PCBP4
gene geneOn this page
Also known as MCG10LIP4
Summary
PCBP4 (poly(rC) binding protein 4, HGNC:8652) is a protein-coding gene on chromosome 3p21.2, encoding Poly(rC)-binding protein 4 (P57723). Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.
This gene encodes a member of the KH-domain protein subfamily. Proteins of this subfamily, also referred to as alpha-CPs, bind to RNA with a specificity for C-rich pyrimidine regions. Alpha-CPs play important roles in post-transcriptional activities and have different cellular distributions. This gene is induced by the p53 tumor suppressor, and the encoded protein can suppress cell proliferation by inducing apoptosis and cell cycle arrest in G(2)-M. This gene’s protein is found in the cytoplasm, yet it lacks the nuclear localization signals found in other subfamily members. Multiple alternatively spliced transcript variants have been described, but the full-length nature for only some has been determined.
Source: NCBI Gene 57060 — RefSeq curated summary.
At a glance
- Clinical variants (ClinVar): 70 total
- MANE Select transcript:
NM_001174100
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:8652 |
| Approved symbol | PCBP4 |
| Name | poly(rC) binding protein 4 |
| Location | 3p21.2 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | MCG10, LIP4 |
| Ensembl gene | ENSG00000090097 |
| Ensembl biotype | protein_coding |
| OMIM | 608503 |
| Entrez | 57060 |
Gene structure
Transcript identifiers
Ensembl transcripts: 97 — 92 protein_coding, 4 retained_intron, 1 nonsense_mediated_decay
ENST00000322099, ENST00000355852, ENST00000428823, ENST00000461544, ENST00000461554, ENST00000466412, ENST00000468324, ENST00000471308, ENST00000471358, ENST00000471622, ENST00000483411, ENST00000484633, ENST00000489595, ENST00000490063, ENST00000492809, ENST00000497390, ENST00000497653, ENST00000498822, ENST00000893872, ENST00000893873, ENST00000893874, ENST00000893875, ENST00000893876, ENST00000893877, ENST00000893878, ENST00000893879, ENST00000893880, ENST00000893881, ENST00000893882, ENST00000893883, ENST00000893884, ENST00000893885, ENST00000893886, ENST00000893887, ENST00000893888, ENST00000893889, ENST00000893890, ENST00000893891, ENST00000893892, ENST00000893893, ENST00000893894, ENST00000913102, ENST00000913103, ENST00000913104, ENST00000913105, ENST00000913106, ENST00000913107, ENST00000913108, ENST00000913109, ENST00000913110, ENST00000913111, ENST00000913112, ENST00000913113, ENST00000913114, ENST00000913115, ENST00000913116, ENST00000913117, ENST00000913118, ENST00000913119, ENST00000913120, ENST00000952276, ENST00000952277, ENST00000952278, ENST00000952279, ENST00000952280, ENST00000952281, ENST00000952282, ENST00000952283, ENST00000952284, ENST00000952285, ENST00000952286, ENST00000952287, ENST00000952288, ENST00000952289, ENST00000952290, ENST00000952291, ENST00000952292, ENST00000952293, ENST00000952294, ENST00000952295, ENST00000952296, ENST00000952297, ENST00000952298, ENST00000952299, ENST00000952300, ENST00000952301, ENST00000952302, ENST00000952303, ENST00000952304, ENST00000952305, ENST00000952306, ENST00000952307, ENST00000952308, ENST00000952309, ENST00000952310, ENST00000952311, ENST00000952312
RefSeq mRNA: 5 — MANE Select: NM_001174100
NM_001174100, NM_001363885, NM_020418, NM_033008, NM_033010
CCDS: CCDS2839, CCDS2840, CCDS87085
Canonical transcript exons
ENST00000461554 — 14 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001938324 | 51967326 | 51967454 |
| ENSE00003477655 | 51959047 | 51959099 |
| ENSE00003498446 | 51959577 | 51959651 |
| ENSE00003506962 | 51960189 | 51960320 |
| ENSE00003628562 | 51959229 | 51959292 |
| ENSE00003649262 | 51959367 | 51959411 |
| ENSE00003655438 | 51957458 | 51958349 |
| ENSE00003677254 | 51959895 | 51960023 |
| ENSE00003683411 | 51958790 | 51958959 |
| ENSE00003708437 | 51961941 | 51962088 |
| ENSE00003780770 | 51961010 | 51961033 |
| ENSE00003781813 | 51961160 | 51961304 |
| ENSE00003781983 | 51960526 | 51960642 |
| ENSE00003785480 | 51960866 | 51960898 |
Expression profiles
Bgee: expression breadth ubiquitous, 273 present calls, max score 99.25.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 29.6100 / max 1314.0799, expressed in 1544 samples.
