SNRNP27

Summary

SNRNP27 (small nuclear ribonucleoprotein U4/U6.U5 subunit 27, HGNC:30240) is a protein-coding gene on chromosome 2p13.3, encoding U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein (Q8WVK2). May play a role in mRNA splicing. It is a common-essential gene (DepMap: required in 99.7% of cancer cell lines).

This gene encodes a serine/arginine-rich (SR) protein. SR proteins play important roles in pre-mRNA splicing by facilitating the recognition and selection of splice sites. The encoded protein associates with the 25S U4/U6.U5 tri-snRNP, a major component of the U2-type spiceosome. The expression of this gene may be altered in cells infected with the human T-cell lymphotropic virus type 1 (HTLV-1) retrovirus. A pseudogene of this gene is located on the long arm of chromosome 5. Alternatively spliced transcript variants have been observed for this gene.

Source: NCBI Gene 11017 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 29 total
• Cancer dependency (DepMap): dependent in 99.7% of screened cell lines (common-essential)
• MANE Select transcript: NM_006857

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30240
Approved symbol	SNRNP27
Name	small nuclear ribonucleoprotein U4/U6.U5 subunit 27
Location	2p13.3
Locus type	gene with protein product
Status	Approved
Aliases	RY1, U4/U6.U5-27K
Ensembl gene	ENSG00000124380
Ensembl biotype	protein_coding
OMIM	619629
Entrez	11017

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 5 protein_coding, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000244227, ENST00000409116, ENST00000450162, ENST00000487029, ENST00000488986, ENST00000911721, ENST00000911722, ENST00000958235

RefSeq mRNA: 1 — MANE Select: NM_006857 NM_006857

CCDS: CCDS33219

Canonical transcript exons

ENST00000244227 — 6 exons

Exon	Start	End
ENSE00000846474	69896436	69896548
ENSE00001006484	69904254	69905236
ENSE00001006485	69895094	69895214
ENSE00001129931	69893956	69894018
ENSE00003482488	69897377	69897456
ENSE00003676464	69903181	69903245

Expression profiles

Bgee: expression breadth ubiquitous, 298 present calls, max score 98.64.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 62.7804 / max 904.2777, expressed in 1824 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
20777	50.3882	1820
20778	12.3922	1796

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	98.64	gold quality
muscle of leg	UBERON:0001383	95.89	gold quality
gastrocnemius	UBERON:0001388	95.87	gold quality
ganglionic eminence	UBERON:0004023	95.37	gold quality
muscle organ	UBERON:0001630	95.24	gold quality
skeletal muscle organ	UBERON:0014892	95.24	gold quality
sural nerve	UBERON:0015488	95.11	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	94.96	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	94.91	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	94.74	gold quality
amygdala	UBERON:0001876	94.71	gold quality
ventricular zone	UBERON:0003053	94.69	gold quality
pigmented layer of retina	UBERON:0001782	94.62	gold quality
retina	UBERON:0000966	94.60	gold quality
biceps brachii	UBERON:0001507	94.59	gold quality
tibialis anterior	UBERON:0001385	94.39	gold quality
skeletal muscle tissue	UBERON:0001134	94.36	gold quality
nucleus accumbens	UBERON:0001882	94.29	gold quality
hindlimb stylopod muscle	UBERON:0004252	94.28	gold quality
mucosa of paranasal sinus	UBERON:0005030	94.20	gold quality
heart right ventricle	UBERON:0002080	94.05	gold quality
spinal cord	UBERON:0002240	94.00	gold quality
hypothalamus	UBERON:0001898	93.87	gold quality
superficial temporal artery	UBERON:0001614	93.82	gold quality
deltoid	UBERON:0001476	93.75	gold quality
choroid plexus epithelium	UBERON:0003911	93.71	gold quality
islet of Langerhans	UBERON:0000006	93.53	gold quality
cortical plate	UBERON:0005343	93.51	gold quality
Brodmann (1909) area 9	UBERON:0013540	93.34	gold quality
buccal mucosa cell	CL:0002336	93.33	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.80

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

65 targeting SNRNP27, 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-5692A	100.00	74.40	6850
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-6755-5P	99.95	65.59	464
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-380-3P	99.89	70.18	1978
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-8080	99.82	67.52	1342
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-5197-5P	99.64	69.08	1494
HSA-MIR-4666B	99.64	68.69	1282
HSA-MIR-875-3P	99.63	69.47	2548
HSA-MIR-3685	99.62	68.83	1621
HSA-MIR-4762-5P	99.57	68.54	1424
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-154-3P	99.50	70.05	831
HSA-MIR-487A-3P	99.50	69.95	840
HSA-MIR-409-3P	99.50	66.33	1192
HSA-MIR-217-5P	99.49	69.93	1419

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.7% of screened cell lines, common-essential.

