SNAPC1

gene
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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

FieldValue
HGNC IDHGNC:11134
Approved symbolSNAPC1
Namesmall nuclear RNA activating complex polypeptide 1
Location14q23.2
Locus typegene with protein product
StatusApproved
AliasesSNAP43, PTFgamma
Ensembl geneENSG00000023608
Ensembl biotypeprotein_coding
OMIM600591
Entrez6617

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

ExonStartEnd
ENSE000006583126177609561776253
ENSE000006583136177807261778140
ENSE000006583146177884861778910
ENSE000006583156178224761782397
ENSE000008675276179280761792902
ENSE000011437836176242061762588
ENSE000012068926179494961796428
ENSE000035539136176863661768740
ENSE000036468336176687661767035
ENSE000036815736176721261767352

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 IDTPM avgSamples expressed
14001118.18851780
1400103.66501585
1400090.4052123

Top tissues by expression

291 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
cartilage tissueUBERON:000241896.00gold quality
oocyteCL:000002394.43gold quality
secondary oocyteCL:000065593.31gold quality
spermCL:000001991.18gold quality
bronchial epithelial cellCL:000232890.77gold quality
male germ cellCL:000001590.12gold quality
calcaneal tendonUBERON:000370187.59gold quality
cauda epididymisUBERON:000436087.41gold quality
epithelium of bronchusUBERON:000203187.21gold quality
bronchusUBERON:000218586.68gold quality
caput epididymisUBERON:000435886.60gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047386.51gold quality
mucosa of paranasal sinusUBERON:000503086.48gold quality
corpus epididymisUBERON:000435986.22gold quality
tibiaUBERON:000097985.15gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099184.21gold quality
testisUBERON:000047383.39gold quality
right testisUBERON:000453483.34gold quality
tendonUBERON:000004382.55gold quality
left testisUBERON:000453382.50gold quality
seminal vesicleUBERON:000099881.89gold quality
choroid plexus epitheliumUBERON:000391181.73gold quality
ventricular zoneUBERON:000305380.77gold quality
islet of LangerhansUBERON:000000680.41gold quality
endometriumUBERON:000129579.92gold quality
visceral pleuraUBERON:000240179.75gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450279.74silver quality
parietal pleuraUBERON:000240079.65gold quality
stromal cell of endometriumCL:000225579.57gold quality
cranial nerve IIUBERON:000094179.39gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes5.62
E-GEOD-124858no348.06

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):

miRNAMax scoreAvg scoremiRNA target_count
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-3646100.0073.565283
HSA-MIR-3924100.0072.092394
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-186-5P99.9970.833707
HSA-MIR-32-5P99.9875.211964
HSA-MIR-92A-3P99.9875.211960
HSA-MIR-92B-3P99.9875.251955
HSA-MIR-25-3P99.9874.601817
HSA-MIR-363-3P99.9874.721821
HSA-MIR-367-3P99.9874.831819
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-381-3P99.9371.872854
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872
HSA-MIR-548AQ-3P99.9372.664867
HSA-MIR-30099.9271.762856
HSA-MIR-338-5P99.9272.342951
HSA-MIR-627-3P99.9071.423316

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

OrganismSymbolGene ID
danio_reriosnapc1bENSDARG00000003827
danio_reriosnapc1aENSDARG00000029569
mus_musculusSnapc1ENSMUSG00000021113
rattus_norvegicusSnapc1ENSRNOG00000009296
drosophila_melanogasterPbp45FBGN0038371
caenorhabditis_elegansWBGENE00012715
caenorhabditis_elegansWBGENE00015513
caenorhabditis_elegansWBGENE00017265
caenorhabditis_elegansWBGENE00019894

Protein

Protein identifiers

snRNA-activating protein complex subunit 1Q16533 (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)

IDNameType
IPR019188SNAPC1Family

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.

