SNAPC1
gene geneOn this page
Also known as SNAP43PTFgamma
Summary
SNAPC1 (small nuclear RNA activating complex polypeptide 1, HGNC:11134) is a protein-coding gene on chromosome 14q23.2, encoding snRNA-activating protein complex subunit 1 (Q16533). Part of the SNAPc complex required for the transcription of both RNA polymerase II and III small-nuclear RNA genes. It is a common-essential gene (DepMap: required in 99.8% of cancer cell lines).
Predicted to enable sequence-specific DNA binding activity. Predicted to be involved in snRNA transcription by RNA polymerase II and snRNA transcription by RNA polymerase III. Located in nucleolus and nucleoplasm.
Source: NCBI Gene 6617 — RefSeq curated summary.
At a glance
- GWAS associations: 5
- Clinical variants (ClinVar): 55 total
- Cancer dependency (DepMap): dependent in 99.8% of screened cell lines (common-essential)
- MANE Select transcript:
NM_003082
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:11134 |
| Approved symbol | SNAPC1 |
| Name | small nuclear RNA activating complex polypeptide 1 |
| Location | 14q23.2 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | SNAP43, PTFgamma |
| Ensembl gene | ENSG00000023608 |
| Ensembl biotype | protein_coding |
| OMIM | 600591 |
| Entrez | 6617 |
Gene structure
Transcript identifiers
Ensembl transcripts: 6 — 6 protein_coding
ENST00000216294, ENST00000923633, ENST00000923634, ENST00000923635, ENST00000923636, ENST00000923637
RefSeq mRNA: 1 — MANE Select: NM_003082
NM_003082
CCDS: CCDS9755
Canonical transcript exons
ENST00000216294 — 10 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000658312 | 61776095 | 61776253 |
| ENSE00000658313 | 61778072 | 61778140 |
| ENSE00000658314 | 61778848 | 61778910 |
| ENSE00000658315 | 61782247 | 61782397 |
| ENSE00000867527 | 61792807 | 61792902 |
| ENSE00001143783 | 61762420 | 61762588 |
| ENSE00001206892 | 61794949 | 61796428 |
| ENSE00003553913 | 61768636 | 61768740 |
| ENSE00003646833 | 61766876 | 61767035 |
| ENSE00003681573 | 61767212 | 61767352 |
Expression profiles
Bgee: expression breadth ubiquitous, 274 present calls, max score 96.00.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.2586 / max 662.2773, expressed in 1792 samples.
FANTOM5 promoters (3 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 140011 | 18.1885 | 1780 |
| 140010 | 3.6650 | 1585 |
| 140009 | 0.4052 | 123 |
Top tissues by expression
291 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| cartilage tissue | UBERON:0002418 | 96.00 | gold quality |
| oocyte | CL:0000023 | 94.43 | gold quality |
| secondary oocyte | CL:0000655 | 93.31 | gold quality |
| sperm | CL:0000019 | 91.18 | gold quality |
| bronchial epithelial cell | CL:0002328 | 90.77 | gold quality |
| male germ cell | CL:0000015 | 90.12 | gold quality |
| calcaneal tendon | UBERON:0003701 | 87.59 | gold quality |
| cauda epididymis | UBERON:0004360 | 87.41 | gold quality |
| epithelium of bronchus | UBERON:0002031 | 87.21 | gold quality |
| bronchus | UBERON:0002185 | 86.68 | gold quality |
| caput epididymis | UBERON:0004358 | 86.60 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 86.51 | gold quality |
| mucosa of paranasal sinus | UBERON:0005030 | 86.48 | gold quality |
| corpus epididymis | UBERON:0004359 | 86.22 | gold quality |
| tibia | UBERON:0000979 | 85.15 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 84.21 | gold quality |
| testis | UBERON:0000473 | 83.39 | gold quality |
| right testis | UBERON:0004534 | 83.34 | gold quality |
| tendon | UBERON:0000043 | 82.55 | gold quality |
| left testis | UBERON:0004533 | 82.50 | gold quality |
| seminal vesicle | UBERON:0000998 | 81.89 | gold quality |
| choroid plexus epithelium | UBERON:0003911 | 81.73 | gold quality |
| ventricular zone | UBERON:0003053 | 80.77 | gold quality |
