SNAPC2

Summary

SNAPC2 (small nuclear RNA activating complex polypeptide 2, HGNC:11135) is a protein-coding gene on chromosome 19p13.2, encoding snRNA-activating protein complex subunit 2 (Q13487). 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 99.5% of cancer cell lines).

This gene encodes a subunit of the snRNA-activating protein complex which is associated with the TATA box-binding protein. The encoded protein is necessary for RNA polymerase II and III dependent small-nuclear RNA gene transcription. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 6618 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 81 total
• Cancer dependency (DepMap): dependent in 99.5% of screened cell lines (common-essential)
• MANE Select transcript: NM_003083

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11135
Approved symbol	SNAPC2
Name	small nuclear RNA activating complex polypeptide 2
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Aliases	SNAP45, PTFdelta
Ensembl gene	ENSG00000104976
Ensembl biotype	protein_coding
OMIM	605076
Entrez	6618

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding, 3 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000221573, ENST00000593598, ENST00000595035, ENST00000595637, ENST00000596520, ENST00000597584, ENST00000704328, ENST00000853925, ENST00000971261

RefSeq mRNA: 1 — MANE Select: NM_003083 NM_003083

CCDS: CCDS12190

Canonical transcript exons

ENST00000221573 — 5 exons

Exon	Start	End
ENSE00001299112	7920338	7920549
ENSE00003512858	7922445	7923250
ENSE00003537926	7921423	7921542
ENSE00003555812	7921705	7921773
ENSE00003627169	7922035	7922347

Expression profiles

Bgee: expression breadth ubiquitous, 189 present calls, max score 95.81.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.2933 / max 223.4080, expressed in 1813 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
173630	27.1264	1810
173631	4.9127	1419
173632	0.2542	87

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	95.81	gold quality
body of uterus	UBERON:0009853	94.00	gold quality
left uterine tube	UBERON:0001303	92.58	gold quality
lower esophagus muscularis layer	UBERON:0035833	92.06	gold quality
lower esophagus	UBERON:0013473	92.03	gold quality
popliteal artery	UBERON:0002250	91.46	gold quality
tibial artery	UBERON:0007610	91.43	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	91.35	gold quality
muscle layer of sigmoid colon	UBERON:0035805	91.15	gold quality
mucosa of stomach	UBERON:0001199	91.07	gold quality
endocervix	UBERON:0000458	90.59	gold quality
aorta	UBERON:0000947	90.15	gold quality
right testis	UBERON:0004534	89.92	gold quality
left testis	UBERON:0004533	89.56	gold quality
granulocyte	CL:0000094	89.23	gold quality
ectocervix	UBERON:0012249	89.06	gold quality
descending thoracic aorta	UBERON:0002345	88.93	gold quality
right hemisphere of cerebellum	UBERON:0014890	88.64	gold quality
thoracic aorta	UBERON:0001515	88.57	gold quality
ascending aorta	UBERON:0001496	88.51	gold quality
right coronary artery	UBERON:0001625	88.49	gold quality
cerebellar hemisphere	UBERON:0002245	88.32	gold quality
cerebellar cortex	UBERON:0002129	88.20	gold quality
left coronary artery	UBERON:0001626	88.19	gold quality
coronary artery	UBERON:0001621	87.75	gold quality
adenohypophysis	UBERON:0002196	87.75	gold quality
apex of heart	UBERON:0002098	87.73	gold quality
nucleus accumbens	UBERON:0001882	87.33	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	87.10	gold quality
pituitary gland	UBERON:0000007	86.96	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.65

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

14 targeting SNAPC2, 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-6794-5P	99.76	66.38	1048
HSA-MIR-4716-3P	99.69	66.73	1022
HSA-MIR-3679-3P	99.64	69.88	1599
HSA-MIR-4311	99.31	70.47	3041
HSA-MIR-6734-3P	99.15	66.27	1627
HSA-MIR-625-5P	99.02	68.64	2031
HSA-MIR-3166	98.24	66.63	1223
HSA-MIR-3179	98.22	65.90	1445
HSA-MIR-10397-5P	97.31	69.06	710
HSA-MIR-6859-3P	97.26	64.69	428
HSA-MIR-874-5P	96.93	63.92	1014
HSA-MIR-3194-5P	96.80	64.90	1027
HSA-MIR-3675-5P	95.90	65.80	474
HSA-MIR-6816-3P	95.05	66.08	459

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.5% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 2)

• SNAP45 plays two roles in the cell, one as a subunit of the transcription factor SNAP(c) and another as a factor required for proper mitotic progression (PMID:18356157)
• The findings invoke a model wherein incomplete DNA synthesis during S phase leads to a DNA damage response and formation of 53BP1-OPT domains in the subsequent G1. (PMID:21444690)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	snapc2	ENSDARG00000036473
mus_musculus	Snapc2	ENSMUSG00000011837
rattus_norvegicus	Snapc2	ENSRNOG00000001056

Protein

Protein identifiers

snRNA-activating protein complex subunit 2 — Q13487 (reviewed: Q13487)

Alternative names: Proximal sequence element-binding transcription factor subunit delta, Small nuclear RNA-activating complex polypeptide 2, snRNA-activating protein complex 45 kDa subunit

All UniProt accessions (3): M0QXY9, M0R1L8, Q13487

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. SNAPC2 interacts with TBP and SNAPC4.

