EDC4
gene geneOn this page
Also known as RCD-8Ge-1HEDLS
Summary
EDC4 (enhancer of mRNA decapping 4, HGNC:17157) is a protein-coding gene on chromosome 16q22.1, encoding Enhancer of mRNA-decapping protein 4 (Q6P2E9). In the process of mRNA degradation, seems to play a role in mRNA decapping. It is a selective cancer dependency (DepMap: 29.8% of cell lines).
Predicted to be involved in deadenylation-independent decapping of nuclear-transcribed mRNA. Located in P-body and nucleoplasm.
Source: NCBI Gene 23644 — RefSeq curated summary.
At a glance
- GWAS associations: 5
- Clinical variants (ClinVar): 188 total
- Cancer dependency (DepMap): dependent in 29.8% of screened cell lines
- MANE Select transcript:
NM_014329
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:17157 |
| Approved symbol | EDC4 |
| Name | enhancer of mRNA decapping 4 |
| Location | 16q22.1 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | RCD-8, Ge-1, HEDLS |
| Ensembl gene | ENSG00000038358 |
| Ensembl biotype | protein_coding |
| OMIM | 606030 |
| Entrez | 23644 |
Gene structure
Transcript identifiers
Ensembl transcripts: 31 — 21 protein_coding, 9 retained_intron, 1 protein_coding_CDS_not_defined
ENST00000358933, ENST00000536072, ENST00000572031, ENST00000572221, ENST00000572724, ENST00000573985, ENST00000573992, ENST00000574770, ENST00000575033, ENST00000575507, ENST00000575514, ENST00000576972, ENST00000577028, ENST00000577105, ENST00000851718, ENST00000851719, ENST00000851720, ENST00000851721, ENST00000851722, ENST00000851723, ENST00000851724, ENST00000851725, ENST00000851726, ENST00000851727, ENST00000851728, ENST00000936214, ENST00000936215, ENST00000936216, ENST00000969096, ENST00000969097, ENST00000969098
RefSeq mRNA: 2 — MANE Select: NM_014329
NM_001427345, NM_014329
CCDS: CCDS10849
Canonical transcript exons
ENST00000358933 — 29 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001550467 | 67883956 | 67884499 |
| ENSE00002669059 | 67873052 | 67873343 |
| ENSE00003468969 | 67878166 | 67878275 |
| ENSE00003482797 | 67880063 | 67880216 |
| ENSE00003486215 | 67882958 | 67883177 |
| ENSE00003497927 | 67881076 | 67881180 |
| ENSE00003509274 | 67881497 | 67881533 |
| ENSE00003510241 | 67875945 | 67876101 |
| ENSE00003520171 | 67879850 | 67879971 |
| ENSE00003523061 | 67876488 | 67876599 |
| ENSE00003527880 | 67879237 | 67879309 |
| ENSE00003528403 | 67882679 | 67882865 |
| ENSE00003563163 | 67881954 | 67882109 |
| ENSE00003563494 | 67882212 | 67882327 |
| ENSE00003569209 | 67877217 | 67877406 |
| ENSE00003571531 | 67881265 | 67881417 |
| ENSE00003589857 | 67878360 | 67878443 |
| ENSE00003595191 | 67876873 | 67876972 |
| ENSE00003595822 | 67878957 | 67879137 |
| ENSE00003597572 | 67880557 | 67880990 |
| ENSE00003629028 | 67877509 | 67877656 |
| ENSE00003644293 | 67879412 | 67879503 |
| ENSE00003651102 | 67882429 | 67882594 |
| ENSE00003661882 | 67877741 | 67877845 |
| ENSE00003668741 | 67879587 | 67879774 |
| ENSE00003669157 | 67881668 | 67881845 |
| ENSE00003678079 | 67878737 | 67878839 |
| ENSE00003682325 | 67878536 | 67878631 |
| ENSE00003690650 | 67883568 | 67883731 |
Expression profiles
Bgee: expression breadth ubiquitous, 134 present calls, max score 96.65.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.5764 / max 123.9643, expressed in 1810 samples.