| islet of Langerhans | UBERON:0000006 | 80.41 | gold quality |
| endometrium | UBERON:0001295 | 79.92 | gold quality |
| visceral pleura | UBERON:0002401 | 79.75 | gold quality |
| skeletal muscle tissue of biceps brachii | UBERON:0004502 | 79.74 | silver quality |
| parietal pleura | UBERON:0002400 | 79.65 | gold quality |
| stromal cell of endometrium | CL:0002255 | 79.57 | gold quality |
| cranial nerve II | UBERON:0000941 | 79.39 | gold quality |
Single-cell (SCXA)
Detected in 2 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 5.62 |
| E-GEOD-124858 | no | 348.06 |
Regulation
Is transcription factor: no
Upstream regulators (CollecTRI, top): GATA3, POU2F1, SP1
miRNA regulators (miRDB)
77 targeting SNAPC1, 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-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-3646 | 100.00 | 73.56 | 5283 |
| HSA-MIR-3924 | 100.00 | 72.09 | 2394 |
| HSA-MIR-200B-3P | 100.00 | 73.31 | 2693 |
| HSA-MIR-200C-3P | 100.00 | 73.35 | 2685 |
| HSA-MIR-429 | 100.00 | 73.44 | 2698 |
| HSA-MIR-4795-3P | 100.00 | 74.62 | 4024 |
| HSA-MIR-186-5P | 99.99 | 70.83 | 3707 |
| HSA-MIR-32-5P | 99.98 | 75.21 | 1964 |
| HSA-MIR-92A-3P | 99.98 | 75.21 | 1960 |
| HSA-MIR-92B-3P | 99.98 | 75.25 | 1955 |
| HSA-MIR-25-3P | 99.98 | 74.60 | 1817 |
| HSA-MIR-363-3P | 99.98 | 74.72 | 1821 |
| HSA-MIR-367-3P | 99.98 | 74.83 | 1819 |
| HSA-MIR-4482-3P | 99.98 | 72.50 | 3147 |
| HSA-MIR-4666A-3P | 99.96 | 71.71 | 3434 |
| HSA-MIR-548AJ-3P | 99.96 | 73.38 | 5345 |
| HSA-MIR-548X-3P | 99.96 | 73.38 | 5345 |
| HSA-MIR-548J-3P | 99.94 | 72.61 | 4881 |
| HSA-MIR-381-3P | 99.93 | 71.87 | 2854 |
| HSA-MIR-548AE-3P | 99.93 | 72.66 | 4867 |
| HSA-MIR-548AH-3P | 99.93 | 72.54 | 4872 |
| HSA-MIR-548AM-3P | 99.93 | 72.54 | 4872 |
| HSA-MIR-548AQ-3P | 99.93 | 72.66 | 4867 |
| HSA-MIR-300 | 99.92 | 71.76 | 2856 |
| HSA-MIR-338-5P | 99.92 | 72.34 | 2951 |
| HSA-MIR-627-3P | 99.90 | 71.42 | 3316 |
Functional genomics
DepMap (CRISPR cell-line fitness): dependent in 99.8% of screened cell lines, common-essential.
Literature-anchored findings (GeneRIF, showing 3)
- CK2 may have the capacity to differentially regulate U1 and U6 transcription even though SNAP(C) is universally utilized for human snRNA gene transcription [SNAPC protein, also called PTF or PSE-binding transcription factor] (PMID:15955816)
- SNAPC1 is a general transcriptional coactivator that functions through elongating RNAPII. (PMID:22966203)
- Results from a study on gene expression variability markers in early-stage human embryos shows that is a putative expression variability marker as well as a differential gene expression marker for the 3-day, 8-cell embryo stage. (PMID:26288249)
Cross-species orthologs
9 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | snapc1b | ENSDARG00000003827 |
| danio_rerio | snapc1a | ENSDARG00000029569 |
| mus_musculus | Snapc1 | ENSMUSG00000021113 |
| rattus_norvegicus | Snapc1 | ENSRNOG00000009296 |
| drosophila_melanogaster | Pbp45 | FBGN0038371 |
| caenorhabditis_elegans | WBGENE00012715 | |
| caenorhabditis_elegans | WBGENE00015513 | |
| caenorhabditis_elegans | WBGENE00017265 | |
| caenorhabditis_elegans | WBGENE00019894 |
Protein
Protein identifiers
snRNA-activating protein complex subunit 1 — Q16533 (reviewed: Q16533)
Alternative names: Proximal sequence element-binding transcription factor subunit gamma, Small nuclear RNA-activating complex polypeptide 1, snRNA-activating protein complex 43 kDa subunit
All UniProt accessions (1): Q16533
UniProt curated annotations — full annotation on UniProt →
Function. Part of the SNAPc complex required for the transcription of both RNA polymerase II and III small-nuclear RNA genes. Binds to the proximal sequence element (PSE), a non-TATA-box basal promoter element common to these 2 types of genes. Recruits TBP and BRF2 to the U6 snRNA TATA box.