FANTOM5 promoters (11 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 42389 | 46.2963 | 1817 |
| 42379 | 22.1146 | 1509 |
| 42378 | 3.4896 | 1137 |
| 42377 | 1.6051 | 718 |
| 42381 | 0.5999 | 294 |
| 42383 | 0.4900 | 58 |
| 42384 | 0.4881 | 160 |
| 42382 | 0.4646 | 209 |
| 42376 | 0.1952 | 86 |
| 42385 | 0.1101 | 71 |
Top tissues by expression
292 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| right hemisphere of cerebellum | UBERON:0014890 | 99.25 | gold quality |
| cerebellar hemisphere | UBERON:0002245 | 99.18 | gold quality |
| cerebellar cortex | UBERON:0002129 | 99.13 | gold quality |
| C1 segment of cervical spinal cord | UBERON:0006469 | 98.35 | gold quality |
| tibial nerve | UBERON:0001323 | 98.21 | gold quality |
| cerebellum | UBERON:0002037 | 98.20 | gold quality |
| sural nerve | UBERON:0015488 | 98.11 | gold quality |
| spinal cord | UBERON:0002240 | 97.74 | gold quality |
| right frontal lobe | UBERON:0002810 | 97.31 | gold quality |
| hindlimb stylopod muscle | UBERON:0004252 | 97.30 | gold quality |
| gastrocnemius | UBERON:0001388 | 97.19 | gold quality |
| ganglionic eminence | UBERON:0004023 | 96.81 | gold quality |
| muscle of leg | UBERON:0001383 | 96.57 | gold quality |
| apex of heart | UBERON:0002098 | 96.48 | gold quality |
| amygdala | UBERON:0001876 | 96.38 | gold quality |
| cortical plate | UBERON:0005343 | 96.20 | gold quality |
| hypothalamus | UBERON:0001898 | 96.06 | gold quality |
| right atrium auricular region | UBERON:0006631 | 95.75 | gold quality |
| inferior vagus X ganglion | UBERON:0005363 | 95.73 | gold quality |
| cingulate cortex | UBERON:0003027 | 95.69 | gold quality |
| anterior cingulate cortex | UBERON:0009835 | 95.62 | gold quality |
| Brodmann (1909) area 9 | UBERON:0013540 | 95.49 | gold quality |
| inferior olivary complex | UBERON:0002127 | 95.11 | gold quality |
| ascending aorta | UBERON:0001496 | 94.95 | gold quality |
| putamen | UBERON:0001874 | 94.93 | gold quality |
| thoracic aorta | UBERON:0001515 | 94.90 | gold quality |
| olfactory bulb | UBERON:0002264 | 94.89 | gold quality |
| dorsal motor nucleus of vagus nerve | UBERON:0002870 | 94.63 | gold quality |
| descending thoracic aorta | UBERON:0002345 | 94.50 | gold quality |
| subthalamic nucleus | UBERON:0001906 | 94.49 | gold quality |
Single-cell (SCXA)
Detected in 8 experiment(s), a significant marker in 6.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-HCAD-5 | yes | 872.19 |
| E-HCAD-56 | yes | 856.68 |
| E-GEOD-93593 | yes | 732.18 |
| E-MTAB-6108 | yes | 621.13 |
| E-GEOD-137537 | yes | 13.09 |
| E-MTAB-11121 | no | 946.22 |
| E-MTAB-7316 | no | 29.29 |
| E-ANND-3 | no | 0.00 |
Regulation
Is transcription factor: no
Upstream regulators (CollecTRI, top): TP53
miRNA regulators (miRDB)
60 targeting PCBP4, 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-145-5P | 99.92 | 71.13 | 1836 |