FANTOM5 promoters (3 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 154689 | 17.6241 | 1807 |
| 154688 | 0.8663 | 588 |
| 154690 | 0.0861 | 27 |
Top tissues by expression
134 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| right hemisphere of cerebellum | UBERON:0014890 | 96.65 | gold quality |
| cerebellum | UBERON:0002037 | 96.54 | gold quality |
| cerebellar cortex | UBERON:0002129 | 96.52 | gold quality |
| cerebellar hemisphere | UBERON:0002245 | 96.50 | gold quality |
| pituitary gland | UBERON:0000007 | 96.04 | gold quality |
| mucosa of transverse colon | UBERON:0004991 | 95.55 | gold quality |
| adenohypophysis | UBERON:0002196 | 95.49 | gold quality |
| left testis | UBERON:0004533 | 95.49 | gold quality |
| granulocyte | CL:0000094 | 95.47 | gold quality |
| right testis | UBERON:0004534 | 95.44 | gold quality |
| left ovary | UBERON:0002119 | 95.12 | gold quality |
| right ovary | UBERON:0002118 | 94.86 | gold quality |
| apex of heart | UBERON:0002098 | 94.85 | gold quality |
| ovary | UBERON:0000992 | 94.81 | gold quality |
| right lobe of thyroid gland | UBERON:0001119 | 94.79 | gold quality |
| ganglionic eminence | UBERON:0004023 | 94.69 | gold quality |
| small intestine Peyer’s patch | UBERON:0003454 | 94.57 | gold quality |
| testis | UBERON:0000473 | 94.51 | gold quality |
| transverse colon | UBERON:0001157 | 94.41 | gold quality |
| spleen | UBERON:0002106 | 94.36 | gold quality |
| metanephros cortex | UBERON:0010533 | 94.36 | gold quality |
| ventricular zone | UBERON:0003053 | 94.27 | gold quality |
| right uterine tube | UBERON:0001302 | 94.25 | gold quality |
| left lobe of thyroid gland | UBERON:0001120 | 94.24 | gold quality |
| small intestine | UBERON:0002108 | 94.23 | gold quality |
| left uterine tube | UBERON:0001303 | 94.22 | gold quality |
| prostate gland | UBERON:0002367 | 94.19 | gold quality |
| stromal cell of endometrium | CL:0002255 | 94.17 | gold quality |
| thyroid gland | UBERON:0002046 | 94.06 | gold quality |
| body of stomach | UBERON:0001161 | 94.02 | gold quality |
Single-cell (SCXA)
Detected in 4 experiment(s), a significant marker in 0.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-GEOD-110499 | no | 456.05 |
| E-GEOD-106540 | no | 455.28 |
| E-GEOD-124858 | no | 81.99 |
| E-ANND-3 | no | 1.88 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
24 targeting EDC4, 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-12136 | 99.98 | 72.81 | 5713 |
| HSA-MIR-607 | 99.97 | 73.62 | 5593 |
| HSA-MIR-3688-3P | 99.97 | 72.02 | 2834 |
| HSA-MIR-335-3P | 99.93 | 73.36 | 4958 |
| HSA-MIR-1305 | 99.91 | 71.43 | 3443 |
| HSA-MIR-4802-3P | 99.72 | 70.13 | 1273 |
| HSA-MIR-4422 | 99.72 | 72.07 | 2908 |
| HSA-MIR-513C-5P | 99.50 | 68.42 | 1730 |
| HSA-MIR-514B-5P | 99.50 | 68.19 | 1766 |
| HSA-MIR-136-5P | 99.50 | 67.26 | 1153 |
| HSA-MIR-6791-5P | 99.16 | 65.92 | 1844 |
| HSA-MIR-4292 | 99.16 | 65.57 | 1767 |
| HSA-MIR-939-3P | 98.97 | 65.07 | 2347 |
| HSA-MIR-4725-5P | 98.67 | 65.42 | 628 |
| HSA-MIR-6509-3P | 98.32 | 67.33 | 1343 |
| HSA-MIR-4518 | 98.12 | 66.82 | 1030 |
| HSA-MIR-12120 | 98.05 | 68.44 | 1768 |
| HSA-MIR-1266-5P | 97.71 | 66.92 | 1052 |
| HSA-MIR-6859-3P | 97.26 | 64.69 | 428 |
| HSA-MIR-6773-5P | 97.04 | 64.30 | 595 |
| HSA-MIR-4436B-5P | 96.71 | 68.37 | 1346 |
| HSA-MIR-6724-5P | 96.41 | 63.11 | 507 |
| HSA-MIR-6777-3P | 95.35 | 64.30 | 699 |
Functional genomics
DepMap (CRISPR cell-line fitness): dependent in 29.8% of screened cell lines.