PDBMethodResolution (Å)
7ZWDELECTRON MICROSCOPY3
7ZX8ELECTRON MICROSCOPY3
9K3UELECTRON MICROSCOPY3
7ZWCELECTRON MICROSCOPY3.2
9FSOELECTRON MICROSCOPY3.28
9LXNELECTRON MICROSCOPY3.3
9FSPELECTRON MICROSCOPY3.39
7ZX7ELECTRON MICROSCOPY3.4
8IUHELECTRON MICROSCOPY3.4
7XURELECTRON MICROSCOPY3.49
7ZXEELECTRON MICROSCOPY3.5
9K3VELECTRON MICROSCOPY3.5
9FSQELECTRON MICROSCOPY3.51
9FSRELECTRON MICROSCOPY3.76
8ITYELECTRON MICROSCOPY3.9
8IUEELECTRON MICROSCOPY4.1
9FSSELECTRON MICROSCOPY4.14
9K3BELECTRON MICROSCOPY4.8

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q16533-F171.910.35

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

IDPathway
R-HSA-6807505RNA polymerase II transcribes snRNA genes
R-HSA-749476RNA Polymerase III Abortive And Retractive Initiation
R-HSA-76071RNA Polymerase III Transcription Initiation From Type 3 Promoter
R-HSA-73857RNA Polymerase II Transcription
R-HSA-74158RNA Polymerase III Transcription
R-HSA-74160Gene expression (Transcription)
R-HSA-76046RNA 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:

CategoryPathways
RNA Polymerase III Transcription2
Gene expression (Transcription)2
RNA Polymerase II Transcription1
RNA Polymerase III Transcription Initiation1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
transcription by RNA polymerase II2
snRNA transcription2
transcription by RNA polymerase III2
general transcription initiation factor activity2
nuclear lumen2
DNA binding1
nucleic acid binding1
binding1
cellular anatomical structure1
intracellular membraneless organelle1
transcription regulator complex1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

586 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SNAPC1SNAPC3Q92966999
SNAPC1SNAPC2Q13487997
SNAPC1SNAPC4Q5SXM2996
SNAPC1SNAPC5O75971984
SNAPC1TBPP20226830
SNAPC1TAF1AQ15573650
SNAPC1BDP1A6H8Y1542
SNAPC1POLIQ9UNA4534
SNAPC1BRF2Q9HAW0506
SNAPC1INTS10Q9NVR2486
SNAPC1POLR3DP05423446
SNAPC1TTC23Q5W5X9392
SNAPC1POLR3FQ9H1D9390
SNAPC1GTF3C1Q12789389
SNAPC1MFFQ9GZY8376

IntAct

52 interactions, top by confidence:

ABTypeScore
SNAPC1SNAPC3psi-mi:“MI:0915”(physical association)0.850
SNAPC1SNAPC3psi-mi:“MI:0914”(association)0.850
SNAPC4SNAPC1psi-mi:“MI:0914”(association)0.790
SNAPC1SNAPC5psi-mi:“MI:0914”(association)0.740
SNAPC1SNAPC5psi-mi:“MI:0915”(physical association)0.740
NAP1L5IQGAP1psi-mi:“MI:0914”(association)0.640
SNAPC4SNAPC5psi-mi:“MI:0914”(association)0.620
HAT1SNAPC1psi-mi:“MI:0915”(physical association)0.560
CCDC6SNAPC1psi-mi:“MI:0915”(physical association)0.560
SNAPC1psi-mi:“MI:0915”(physical association)0.560
SNAPC1EXOC8psi-mi:“MI:0915”(physical association)0.560
HSF2BPSNAPC1psi-mi:“MI:0915”(physical association)0.560
SNAPC1psi-mi:“MI:0914”(association)0.540
SNAPC1psi-mi:“MI:0915”(physical association)0.540
CSPP1SNAPC1psi-mi:“MI:0915”(physical association)0.400
SNAPC1NR2E3psi-mi:“MI:0915”(physical association)0.370
SNAPC1TRIM29psi-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.

AEffectBMechanism
SNAPC1“form complex”SNAPCbinding

Disease & clinical

Clinical variants and AI predictions

ClinVar

55 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance44
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1755 predictions. Top by Δscore:

VariantEffectΔscore
14:61762568:G:GTdonor_gain1.0000
14:61762589:GTGG:Gdonor_loss1.0000
14:61762590:T:Adonor_loss1.0000
14:61767203:T:Aacceptor_gain1.0000
14:61776249:GAAAG:Gdonor_gain1.0000
14:61776250:AAAGG:Adonor_loss1.0000
14:61776252:AGG:Adonor_loss1.0000
14:61776253:GGT:Gdonor_loss1.0000
14:61776254:G:Tdonor_loss1.0000
14:61776255:T:Adonor_loss1.0000
14:61778070:A:AGacceptor_gain1.0000
14:61778071:G:GGacceptor_gain1.0000
14:61778138:G:GTdonor_gain1.0000
14:61778835:A:AGacceptor_gain1.0000
14:61778836:T:Gacceptor_gain1.0000
14:61778840:A:AGacceptor_gain1.0000
14:61778842:A:AGacceptor_gain1.0000
14:61778843:T:Gacceptor_gain1.0000
14:61778845:CA:Cacceptor_loss1.0000
14:61778846:A:ACacceptor_loss1.0000
14:61778846:A:AGacceptor_gain1.0000
14:61778847:G:GGacceptor_gain1.0000
14:61778847:GA:Gacceptor_gain1.0000
14:61778847:GAGAT:Gacceptor_gain1.0000
14:61778911:G:Adonor_loss1.0000
14:61778912:TAAG:Tdonor_loss1.0000
14:61782395:AAGG:Adonor_loss1.0000
14:61782398:GTAA:Gdonor_loss1.0000
14:61782399:T:Adonor_loss1.0000
14:61794947:A:AGacceptor_gain1.0000

AlphaMissense

2458 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
14:61766989:T:CL81P0.996
14:61767309:T:CL129P0.996
14:61762557:T:AW33R0.995
14:61762557:T:CW33R0.995
14:61766977:G:AG77D0.994
14:61767339:C:AA139E0.993
14:61778883:A:CK266N0.993
14:61778883:A:TK266N0.993
14:61766985:T:GY80D0.992
14:61767219:T:AV99D0.992
14:61762545:T:CF29L0.990
14:61762547:C:AF29L0.990
14:61762547:C:GF29L0.990
14:61766976:G:CG77R0.990
14:61782261:A:CR280S0.989
14:61782261:A:TR280S0.989
14:61782264:G:CR281S0.989
14:61782264:G:TR281S0.989
14:61762546:T:CF29S0.988
14:61766974:T:AV76D0.988
14:61766998:G:AG84E0.988
14:61767233:T:AW104R0.988
14:61767233:T:CW104R0.988
14:61767324:C:AA134E0.988
14:61762501:T:CL14P0.987
14:61762512:T:CF18L0.987
14:61762514:C:AF18L0.987
14:61762514:C:GF18L0.987
14:61767327:T:CF135S0.986
14:61782263:G:CR281T0.986

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):

StudyTraitp-value
GCST007576_180Chronotype7.000000e-09
GCST009391_1321Metabolite levels7.000000e-06
GCST009391_1410Metabolite levels8.000000e-06
GCST009391_310Metabolite levels3.000000e-06
GCST009391_316Metabolite levels4.000000e-07

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0008328chronotype measurement
EFO:0010519pantothenic acid measurement
EFO:00051325-HIAA measurement
EFO:0010430triacylglycerol 56:3 measurement
EFO:0010431triacylglycerol 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.

ChemicalActions (top 5)PubMed papers
Cyclosporineincreases expression3
Fluorouracildecreases expression2
Oxygenincreases expression2
Valproic Acidincreases expression2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression2
aristolochic acid Idecreases expression1
testosterone enanthateaffects expression1
methylmercuric chlorideincreases expression1
glycidyl methacrylateincreases expression1
sodium arsenateincreases abundance, increases expression1
nickel chlorideincreases expression1
CGP 52608affects binding, increases reaction1
monomethylarsonous acidincreases expression1
torcetrapibincreases expression1
ICG 001increases expression1
abrineincreases expression1
jinfukangaffects cotreatment, decreases expression1
(+)-JQ1 compounddecreases expression1
MT19c compoundincreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases expression1
2,3,5-trichloro-6-phenyl-(1,4)benzoquinonedecreases expression1
Leflunomideincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicincreases abundance, increases expression1
Benzo(a)pyrenedecreases methylation1
Calcitriolaffects cotreatment, increases expression1
Carmustineincreases expression1
Cisplatinaffects cotreatment, decreases expression1
Estradiolincreases expression1
Hydrogen Peroxideaffects expression1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_A6K5SEES3-1V human SNAPC1, clone1Embryonic stem cellMale
CVCL_A6K6SEES3-1V human SNAPC1, clone2Embryonic stem cellMale
CVCL_A6K7SEES3-1V human SNAPC1, clone3Embryonic stem cellMale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.