| HSA-MIR-5195-3P | 99.92 | 70.92 | 1877 |
| HSA-MIR-497-5P | 99.92 | 71.83 | 2674 |
| HSA-MIR-15A-5P | 99.90 | 72.80 | 2787 |
| HSA-MIR-15B-5P | 99.90 | 72.78 | 2798 |
| HSA-MIR-16-5P | 99.90 | 72.80 | 2780 |
| HSA-MIR-195-5P | 99.90 | 72.81 | 2805 |
| HSA-MIR-424-5P | 99.89 | 71.90 | 2641 |
| HSA-MIR-6838-5P | 99.89 | 71.94 | 2690 |
| HSA-MIR-548AR-3P | 99.85 | 71.26 | 3889 |
| HSA-MIR-548AZ-3P | 99.82 | 70.56 | 3549 |
| HSA-MIR-548BC | 99.82 | 70.61 | 3524 |
| HSA-MIR-548E-3P | 99.82 | 70.59 | 3514 |
| HSA-MIR-548F-3P | 99.82 | 70.59 | 3540 |
| HSA-MIR-548A-3P | 99.76 | 70.58 | 3524 |
| HSA-MIR-92A-2-5P | 99.75 | 67.01 | 2164 |
| HSA-MIR-2116-3P | 99.74 | 64.32 | 889 |
| HSA-MIR-6752-3P | 99.72 | 66.71 | 1587 |
| HSA-MIR-580-3P | 99.67 | 69.23 | 1841 |
| HSA-MIR-10394-5P | 99.65 | 66.83 | 1852 |
| HSA-MIR-1205 | 99.65 | 66.76 | 1826 |
| HSA-MIR-3175 | 99.65 | 66.30 | 2031 |
| HSA-MIR-1827 | 99.63 | 68.57 | 3265 |
| HSA-MIR-12123 | 99.52 | 71.79 | 2990 |
| HSA-MIR-671-5P | 99.52 | 67.11 | 1277 |
| HSA-MIR-548G-3P | 99.48 | 68.67 | 2159 |
| HSA-MIR-4251 | 99.40 | 69.19 | 3363 |
| HSA-MIR-4797-5P | 99.39 | 68.01 | 1354 |
| HSA-MIR-532-3P | 99.34 | 65.76 | 1195 |
Literature-anchored findings (GeneRIF, showing 2)
- expression of alpha CP-4 can inhibit proliferation and tumorigenesis of lung cancer cells, both in vivo and in vitro, by delaying the progression of the cell cycle (PMID:17973258)
- PCBP4 plays important roles in the induction of cisplatin resistance in human maxillary cancers. (PMID:26196957)
Cross-species orthologs
11 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | pcbp4 | ENSDARG00000024276 |
| mus_musculus | Pcbp4 | ENSMUSG00000023495 |
| rattus_norvegicus | Pcbp4 | ENSRNOG00000012406 |
| drosophila_melanogaster | ps | FBGN0261552 |
| drosophila_melanogaster | mub | FBGN0262737 |
| drosophila_melanogaster | Imp | FBGN0285926 |
| caenorhabditis_elegans | WBGENE00003978 | |
| caenorhabditis_elegans | WBGENE00010908 | |
| caenorhabditis_elegans | WBGENE00013347 | |
| caenorhabditis_elegans | WBGENE00016489 | |
| caenorhabditis_elegans | fubl-4 | WBGENE00019692 |
Paralogs (12): IGF2BP2 (ENSG00000073792), KHSRP (ENSG00000088247), NOVA2 (ENSG00000104967), FUBP3 (ENSG00000107164), IGF2BP3 (ENSG00000136231), NOVA1 (ENSG00000139910), IGF2BP1 (ENSG00000159217), FUBP1 (ENSG00000162613), HNRNPK (ENSG00000165119), PCBP1 (ENSG00000169564), PCBP3 (ENSG00000183570), PCBP2 (ENSG00000197111)
Protein
Protein identifiers
Poly(rC)-binding protein 4 — P57723 (reviewed: P57723)
Alternative names: Alpha-CP4
All UniProt accessions (10): P57723, C9IZV9, C9J0A4, C9J5V4, C9J7A9, C9JSA6, C9JTY5, C9JZY3, C9K0A2, F8WC71
UniProt curated annotations — full annotation on UniProt →
Function. Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.