Subunit / interactions. Part of the SNAPc complex composed of 5 subunits: SNAPC1, SNAPC2, SNAPC3, SNAPC4 and SNAPC5. SNAPC1 interacts with SNAPC3, SNAPC4 and TBP.
Subcellular location. Nucleus.
RefSeq proteins (1): NP_003073* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR019188 | SNAPC1 | Family |
Pfam: PF09808
UniProt features (24 total): helix 10, strand 5, region of interest 4, modified residue 2, chain 1, compositionally biased region 1, turn 1
Structure
Experimental structures (PDB)
18 structures.
| PDB | Method | Resolution (Å) |
|---|---|---|
| 7ZWD | ELECTRON MICROSCOPY | 3 |
| 7ZX8 | ELECTRON MICROSCOPY | 3 |
| 9K3U | ELECTRON MICROSCOPY | 3 |
| 7ZWC | ELECTRON MICROSCOPY | 3.2 |
| 9FSO | ELECTRON MICROSCOPY | 3.28 |
| 9LXN | ELECTRON MICROSCOPY | 3.3 |
| 9FSP | ELECTRON MICROSCOPY | 3.39 |
| 7ZX7 | ELECTRON MICROSCOPY | 3.4 |
| 8IUH | ELECTRON MICROSCOPY | 3.4 |
| 7XUR | ELECTRON MICROSCOPY | 3.49 |
| 7ZXE | ELECTRON MICROSCOPY | 3.5 |
| 9K3V | ELECTRON MICROSCOPY | 3.5 |
| 9FSQ | ELECTRON MICROSCOPY | 3.51 |
| 9FSR | ELECTRON MICROSCOPY | 3.76 |
| 8ITY | ELECTRON MICROSCOPY | 3.9 |
| 8IUE | ELECTRON MICROSCOPY | 4.1 |
| 9FSS | ELECTRON MICROSCOPY | 4.14 |
| 9K3B | ELECTRON MICROSCOPY | 4.8 |
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q16533-F1 | 71.91 | 0.35 |
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 (2): 289, 290
Function
Pathways and Gene Ontology
Reactome pathways
7 pathways
| ID | Pathway |
|---|---|
| R-HSA-6807505 | RNA polymerase II transcribes snRNA genes |
| R-HSA-749476 | RNA Polymerase III Abortive And Retractive Initiation |
| R-HSA-76071 | RNA Polymerase III Transcription Initiation From Type 3 Promoter |
| R-HSA-73857 | RNA Polymerase II Transcription |
| R-HSA-74158 | RNA Polymerase III Transcription |
| R-HSA-74160 | Gene expression (Transcription) |
| R-HSA-76046 | RNA Polymerase III Transcription Initiation |
MSigDB gene sets: 168 (showing top):
GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_DN, REACTOME_RNA_POLYMERASE_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, ENK_UV_RESPONSE_KERATINOCYTE_UP, GOBP_TRANSCRIPTION_BY_RNA_POLYMERASE_III, BLALOCK_ALZHEIMERS_DISEASE_UP, MODULE_123, SCHLOSSER_SERUM_RESPONSE_DN, DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_UP, chr14q23, BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_24HR_UP, DANG_BOUND_BY_MYC, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, SENESE_HDAC3_TARGETS_DN, GOCC_TRANSCRIPTION_REGULATOR_COMPLEX
GO Biological Process (2): snRNA transcription by RNA polymerase II (GO:0042795), snRNA transcription by RNA polymerase III (GO:0042796)
GO Molecular Function (5): RNA polymerase III general transcription initiation factor activity (GO:0000995), RNA polymerase II general transcription initiation factor activity (GO:0016251), sequence-specific DNA binding (GO:0043565), DNA binding (GO:0003677), protein binding (GO:0005515)
GO Cellular Component (4): nucleoplasm (GO:0005654), nucleolus (GO:0005730), snRNA-activating protein complex (GO:0019185), nucleus (GO:0005634)
Reactome top-level categories
Rollup of top-4 pathways:
| Category | Pathways |
|---|---|
| RNA Polymerase III Transcription | 2 |
| Gene expression (Transcription) | 2 |