Subcellular location. Nucleus.

RefSeq proteins (1): NP_003074* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR021281	SNAPC2	Family

Pfam: PF11035

UniProt features (5 total): region of interest 2, chain 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q13487-F1	67.10	0.05

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: 106 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_DN, REACTOME_RNA_POLYMERASE_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GOBP_TRANSCRIPTION_BY_RNA_POLYMERASE_III, BLALOCK_ALZHEIMERS_DISEASE_UP, SANSOM_APC_TARGETS_UP, WANG_CISPLATIN_RESPONSE_AND_XPC_DN, MEDINA_SMARCA4_TARGETS, HAMAI_APOPTOSIS_VIA_TRAIL_DN, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, CHIARADONNA_NEOPLASTIC_TRANSFORMATION_CDC25_DN, GOCC_NUCLEAR_BODY, GOCC_TRANSCRIPTION_REGULATOR_COMPLEX, chr19p13, MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP

GO Biological Process (3): transcription by RNA polymerase II (GO:0006366), transcription by RNA polymerase III (GO:0006383), snRNA transcription (GO:0009301)

GO Molecular Function (1): RNA polymerase II general transcription initiation factor activity (GO:0016251)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829), nuclear body (GO:0016604)

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
DNA-templated transcription	3
cellular anatomical structure	2
snRNA metabolic process	1
transcription by RNA polymerase II	1
general transcription initiation factor activity	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cytoplasm	1
nucleoplasm	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

382 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SNAPC2	SNAPC3	Q92966	999
SNAPC2	SNAPC1	Q16533	997
SNAPC2	SNAPC4	Q5SXM2	997
SNAPC2	SNAPC5	O75971	988
SNAPC2	TBP	P20226	709
SNAPC2	TAF1A	Q15573	650
SNAPC2	POLI	Q9UNA4	534
SNAPC2	INTS10	Q9NVR2	490
SNAPC2	TM9SF1	O15321	452
SNAPC2	BRF2	Q9HAW0	404
SNAPC2	BDP1	A6H8Y1	399
SNAPC2	ZNF865	P0CJ78	377
SNAPC2	ZNF524	Q96C55	370
SNAPC2	TM9SF4	Q92544	367
SNAPC2	ZC3H8	Q8N5P1	365

IntAct

10 interactions, top by confidence:

A	B	Type	Score
SNAPC1	SNAPC5	psi-mi:“MI:0914”(association)	0.740
SNAPC4	KDM5C	psi-mi:“MI:0914”(association)	0.530
SNAPC2	MBD1	psi-mi:“MI:0915”(physical association)	0.370
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
ANKRD36B	CCDC66	psi-mi:“MI:0914”(association)	0.350
SNAPC4	PIK3C2A	psi-mi:“MI:0914”(association)	0.350
SNAPC1	RP2	psi-mi:“MI:0914”(association)	0.350

BioGRID (19): SNAPC2 (Affinity Capture-MS), SNAPC2 (Affinity Capture-MS), SNAPC2 (Affinity Capture-MS), TBP (Reconstituted Complex), SNAPC2 (Negative Genetic), SNAPC2 (Reconstituted Complex), SNAPC4 (Reconstituted Complex), SNAPC2 (Two-hybrid), SNAPC2 (Affinity Capture-MS), SNAPC2 (Affinity Capture-MS), SNAPC2 (Affinity Capture-MS), SNAPC2 (Reconstituted Complex), SNAPC2 (Negative Genetic), SNAPC2 (Negative Genetic), TBP (Affinity Capture-Western)

ESM2 similar proteins: A0A1B0GUA5, A0A494C0Y3, A0JNN8, A2A9F4, A2ARS0, A2VDX9, A5A769, A5PJP1, A8MTW9, C9JTQ0, O54887, P0C171, P0DJK0, P0DPE3, P36343, P60531, P98162, Q13487, Q1HCM0, Q1LZC5, Q2TBK3, Q2VPJ9, Q566C8, Q5BLP8, Q5JTB6, Q5NRQ0, Q64322, Q68FX5, Q6F5E0, Q6QNY0, Q6VUP9, Q7TN12, Q7TPD7, Q867D0, Q8K025, Q8MJW9, Q8NAX2, Q8NG41, Q8TAP8, Q8TEF2

Diamond homologs: Q13487, Q68FX5, Q91XA5

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
SNAPC2	“form complex”	SNAPC	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	62
Likely benign	11
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

542 predictions. Top by Δscore:

Variant	Effect	Δscore
19:7920546:TGAGG:T	donor_loss	1.0000
19:7920547:GAG:G	donor_gain	1.0000
19:7920550:G:GG	donor_gain	1.0000
19:7921418:TCTA:T	acceptor_loss	1.0000
19:7921420:TA:T	acceptor_loss	1.0000
19:7921421:A:AG	acceptor_gain	1.0000
19:7921422:G:A	acceptor_loss	1.0000
19:7921422:G:GC	acceptor_gain	1.0000
19:7921422:GATC:G	acceptor_gain	1.0000
19:7921422:GATCC:G	acceptor_gain	1.0000
19:7921539:AGAG:A	donor_loss	1.0000
19:7921540:GAG:G	donor_gain	1.0000
19:7921540:GAGG:G	donor_loss	1.0000
19:7921541:AG:A	donor_loss	1.0000
19:7921544:T:A	donor_loss	1.0000
19:7921700:C:G	acceptor_gain	1.0000
19:7921700:CTCA:C	acceptor_loss	1.0000
19:7921701:TCAG:T	acceptor_loss	1.0000
19:7921702:CAG:C	acceptor_loss	1.0000
19:7921703:A:AG	acceptor_gain	1.0000
19:7921703:A:C	acceptor_loss	1.0000
19:7921704:G:GG	acceptor_gain	1.0000
19:7921704:GGTCT:G	acceptor_gain	1.0000
19:7921772:AGGTA:A	donor_loss	1.0000
19:7921773:GG:G	donor_loss	1.0000
19:7921775:T:G	donor_loss	1.0000
19:7922016:T:TA	acceptor_gain	1.0000
19:7922025:T:TA	acceptor_gain	1.0000
19:7922031:CCAGG:C	acceptor_loss	1.0000
19:7922032:CAGGT:C	acceptor_loss	1.0000

AlphaMissense

2087 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:7921708:T:A	W103R	0.993
19:7921708:T:C	W103R	0.993
19:7920436:T:A	W24R	0.991
19:7920436:T:C	W24R	0.991
19:7922466:T:C	L236P	0.991
19:7920438:G:C	W24C	0.989
19:7920438:G:T	W24C	0.989
19:7922457:T:A	V233D	0.988
19:7920383:G:T	R6M	0.981
19:7921710:G:C	W103C	0.981
19:7921710:G:T	W103C	0.981
19:7922450:G:C	A231P	0.980
19:7922447:T:C	S230P	0.978
19:7921765:T:C	F122L	0.970
19:7921767:C:A	F122L	0.970
19:7921767:C:G	F122L	0.970
19:7922278:T:C	F206L	0.970
19:7922280:T:A	F206L	0.970
19:7922280:T:G	F206L	0.970
19:7922710:C:A	N317K	0.970
19:7922710:C:G	N317K	0.970
19:7922469:T:C	L237P	0.968
19:7922336:T:A	L225H	0.967
19:7920384:G:C	R6S	0.965
19:7920384:G:T	R6S	0.965
19:7922460:T:C	L234P	0.965
19:7921709:G:C	W103S	0.963
19:7922451:C:A	A231D	0.963
19:7921766:T:C	F122S	0.961
19:7922045:T:A	I128N	0.961

dbSNP variants (sampled 300 via entrez): RS1000267087 (19:7918731 G>A), RS1000281750 (19:7923365 G>A,C), RS1000382049 (19:7923473 C>T), RS1001690595 (19:7919835 T>C), RS1002273648 (19:7921338 G>A,C), RS1002534650 (19:7921833 A>G), RS1002853325 (19:7919335 G>T), RS1003805846 (19:7920739 G>A), RS1004159050 (19:7918346 C>G), RS1004538830 (19:7923483 A>G), RS1004584633 (19:7923111 C>A,T), RS1005135048 (19:7919250 C>G,T), RS1005166253 (19:7919668 C>A,T), RS1006140935 (19:7921059 A>G), RS1006172041 (19:7921259 G>A)

Disease associations

OMIM: gene MIM:605076 | 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
GCST008987_6	HDL cholesterol	3.000000e-07
GCST008988_4	LDL cholesterol	5.000000e-07

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004611	low density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression, affects cotreatment, increases abundance	3
manganese chloride	affects cotreatment, increases abundance, increases expression	1
di-n-butylphosphoric acid	affects expression	1
ICG 001	increases expression	1
Temozolomide	decreases expression	1
Fulvestrant	increases methylation	1
Acetaminophen	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	increases abundance, increases expression, affects cotreatment	1
Atrazine	increases expression	1
Benzo(a)pyrene	affects methylation	1
Cadmium	decreases expression	1
Diazinon	increases methylation	1
Doxorubicin	decreases expression	1
Manganese	increases expression, affects cotreatment, increases abundance	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases methylation	1
Urethane	increases expression	1
Valproic Acid	increases methylation	1
Particulate Matter	increases expression, increases abundance	1

Clinical trials (associated diseases)

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