Subcellular location. Cytoplasm.
Isoforms (2)
| UniProt ID | Names | Canonical? |
|---|---|---|
| P57723-1 | 1 | yes |
| P57723-2 | 2 |
RefSeq proteins (5): NP_001167571, NP_001350814, NP_065151, NP_127501, NP_127503 (=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR004087 | KH_dom | Domain |
| IPR004088 | KH_dom_type_1 | Domain |
| IPR036612 | KH_dom_type_1_sf | Homologous_superfamily |
Pfam: PF00013
UniProt features (6 total): domain 3, chain 1, splice variant 1, sequence variant 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-P57723-F1 | 67.18 | 0.08 |
Function
Pathways and Gene Ontology
Reactome pathways
3 pathways
| ID | Pathway |
|---|---|
| R-HSA-6804116 | TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest |
| R-HSA-69895 | Transcriptional activation of cell cycle inhibitor p21 |
| R-HSA-9617828 | FOXO-mediated transcription of cell cycle genes |
MSigDB gene sets: 231 (showing top):
RNGTGGGC_UNKNOWN, CREL_01, GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GCANCTGNY_MYOD_Q6, GOBP_NEGATIVE_REGULATION_OF_RNA_SPLICING, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, TGACCTY_ERR1_Q2, GGGTGGRR_PAX4_03, CAGCTG_AP4_Q5, YY1_Q6, NFKB_Q6, MODULE_66, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION
GO Biological Process (5): regulation of transcription by RNA polymerase II (GO:0006357), regulation of mRNA stability (GO:0043488), negative regulation of mRNA splicing, via spliceosome (GO:0048025), regulation of gene expression (GO:0010468), regulation of mRNA metabolic process (GO:1903311)
GO Molecular Function (6): DNA binding (GO:0003677), RNA binding (GO:0003723), mRNA binding (GO:0003729), mRNA 3’-UTR binding (GO:0003730), nucleic acid binding (GO:0003676), protein binding (GO:0005515)
GO Cellular Component (4): nucleus (GO:0005634), cytoplasm (GO:0005737), cytosol (GO:0005829), ribonucleoprotein complex (GO:1990904)
Reactome top-level categories
Rollup of top-3 pathways:
| Category | Pathways |
|---|---|
| TP53 Regulates Transcription of Cell Cycle Genes | 1 |
| Transcriptional activation of p53 responsive genes | 1 |
| FOXO-mediated transcription | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| nucleic acid binding | 2 |
| binding | 2 |
| cellular anatomical structure | 2 |
| regulation of DNA-templated transcription | 1 |
| transcription by RNA polymerase II | 1 |
| regulation of RNA stability | 1 |
| regulation of mRNA catabolic process | 1 |
| mRNA splicing, via spliceosome | 1 |
| negative regulation of RNA splicing | 1 |
| regulation of mRNA splicing, via spliceosome | 1 |
| negative regulation of mRNA processing | 1 |
| gene expression | 1 |
| regulation of macromolecule biosynthetic process | 1 |
| mRNA metabolic process | 1 |
| regulation of RNA metabolic process | 1 |
| RNA binding | 1 |
| mRNA binding | 1 |
| intracellular membrane-bounded organelle | 1 |
| intracellular anatomical structure | 1 |
| cytoplasm | 1 |