Literature-anchored findings (GeneRIF, showing 8)
- EDC4 might contribute to regulation of CoA biosynthesis in addition to its scaffold function in processing bodies (PMID:22982864)
- The data indicates that DCP2 activation by DCP1 occurs preferentially on the EDC4 scaffold, which may serve to couple DCP2 activation by DCP1 with 5’-to-3’ mRNA degradation by XRN1 in human cells. (PMID:24510189)
- LMKB is the first protein identified to date that interacts with this portion of Ge-1. LMKB was expressed in human B and T lymphocyte cell lines; depletion of LMKB increased expression of IFI44L. (PMID:24755989)
- EDC4 is a processing body (P-body) component. (PMID:24858563)
- The assembly of EDC4 and Dcp1a into processing bodies is critical for the translational regulation of IL-6. (PMID:25970328)
- EDC4 plays a key role in homologous recombination by stimulating end resection at double-strand breaks. (PMID:29511213)
- A non-canonical role for the EDC4 decapping factor in regulating MARF1-mediated mRNA decay. (PMID:32510323)
- Enhancer of mRNA Decapping protein 4 (EDC4) interacts with replication protein a (RPA) and contributes to Cisplatin resistance in cervical Cancer by alleviating DNA damage. (PMID:33054858)
Cross-species orthologs
5 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | edc4 | ENSDARG00000062266 |
| mus_musculus | Edc4 | ENSMUSG00000036270 |
| rattus_norvegicus | Edc4 | ENSRNOG00000024025 |
| drosophila_melanogaster | Ge-1 | FBGN0283682 |
| caenorhabditis_elegans | edc-4 | WBGENE00021551 |
Protein
Protein identifiers
Enhancer of mRNA-decapping protein 4 — Q6P2E9 (reviewed: Q6P2E9)
Alternative names: Autoantigen Ge-1, Autoantigen RCD-8, Human enhancer of decapping large subunit
All UniProt accessions (4): Q6P2E9, I3L0V0, I3L2F4, I3L3M2
UniProt curated annotations — full annotation on UniProt →
Function. In the process of mRNA degradation, seems to play a role in mRNA decapping. Component of a complex containing DCP2 and DCP1A which functions in decapping of ARE-containing mRNAs. Promotes complex formation between DCP1A and DCP2. Enhances the catalytic activity of DCP2 (in vitro).
Subunit / interactions. Part of a decapping complex consisting of DCP1A, DCP2, EDC3, EDC4 and probably DDX6. Part of a complex consisting of DCP1A, EDC3, EDC4 and DDX6. Part of a complex consisting of DCP1B, EDC3, EDC4 and DDX6. Interacts with DCP2. Interacts with RC3H1. Interacts with NBDY. Interacts with TEX19. Interacts with LSM14A. Interacts with DDX6. Interacts with HELZ. (Microbial infection) Interacts with rotavirus A non-structural protein 2; this interaction probably plays a role in the sequestration of EDC4 in viral factories. Interacts with rotavirus A non-structural protein 5; this interaction probably plays a role in its sequestration in viral factories.