| RNA Polymerase II Transcription | 1 |
| RNA Polymerase III Transcription Initiation | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| transcription by RNA polymerase II | 2 |
| snRNA transcription | 2 |
| transcription by RNA polymerase III | 2 |
| general transcription initiation factor activity | 2 |
| nuclear lumen | 2 |
| DNA binding | 1 |
| nucleic acid binding | 1 |
| binding | 1 |
| cellular anatomical structure | 1 |
| intracellular membraneless organelle | 1 |
| transcription regulator complex | 1 |
| intracellular membrane-bounded organelle | 1 |
Protein interactions and networks
STRING
586 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| SNAPC1 | SNAPC3 | Q92966 | 999 |
| SNAPC1 | SNAPC2 | Q13487 | 997 |
| SNAPC1 | SNAPC4 | Q5SXM2 | 996 |
| SNAPC1 | SNAPC5 | O75971 | 984 |
| SNAPC1 | TBP | P20226 | 830 |
| SNAPC1 | TAF1A | Q15573 | 650 |
| SNAPC1 | BDP1 | A6H8Y1 | 542 |
| SNAPC1 | POLI | Q9UNA4 | 534 |
| SNAPC1 | BRF2 | Q9HAW0 | 506 |
| SNAPC1 | INTS10 | Q9NVR2 | 486 |
| SNAPC1 | POLR3D | P05423 | 446 |
| SNAPC1 | TTC23 | Q5W5X9 | 392 |
| SNAPC1 | POLR3F | Q9H1D9 | 390 |
| SNAPC1 | GTF3C1 | Q12789 | 389 |
| SNAPC1 | MFF | Q9GZY8 | 376 |
IntAct
52 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| SNAPC1 | SNAPC3 | psi-mi:“MI:0915”(physical association) | 0.850 |
| SNAPC1 | SNAPC3 | psi-mi:“MI:0914”(association) | 0.850 |
| SNAPC4 | SNAPC1 | psi-mi:“MI:0914”(association) | 0.790 |
| SNAPC1 | SNAPC5 | psi-mi:“MI:0914”(association) | 0.740 |
| SNAPC1 | SNAPC5 | psi-mi:“MI:0915”(physical association) | 0.740 |
| NAP1L5 | IQGAP1 | psi-mi:“MI:0914”(association) | 0.640 |
| SNAPC4 | SNAPC5 | psi-mi:“MI:0914”(association) | 0.620 |
| HAT1 | SNAPC1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CCDC6 | SNAPC1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| SNAPC1 | psi-mi:“MI:0915”(physical association) | 0.560 | |
| SNAPC1 | EXOC8 | psi-mi:“MI:0915”(physical association) | 0.560 |
| HSF2BP | SNAPC1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| SNAPC1 | psi-mi:“MI:0914”(association) | 0.540 | |
| SNAPC1 | psi-mi:“MI:0915”(physical association) | 0.540 | |
| CSPP1 | SNAPC1 | psi-mi:“MI:0915”(physical association) | 0.400 |
| SNAPC1 | NR2E3 | psi-mi:“MI:0915”(physical association) | 0.370 |
| SNAPC1 | TRIM29 | psi-mi:“MI:0915”(physical association) | 0.370 |
BioGRID (140): SNAPC1 (Affinity Capture-MS), SNAPC5 (Affinity Capture-MS), SNAPC4 (Affinity Capture-MS), SNAPC2 (Affinity Capture-MS), SNAPC3 (Affinity Capture-MS), ZG16B (Affinity Capture-MS), CST4 (Affinity Capture-MS), SNAPC3 (Affinity Capture-MS), SNAPC4 (Affinity Capture-MS), SNAPC1 (Affinity Capture-MS), SNAPC2 (Affinity Capture-MS), SNAPC5 (Affinity Capture-MS), ZG16B (Affinity Capture-MS), SNAPC1 (Affinity Capture-MS), SNAPC1 (Positive Genetic)
ESM2 similar proteins: A0A0M3U1B0, A0A1L8EYB2, A0JMF7, A1L2Y1, A2ALV5, A9JRX0, B2GUZ2, D3ZSP7, F1QB81, O35892, O70608, O75113, P23497, P70347, Q0P5X5, Q13129, Q16533, Q2T9I9, Q3U1D0, Q5CZC0, Q5H9M0, Q5REF4, Q5RHB5, Q5SW75, Q5T4T6, Q5T5J6, Q5XG69, Q5ZLE9, Q60664, Q63HN8, Q7M6U3, Q7Z4H7, Q80VH0, Q8BVK9, Q8C263, Q8CCC3, Q8NA03, Q90WN7, Q92844, Q96QP1
Diamond homologs: Q16533, Q4R6W9, Q8K0S9
SIGNOR signaling
1 interactions.