| protein-containing complex | 1 |
Protein interactions and networks
STRING
1011 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| PCBP4 | TP53 | P04637 | 653 |
| PCBP4 | ZNF521 | Q96K83 | 620 |
| PCBP4 | VTA1 | Q9NP79 | 545 |
| PCBP4 | DNAJC14 | Q6Y2X3 | 526 |
| PCBP4 | RBM38 | Q9H0Z9 | 461 |
| PCBP4 | RBFOX2 | O43251 | 454 |
| PCBP4 | HNRNPDL | O14979 | 444 |
| PCBP4 | MBNL2 | Q5VZF2 | 418 |
| PCBP4 | ULK3 | Q6PHR2 | 415 |
| PCBP4 | ZNF709 | Q8N972 | 407 |
| PCBP4 | MBNL1 | Q9NR56 | 400 |
| PCBP4 | CNTROB | Q8N137 | 392 |
| PCBP4 | IP6K3 | Q96PC2 | 388 |
| PCBP4 | RBM8A | Q9Y5S9 | 377 |
| PCBP4 | SAMD7 | Q7Z3H4 | 364 |
IntAct
25 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| PCBP4 | HSPA8 | psi-mi:“MI:0915”(physical association) | 0.560 |
| MRPS18C | MRPS14 | psi-mi:“MI:0914”(association) | 0.530 |
| MIEN1 | PCBP4 | psi-mi:“MI:0915”(physical association) | 0.400 |
| PPDPFL | PCBP4 | psi-mi:“MI:0915”(physical association) | 0.400 |
| MRPL53 | psi-mi:“MI:0914”(association) | 0.350 | |
| ZNF664 | GAPDHS | psi-mi:“MI:0914”(association) | 0.350 |
| PHF5A | VPS26C | psi-mi:“MI:0914”(association) | 0.350 |
| TMEM126A | IPO7 | psi-mi:“MI:0914”(association) | 0.350 |
| GTF2A2 | S100P | psi-mi:“MI:0914”(association) | 0.350 |
| TXNDC8 | S100P | psi-mi:“MI:0914”(association) | 0.350 |
| ABCB9 | PIK3CA | psi-mi:“MI:0914”(association) | 0.350 |
| SSR3 | HMGCS2 | psi-mi:“MI:0914”(association) | 0.350 |
| SPMIP9 | PCBP4 | psi-mi:“MI:0914”(association) | 0.350 |
| PCBP4 | PPID | psi-mi:“MI:0914”(association) | 0.350 |
| PCBP4 | TUSC2 | psi-mi:“MI:0914”(association) | 0.350 |
| AFG2A | ESYT2 | psi-mi:“MI:0914”(association) | 0.350 |
| AFG2B | MMP24OS | psi-mi:“MI:0914”(association) | 0.350 |
| INSR | ATOX1 | psi-mi:“MI:0914”(association) | 0.350 |
| INSR | RIMOC1 | psi-mi:“MI:0914”(association) | 0.350 |
| RBFOX1 | PCBP4 | psi-mi:“MI:0915”(physical association) | 0.000 |
| PCBP1 | PCBP4 | psi-mi:“MI:0915”(physical association) | 0.000 |
| QKI | PCBP4 | psi-mi:“MI:0915”(physical association) | 0.000 |
| RNF138 | PCBP4 | psi-mi:“MI:0915”(physical association) | 0.000 |
BioGRID (55): PCBP1 (Affinity Capture-Western), PCBP4 (Affinity Capture-MS), PPID (Affinity Capture-MS), TRIM11 (Affinity Capture-MS), CSPG4 (Affinity Capture-MS), PPID (Affinity Capture-MS), TRIM11 (Affinity Capture-MS), CSPG4 (Affinity Capture-MS), PCBP4 (Affinity Capture-MS), DYNC1LI2 (Affinity Capture-MS), PCBP4 (Affinity Capture-MS), PCBP4 (Affinity Capture-MS), PCBP4 (Affinity Capture-MS), PCBP4 (Protein-RNA), PCBP4 (Proximity Label-MS)
ESM2 similar proteins: A0A1W2P872, A1L1C7, A4IIM2, B2RYD2, F1LQ48, O57406, O88532, O95319, P14866, P28659, P51513, P57723, P57724, Q28HE9, Q2PFW9, Q32PX7, Q3U0V1, Q3US41, Q4QQT3, Q4R535, Q58A45, Q5F3T7, Q5NVC8, Q5R8Y8, Q5R995, Q5U231, Q640Q5, Q6DGV1, Q6GPM1, Q6NXG1, Q6P0B1, Q6PF35, Q792H5, Q7T2T1, Q7TSY6, Q7ZXE2, Q80WA4, Q8R081, Q8UVD9, Q91WJ8