Subcellular location. Cytoplasm. P-body. Nucleus.
Similarity. Belongs to the WD repeat EDC4 family.
Isoforms (2)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q6P2E9-1 | 1 | yes |
| Q6P2E9-2 | 2 |
RefSeq proteins (2): NP_001414274, NP_055144* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR001680 | WD40_rpt | Repeat |
| IPR015943 | WD40/YVTN_repeat-like_dom_sf | Homologous_superfamily |
| IPR032401 | EDC4_WD40 | Domain |
| IPR036322 | WD40_repeat_dom_sf | Homologous_superfamily |
| IPR044938 | EDC4_C_sf | Homologous_superfamily |
| IPR045152 | EDC4-like | Family |
| IPR049404 | EDC4_C | Domain |
Pfam: PF16529, PF21289
UniProt features (53 total): modified residue 26, region of interest 8, repeat 7, compositionally biased region 4, sequence conflict 4, initiator methionine 1, chain 1, coiled-coil region 1, splice variant 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q6P2E9-F1 | 63.18 | 0.22 |
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 (26): 2, 3, 6, 125, 560, 565, 583, 585, 676, 693, 708, 723, 725, 727, 729, 741, 821, 844, 871, 875 …
Function
Pathways and Gene Ontology
Reactome pathways
1 pathways
| ID | Pathway |
|---|---|
| R-HSA-430039 | mRNA decay by 5’ to 3’ exoribonuclease |
MSigDB gene sets: 171 (showing top):
GSE45365_NK_CELL_VS_CD8A_DC_UP, YAATNRNNNYNATT_UNKNOWN, MYOGENIN_Q6, chr16q22, GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, GCANCTGNY_MYOD_Q6, CMYB_01, MODULE_45, REACTOME_MRNA_DECAY_BY_5_TO_3_EXORIBONUCLEASE, MORF_HDAC1, MORF_UBE2N, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, AREB6_01, RACCACAR_AML_Q6, MORF_HDAC2
GO Biological Process (1): deadenylation-independent decapping of nuclear-transcribed mRNA (GO:0031087)
GO Molecular Function (1): protein binding (GO:0005515)
GO Cellular Component (7): P-body (GO:0000932), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), membrane (GO:0016020), cytoplasmic ribonucleoprotein granule (GO:0036464)
Reactome top-level categories
Rollup of top-1 pathways:
| Category | Pathways |
|---|---|
| Deadenylation-dependent mRNA decay | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cellular anatomical structure | 4 |
| cytoplasm | 2 |
| nuclear-transcribed mRNA catabolic process, deadenylation-independent decay | 1 |
| mRNA methylguanosine-cap decapping | 1 |
| binding | 1 |
| cytoplasmic ribonucleoprotein granule | 1 |
| intracellular membrane-bounded organelle | 1 |
| nuclear lumen | 1 |
| intracellular anatomical structure | 1 |
| ribonucleoprotein granule | 1 |
Protein interactions and networks
STRING
