyl)phosphate | increases expression | 1 |
| butyraldehyde | decreases expression | 1 |
| perfluorooctane sulfonic acid | decreases expression | 1 |
| CGP 52608 | increases reaction, affects binding | 1 |
| monomethylarsonous acid | increases expression | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | affects cotreatment, increases expression | 1 |
| ICG 001 | decreases expression | 1 |
| abrine | increases expression | 1 |
| dorsomorphin | affects cotreatment, increases expression | 1 |
| jinfukang | decreases expression, affects cotreatment | 1 |
| Resveratrol | affects cotreatment, increases expression | 1 |
| Sunitinib | increases expression | 1 |
| Air Pollutants | decreases expression, increases abundance | 1 |
| Cadmium | increases abundance, increases expression | 1 |
| Cisplatin | affects cotreatment, decreases expression | 1 |
| Dexamethasone | increases expression, affects cotreatment | 1 |
| Diazinon | increases methylation | 1 |
| Doxorubicin | decreases expression | 1 |
| Endosulfan | increases expression | 1 |
| Ethyl Methanesulfonate | increases expression | 1 |
| Indomethacin | affects cotreatment, increases expression | 1 |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.