| A | Effect | B | Mechanism |
|---|---|---|---|
| SNAPC1 | “form complex” | SNAPC | binding |
Disease & clinical
Clinical variants and AI predictions
ClinVar
55 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 44 |
| Likely benign | 0 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
1755 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 14:61762568:G:GT | donor_gain | 1.0000 |
| 14:61762589:GTGG:G | donor_loss | 1.0000 |
| 14:61762590:T:A | donor_loss | 1.0000 |
| 14:61767203:T:A | acceptor_gain | 1.0000 |
| 14:61776249:GAAAG:G | donor_gain | 1.0000 |
| 14:61776250:AAAGG:A | donor_loss | 1.0000 |
| 14:61776252:AGG:A | donor_loss | 1.0000 |
| 14:61776253:GGT:G | donor_loss | 1.0000 |
| 14:61776254:G:T | donor_loss | 1.0000 |
| 14:61776255:T:A | donor_loss | 1.0000 |
| 14:61778070:A:AG | acceptor_gain | 1.0000 |
| 14:61778071:G:GG | acceptor_gain | 1.0000 |
| 14:61778138:G:GT | donor_gain | 1.0000 |
| 14:61778835:A:AG | acceptor_gain | 1.0000 |
| 14:61778836:T:G | acceptor_gain | 1.0000 |
| 14:61778840:A:AG | acceptor_gain | 1.0000 |
| 14:61778842:A:AG | acceptor_gain | 1.0000 |
| 14:61778843:T:G | acceptor_gain | 1.0000 |
| 14:61778845:CA:C | acceptor_loss | 1.0000 |
| 14:61778846:A:AC | acceptor_loss | 1.0000 |
| 14:61778846:A:AG | acceptor_gain | 1.0000 |
| 14:61778847:G:GG | acceptor_gain | 1.0000 |
| 14:61778847:GA:G | acceptor_gain | 1.0000 |
| 14:61778847:GAGAT:G | acceptor_gain | 1.0000 |
| 14:61778911:G:A | donor_loss | 1.0000 |
| 14:61778912:TAAG:T | donor_loss | 1.0000 |
| 14:61782395:AAGG:A | donor_loss | 1.0000 |
| 14:61782398:GTAA:G | donor_loss | 1.0000 |
| 14:61782399:T:A | donor_loss | 1.0000 |
| 14:61794947:A:AG | acceptor_gain | 1.0000 |
AlphaMissense
2458 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 14:61766989:T:C | L81P | 0.996 |
| 14:61767309:T:C | L129P | 0.996 |
| 14:61762557:T:A | W33R | 0.995 |
| 14:61762557:T:C | W33R | 0.995 |
| 14:61766977:G:A | G77D | 0.994 |
| 14:61767339:C:A | A139E | 0.993 |
| 14:61778883:A:C | K266N | 0.993 |
| 14:61778883:A:T | K266N | 0.993 |
| 14:61766985:T:G | Y80D | 0.992 |
| 14:61767219:T:A | V99D | 0.992 |
| 14:61762545:T:C | F29L | 0.990 |
| 14:61762547:C:A | F29L | 0.990 |
| 14:61762547:C:G | F29L | 0.990 |
| 14:61766976:G:C | G77R | 0.990 |
| 14:61782261:A:C | R280S | 0.989 |
| 14:61782261:A:T | R280S | 0.989 |
| 14:61782264:G:C | R281S | 0.989 |
| 14:61782264:G:T | R281S | 0.989 |
| 14:61762546:T:C | F29S | 0.988 |
| 14:61766974:T:A | V76D | 0.988 |
| 14:61766998:G:A | G84E | 0.988 |
| 14:61767233:T:A | W104R | 0.988 |
| 14:61767233:T:C | W104R | 0.988 |
| 14:61767324:C:A | A134E | 0.988 |
| 14:61762501:T:C | L14P | 0.987 |
| 14:61762512:T:C | F18L | 0.987 |
| 14:61762514:C:A | F18L | 0.987 |
| 14:61762514:C:G | F18L | 0.987 |
| 14:61767327:T:C | F135S | 0.986 |
| 14:61782263:G:C | R281T | 0.986 |