1856 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| EDC4 | DCP1A | Q9NPI6 | 999 |
| EDC4 | DCP2 | Q8IU60 | 998 |
| EDC4 | EDC3 | Q96F86 | 998 |
| EDC4 | DDX6 | P26196 | 994 |
| EDC4 | XRN1 | Q8IZH2 | 978 |
| EDC4 | LSM14A | Q8ND56 | 936 |
| EDC4 | LSM1 | O15116 | 882 |
| EDC4 | UPF1 | Q92900 | 877 |
| EDC4 | AGO2 | Q9UKV8 | 786 |
| EDC4 | DCP1B | Q8IZD4 | 780 |
| EDC4 | PATL1 | Q86TB9 | 728 |
| EDC4 | TNRC6A | Q8NDV7 | 725 |
| EDC4 | CNOT1 | A5YKK6 | 723 |
| EDC4 | EIF4ENIF1 | Q9NRA8 | 713 |
| EDC4 | LSM4 | Q9Y4Z0 | 696 |
IntAct
219 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| EDC3 | DDX6 | psi-mi:“MI:0914”(association) | 0.960 |
| MED4 | MED19 | psi-mi:“MI:2364”(proximity) | 0.900 |
| DCP2 | EDC4 | psi-mi:“MI:0915”(physical association) | 0.890 |
| EDC4 | DCP2 | psi-mi:“MI:0914”(association) | 0.890 |
| EDC4 | DCP2 | psi-mi:“MI:0915”(physical association) | 0.890 |
| DCP1A | EDC4 | psi-mi:“MI:0914”(association) | 0.880 |
| EDC4 | DCP1A | psi-mi:“MI:0403”(colocalization) | 0.880 |
| DCP1A | EDC4 | psi-mi:“MI:0403”(colocalization) | 0.880 |
| DCP1A | EDC4 | psi-mi:“MI:0915”(physical association) | 0.880 |
| EDC4 | DCP1A | psi-mi:“MI:0915”(physical association) | 0.880 |
| SGF29 | NDC80 | psi-mi:“MI:0914”(association) | 0.840 |
| ATXN2 | PABPC1 | psi-mi:“MI:0915”(physical association) | 0.820 |
| DDX6 | EDC4 | psi-mi:“MI:0914”(association) | 0.820 |
| PATL1 | LSM1 | psi-mi:“MI:0914”(association) | 0.770 |
| EDC4 | XRN1 | psi-mi:“MI:0915”(physical association) | 0.750 |
| XRN1 | EDC4 | psi-mi:“MI:0914”(association) | 0.750 |
| CFTR | ESYT2 | psi-mi:“MI:2364”(proximity) | 0.710 |
| EDC3 | EDC4 | psi-mi:“MI:0914”(association) | 0.640 |
BioGRID (327): EDC4 (Affinity Capture-RNA), EDC4 (Affinity Capture-RNA), EDC4 (Affinity Capture-RNA), EDC4 (Affinity Capture-MS), EDC4 (Affinity Capture-MS), EDC4 (Affinity Capture-MS), EDC4 (Affinity Capture-MS), EDC4 (Affinity Capture-MS), EDC4 (Affinity Capture-MS), EDC4 (Affinity Capture-MS), EDC4 (Affinity Capture-MS), EDC4 (Affinity Capture-MS), EDC4 (Co-fractionation), EDC4 (Affinity Capture-MS), EDC4 (Proximity Label-MS)
ESM2 similar proteins: A0A140LI67, A0A1W2PR48, A0JP70, D3YYM4, F1LW30, O13034, O15040, O70173, Q15345, Q3SXM0, Q3UDP0, Q3UJB9, Q3ULW6, Q3V129, Q3ZAV8, Q58DC2, Q5F479, Q5JV73, Q5M9H0, Q5M9H1, Q5R6T6, Q5R9H2, Q68DX3, Q6IRN0, Q6NV72, Q6P2E9, Q6P4K6, Q6PCD5, Q6ZPG2, Q6ZW76, Q7TNH6, Q80TQ5, Q8BLD6, Q8C008, Q8C5V5, Q8CBW4, Q8CIK8, Q8IWE5, Q8JZL1, Q8K1C9
Diamond homologs: Q1LUT1, Q3UJB9, Q3ZAV8, Q6P2E9, Q7ZXT3
SIGNOR signaling
0 interactions.