Diamond homologs: A0A0B4KGY6, A0A1W2P872, O00425, O19048, P38151, P51513, P57721, P57722, P57723, P57724, P60335, Q0VCU0, Q15365, Q15366, Q21920, Q2PFW9, Q5E9A3, Q5ZLP8, Q61990, Q80WA4, Q9CPN8, Q9JKN6, Q9SR13, Q9UNW9, A6ZKR5, A7TT46, B3LNH0, C5DIR2, C5E0I9, C7GND0, C8Z3W4, P38199, Q6CNI6, Q6FUD8, Q756R8, O42254, O57526, O73932, O75179, O88477
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
70 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 50 |
| Likely benign | 4 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
2225 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 3:51958783:CGCT:C | donor_loss | 1.0000 |
| 3:51958784:GCTCA:G | donor_loss | 1.0000 |
| 3:51958785:CT:C | donor_loss | 1.0000 |
| 3:51958786:TCACC:T | donor_loss | 1.0000 |
| 3:51958787:CA:C | donor_loss | 1.0000 |
| 3:51958788:A:AC | donor_gain | 1.0000 |
| 3:51958788:A:C | donor_loss | 1.0000 |
| 3:51958789:C:CC | donor_gain | 1.0000 |
| 3:51958789:CCAGG:C | donor_gain | 1.0000 |
| 3:51958955:ATCAA:A | acceptor_gain | 1.0000 |
| 3:51958956:TCAA:T | acceptor_gain | 1.0000 |
| 3:51958957:CAA:C | acceptor_gain | 1.0000 |
| 3:51958957:CAAC:C | acceptor_gain | 1.0000 |
| 3:51958958:A:T | acceptor_gain | 1.0000 |
| 3:51958958:AA:A | acceptor_gain | 1.0000 |
| 3:51958959:AC:A | acceptor_loss | 1.0000 |
| 3:51958960:C:CA | acceptor_loss | 1.0000 |
| 3:51958960:C:CC | acceptor_gain | 1.0000 |
| 3:51959041:GCTCA:G | donor_loss | 1.0000 |
| 3:51959042:CTCA:C | donor_loss | 1.0000 |
| 3:51959043:TCAC:T | donor_loss | 1.0000 |
| 3:51959044:CA:C | donor_loss | 1.0000 |
| 3:51959045:A:AC | donor_gain | 1.0000 |
| 3:51959045:A:C | donor_loss | 1.0000 |
| 3:51959046:C:CC | donor_gain | 1.0000 |
| 3:51959046:CATCG:C | donor_gain | 1.0000 |
| 3:51959095:CAGTC:C | acceptor_gain | 1.0000 |
| 3:51959097:GTC:G | acceptor_gain | 1.0000 |
| 3:51959098:TC:T | acceptor_gain | 1.0000 |
| 3:51959099:CC:C | acceptor_gain | 1.0000 |
AlphaMissense
2567 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 3:51958802:A:G | L304P | 1.000 |
| 3:51958811:G:T | A301D | 1.000 |
| 3:51958836:C:G | G293R | 1.000 |
| 3:51958841:A:T | I291N | 1.000 |
| 3:51958847:A:T | V289D | 1.000 |
| 3:51958889:A:C | I275S | 1.000 |
| 3:51958889:A:G | I275T | 1.000 |
| 3:51958889:A:T | I275N | 1.000 |
| 3:51958910:C:G | R268P | 1.000 |
| 3:51958913:A:C | I267S | 1.000 |
| 3:51958922:A:C | I264S | 1.000 |
| 3:51958922:A:G | I264T | 1.000 |
| 3:51958922:A:T | I264N | 1.000 |
| 3:51958931:C:T | G261D | 1.000 |
| 3:51958940:C:A | G258V | 1.000 |
| 3:51958940:C:T | G258E | 1.000 |
| 3:51958943:A:T | I257N | 1.000 |
| 3:51958952:C:T | G254D | 1.000 |
| 3:51959057:A:T | V248D | 1.000 |
| 3:51959624:A:C | Y182D | 1.000 |
| 3:51959925:A:C | C162W | 1.000 |
| 3:51959926:C:T | C162Y | 1.000 |
| 3:51959927:A:G | C162R | 1.000 |
| 3:51959950:C:A | G154V | 1.000 |
| 3:51959950:C:T | G154E | 1.000 |
| 3:51959951:C:A | G154W | 1.000 |
| 3:51959951:C:G | G154R | 1.000 |