dbSNP variants (sampled 300 via entrez): RS1000027745 (14:61772543 C>T), RS1000081466 (14:61787451 A>T), RS1000252268 (14:61779582 T>G), RS1000306311 (14:61790010 A>G), RS1000416368 (14:61784621 A>T), RS1000420749 (14:61790271 A>G), RS1000591090 (14:61777962 T>C), RS1000642265 (14:61788777 A>G), RS1000730038 (14:61788214 G>T), RS1000756680 (14:61789004 A>T), RS1000761644 (14:61787838 A>C), RS1000832247 (14:61766953 C>T), RS1001043531 (14:61763674 A>T), RS1001059288 (14:61793475 T>C), RS1001211666 (14:61763940 A>T)
Disease associations
OMIM: gene MIM:600591 | 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 |
|---|---|---|
| GCST007576_180 | Chronotype | 7.000000e-09 |
| GCST009391_1321 | Metabolite levels | 7.000000e-06 |
| GCST009391_1410 | Metabolite levels | 8.000000e-06 |
| GCST009391_310 | Metabolite levels | 3.000000e-06 |
| GCST009391_316 | Metabolite levels | 4.000000e-07 |
EFO canonical traits (5, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0008328 | chronotype measurement |
| EFO:0010519 | pantothenic acid measurement |
| EFO:0005132 | 5-HIAA measurement |
| EFO:0010430 | triacylglycerol 56:3 measurement |
| EFO:0010431 | triacylglycerol 56:4 measurement |
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 |
|---|---|---|
| Cyclosporine | increases expression | 3 |
| Fluorouracil | decreases expression | 2 |
| Oxygen | increases expression | 2 |
| Valproic Acid | increases expression | 2 |
| 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide | decreases expression | 2 |
| aristolochic acid I | decreases expression | 1 |
| testosterone enanthate | affects expression | 1 |
| methylmercuric chloride | increases expression | 1 |
| glycidyl methacrylate | increases expression | 1 |
| sodium arsenate | increases abundance, increases expression | 1 |
| nickel chloride | increases expression | 1 |
| CGP 52608 | affects binding, increases reaction | 1 |
| monomethylarsonous acid | increases expression | 1 |
| torcetrapib | increases expression | 1 |
| ICG 001 | increases expression | 1 |
| abrine | increases expression | 1 |
| jinfukang | affects cotreatment, decreases expression | 1 |
| (+)-JQ1 compound | decreases expression | 1 |
| MT19c compound | increases expression | 1 |
| 4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid | increases expression | 1 |
| 2,3,5-trichloro-6-phenyl-(1,4)benzoquinone | decreases expression | 1 |
| Leflunomide | increases expression | 1 |
| Air Pollutants | decreases expression, increases abundance | 1 |
| Arsenic | increases abundance, increases expression | 1 |
| Benzo(a)pyrene | decreases methylation | 1 |
| Calcitriol | affects cotreatment, increases expression | 1 |
| Carmustine | increases expression | 1 |
| Cisplatin | affects cotreatment, decreases expression | 1 |
| Estradiol | increases expression | 1 |
| Hydrogen Peroxide | affects expression | 1 |
Cellosaurus cell lines
3 cell lines: 3 embryonic stem cell
First 10 cell lines (id-ordered, not curated):
| Cellosaurus | Name | Category | Sex |
|---|---|---|---|
| CVCL_A6K5 | SEES3-1V human SNAPC1, clone1 | Embryonic stem cell | Male |
| CVCL_A6K6 | SEES3-1V human SNAPC1, clone2 | Embryonic stem cell | Male |
| CVCL_A6K7 | SEES3-1V human SNAPC1, clone3 | Embryonic stem cell | Male |
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.