Enriched among interaction partners
Reactome pathways and GO biological processes over-represented among this gene’s 193 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 decay by 5’ to 3’ exoribonuclease | 7 | 40.4× | 9e-08 |
| Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA | 5 | 24.0× | 3e-04 |
| SARS-CoV-1-host interactions | 9 | 12.0× | 2e-05 |
| SARS-CoV-1 modulates host translation machinery | 5 | 11.7× | 5e-03 |
| SARS-CoV-1 Infection | 8 | 8.7× | 6e-04 |
| Translation initiation complex formation | 6 | 8.7× | 5e-03 |
| SARS-CoV-2-host interactions | 7 | 6.3× | 7e-03 |
| Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) | 8 | 5.9× | 5e-03 |
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| P-body assembly | 5 | 31.5× | 4e-04 |
| nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | 6 | 16.8× | 6e-04 |
| mRNA transport | 7 | 11.0× | 8e-04 |
| negative regulation of translation | 7 | 8.2× | 3e-03 |
| translation | 9 | 5.5× | 4e-03 |
| mRNA splicing, via spliceosome | 10 | 5.5× | 2e-03 |
| mRNA processing | 10 | 4.7× | 5e-03 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
188 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 151 |
| Likely benign | 9 |
| Benign | 2 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
4524 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 16:67873339:GGGCG:G | donor_gain | 1.0000 |
| 16:67873340:GGCG:G | donor_gain | 1.0000 |
| 16:67873340:GGCGG:G | donor_gain | 1.0000 |
| 16:67873341:GCGG:G | donor_gain | 1.0000 |
| 16:67875839:T:G | donor_gain | 1.0000 |
| 16:67875940:CCCA:C | acceptor_loss | 1.0000 |
| 16:67875942:CA:C | acceptor_loss | 1.0000 |
| 16:67875943:A:AG | acceptor_gain | 1.0000 |
| 16:67875943:A:AT | acceptor_loss | 1.0000 |
| 16:67875943:AG:A | acceptor_gain | 1.0000 |
| 16:67875944:G:GT | acceptor_gain | 1.0000 |
| 16:67875944:GG:G | acceptor_gain | 1.0000 |
| 16:67875944:GGC:G | acceptor_gain | 1.0000 |
| 16:67875944:GGCC:G | acceptor_gain | 1.0000 |
| 16:67875944:GGCCC:G | acceptor_gain | 1.0000 |
| 16:67876097:GTCAT:G | donor_gain | 1.0000 |
| 16:67876102:G:GG | donor_gain | 1.0000 |
| 16:67876485:CAG:C | acceptor_loss | 1.0000 |
| 16:67876486:A:AG | acceptor_gain | 1.0000 |
| 16:67876486:AGCT:A | acceptor_gain | 1.0000 |
| 16:67876487:G:GG | acceptor_gain | 1.0000 |
| 16:67876487:G:GT | acceptor_loss | 1.0000 |
| 16:67876487:GCT:G | acceptor_gain | 1.0000 |
| 16:67876487:GCTG:G | acceptor_gain | 1.0000 |
| 16:67876487:GCTGT:G | acceptor_gain | 1.0000 |
| 16:67876862:T:A | acceptor_gain | 1.0000 |
| 16:67876863:G:A | acceptor_gain | 1.0000 |
| 16:67876868:CTCAG:C | acceptor_loss | 1.0000 |
| 16:67876870:CA:C | acceptor_loss | 1.0000 |
| 16:67876871:A:AC | acceptor_loss | 1.0000 |
AlphaMissense
9136 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 16:67873308:T:C | L16P | 1.000 |
| 16:67873320:T:C | L20P | 1.000 |
| 16:67876903:T:A | W128R | 1.000 |
| 16:67876903:T:C | W128R | 1.000 |
| 16:67878206:T:C | L312P | 1.000 |
| 16:67878209:C:A | A313D | 1.000 |
| 16:67878239:T:C | F323S | 1.000 |
| 16:67878412:T:C | F353L | 1.000 |
| 16:67878413:T:C | F353S | 1.000 |
| 16:67878414:C:A | F353L | 1.000 |
| 16:67878414:C:G | F353L | 1.000 |
| 16:67878419:A:T | D355V | 1.000 |