| 3:51959951:C:T | G154R | 1.000 |
| 3:51959956:A:T | V152E | 1.000 |
| 3:51959962:A:T | V150D | 1.000 |
dbSNP variants (sampled 300 via entrez): RS1000387144 (3:51962201 T>C), RS1000596514 (3:51966673 C>T), RS1000651797 (3:51957116 G>A,T), RS1000663011 (3:51959748 G>A), RS1000814477 (3:51963546 A>T), RS1000883490 (3:51961888 G>A,T), RS1000931956 (3:51966408 G>C,T), RS1001118988 (3:51963914 CT>C), RS1001217335 (3:51957657 G>T), RS1001224577 (3:51962657 C>T), RS1001359207 (3:51969037 G>A), RS1001369210 (3:51968676 C>G), RS1001483241 (3:51963280 G>A), RS1001716686 (3:51962348 C>G), RS1002056785 (3:51957968 G>C)
Disease associations
OMIM: gene MIM:608503 | disease phenotypes:
GenCC curated gene-disease
Mondo (0):
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
0 associations (top):
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
44 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| trichostatin A | affects cotreatment, increases expression | 3 |
| Cyclosporine | increases expression, decreases expression | 3 |
| Air Pollutants | increases expression, decreases expression, affects cotreatment, increases abundance | 2 |
| Benzo(a)pyrene | decreases methylation, increases expression, increases methylation | 2 |
| Valproic Acid | increases methylation, affects expression, decreases expression | 2 |
| alpha-pinene | affects cotreatment, increases expression, increases abundance | 1 |
| pirinixic acid | affects binding, decreases expression, increases activity | 1 |
| bisphenol A | affects cotreatment, decreases methylation | 1 |
| bromoacetate | decreases expression | 1 |
| sulforaphane | decreases expression | 1 |
| delphinidin | affects expression | 1 |
| potassium chromate(VI) | decreases expression | 1 |
| methacrylaldehyde | affects cotreatment, increases expression, increases abundance | 1 |
| beta-methylcholine | affects expression | 1 |
| di-n-butylphosphoric acid | affects expression | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | affects cotreatment, decreases expression, increases expression | 1 |
| dorsomorphin | decreases expression, increases expression, affects cotreatment | 1 |
| SRT2183 | increases expression | 1 |
| jinfukang | affects cotreatment, increases expression | 1 |
| brevetoxin 2 | increases expression | 1 |
| MT19c compound | decreases expression | 1 |
| Resveratrol | affects cotreatment, decreases expression | 1 |
| Sunitinib | decreases expression | 1 |
| Fulvestrant | affects cotreatment, decreases methylation | 1 |
| Acrolein | affects cotreatment, increases expression, increases abundance | 1 |
| Cisplatin | affects cotreatment, increases expression | 1 |
| Diazinon | increases methylation | 1 |
| Ethyl Methanesulfonate | increases expression | 1 |
| Methyl Methanesulfonate | increases expression | 1 |
| Ozone | affects cotreatment, increases expression, increases abundance | 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.