| 16:67878546:T:A | W367R | 1.000 |
| 16:67878546:T:C | W367R | 1.000 |
| 16:67878552:T:C | F369L | 1.000 |
| 16:67878554:C:A | F369L | 1.000 |
| 16:67878554:C:G | F369L | 1.000 |
| 16:67878556:T:C | L370P | 1.000 |
| 16:67878594:T:A | W383R | 1.000 |
| 16:67878594:T:C | W383R | 1.000 |
| 16:67878609:T:A | W388R | 1.000 |
| 16:67878609:T:C | W388R | 1.000 |
| 16:67878611:G:C | W388C | 1.000 |
| 16:67878611:G:T | W388C | 1.000 |
| 16:67878814:T:C | L421P | 1.000 |
| 16:67878961:T:C | L431P | 1.000 |
| 16:67879291:T:C | L508P | 1.000 |
| 16:67883170:T:C | F1281S | 1.000 |
| 16:67883572:T:C | L1285P | 1.000 |
| 16:67883671:T:C | L1318P | 1.000 |
dbSNP variants (sampled 300 via entrez): RS1000217523 (16:67880426 G>A), RS1000491813 (16:67873193 G>A,C,T), RS1000842486 (16:67873411 A>G,T), RS1001072909 (16:67876814 G>A), RS1001232055 (16:67872067 G>T), RS1001308848 (16:67883857 C>T), RS1001516286 (16:67874270 C>A,G,T), RS1001946610 (16:67872663 T>A), RS1002011024 (16:67873800 C>T), RS1002301810 (16:67875653 A>G,T), RS1002344442 (16:67879424 T>C), RS1002605561 (16:67875657 C>G,T), RS1002632472 (16:67873644 A>T), RS1002924613 (16:67875874 G>A,T), RS1003296910 (16:67881065 T>C)
Disease associations
OMIM: gene MIM:606030 | disease phenotypes:
GenCC curated gene-disease
Mondo (0):
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
5 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST000974_8 | HDL cholesterol | 8.000000e-06 |
| GCST001436_3 | Metabolic syndrome | 2.000000e-10 |
| GCST002539_84 | Schizophrenia | 2.000000e-08 |
| GCST006803_42 | Schizophrenia | 4.000000e-08 |
| GCST010002_113 | Refractive error | 2.000000e-14 |
EFO canonical traits (2, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0004612 | high density lipoprotein cholesterol measurement |
| EFO:0000195 | metabolic syndrome |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
24 total (human), top 24 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| sodium arsenite | increases abundance, increases expression, decreases expression | 3 |
| Smoke | increases abundance, increases expression, decreases expression | 2 |
| FR900359 | affects phosphorylation | 1 |
| bisphenol A | decreases expression | 1 |
| perfluorooctanoic acid | decreases expression | 1 |
| coumarin | increases phosphorylation | 1 |
| beta-methylcholine | affects expression | 1 |
| di-n-butylphosphoric acid | affects expression | 1 |
| CGP 52608 | affects binding, increases reaction | 1 |
| 2-palmitoylglycerol | increases expression | 1 |
| Fulvestrant | increases methylation | 1 |
| Leflunomide | decreases expression | 1 |
| Air Pollutants | increases abundance, increases expression | 1 |
| Arsenic | decreases expression, increases abundance | 1 |
| Benzo(a)pyrene | affects methylation | 1 |
| Caffeine | decreases phosphorylation | 1 |
| Clozapine | increases expression | 1 |
| Diazinon | increases methylation | 1 |
| Enzyme Inhibitors | decreases activity, increases O-linked glycosylation | 1 |
| Ivermectin | decreases expression | 1 |
| Ribonucleotides | affects binding | 1 |
| Rotenone | decreases expression | 1 |
| Aflatoxin B1 | increases methylation | 1 |
| Genistein | decreases 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.