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	snrnp27	ENSDARG00000035625
mus_musculus	Snrnp27	ENSMUSG00000001158
rattus_norvegicus	Snrnp27	ENSRNOG00000065135
rattus_norvegicus	LOC100910341	ENSRNOG00000070440
caenorhabditis_elegans	snrp-27	WBGENE00011035

Protein

Protein identifiers

U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein — Q8WVK2 (reviewed: Q8WVK2)

Alternative names: Nucleic acid-binding protein RY-1, U4/U6.U5 tri-snRNP-associated 27 kDa protein, U4/U6.U5 tri-snRNP-associated protein 3

All UniProt accessions (4): A8K513, B8ZZ98, Q8WVK2, H0YBW5

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in mRNA splicing.

Subunit / interactions. Part of a tri-snRNP complex.

Subcellular location. Nucleus.

Post-translational modifications. Phosphorylated in vitro by snRNP-associated protein kinase.

Similarity. Belongs to the SNUT3 family.

RefSeq proteins (1): NP_006848* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013957	SNRNP27	Domain

Pfam: PF08648

UniProt features (12 total): modified residue 5, compositionally biased region 3, sequence variant 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

10 structures.

PDB	Method	Resolution (Å)
6QW6	ELECTRON MICROSCOPY	2.92
8H6E	ELECTRON MICROSCOPY	3.2
8H6J	ELECTRON MICROSCOPY	3.25
6QX9	ELECTRON MICROSCOPY	3.28
8QP8	ELECTRON MICROSCOPY	3.5
8QP9	ELECTRON MICROSCOPY	4.1
8QPK	ELECTRON MICROSCOPY	4.2
8R0A	ELECTRON MICROSCOPY	5.8
8R08	ELECTRON MICROSCOPY	6.1
8QXD	ELECTRON MICROSCOPY	9.6

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WVK2-F1	59.22	0.00

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 (5): 61, 65, 111, 114, 132

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-72163	mRNA Splicing - Major Pathway
R-HSA-72172	mRNA Splicing
R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854	Metabolism of RNA

MSigDB gene sets: 144 (showing top): HORIUCHI_WTAP_TARGETS_DN, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, MARTINEZ_RB1_TARGETS_DN, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_RNA_SPLICING, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13, MCBRYAN_PUBERTAL_BREAST_5_6WK_UP, REACTOME_MRNA_SPLICING, WANG_CISPLATIN_RESPONSE_AND_XPC_DN, MARTINEZ_RB1_AND_TP53_TARGETS_UP, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOBP_SPLICEOSOMAL_SNRNP_ASSEMBLY, REACTOME_METABOLISM_OF_RNA, GOCC_PRECATALYTIC_SPLICEOSOME

GO Biological Process (3): mRNA splicing, via spliceosome (GO:0000398), mRNA processing (GO:0006397), RNA splicing (GO:0008380)

GO Molecular Function (2): nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), spliceosomal complex (GO:0005681), U4/U6 x U5 tri-snRNP complex (GO:0046540)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
mRNA Splicing	1
Processing of Capped Intron-Containing Pre-mRNA	1
Metabolism of RNA	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
binding	2
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
mRNA metabolic process	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1
nuclear protein-containing complex	1
ribonucleoprotein complex	1
U5 snRNP	1
U4/U6 snRNP	1
spliceosomal tri-snRNP complex	1

Protein interactions and networks

STRING

1648 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SNRNP27	USP39	Q53GS9	940
SNRNP27	SNRNP70	P08621	758
SNRNP27	GPATCH1	Q9BRR8	487
SNRNP27	SART1	O43290	478
SNRNP27	KCNJ5-AS1	Q8TAV5	478
SNRNP27	LSM7	Q9UK45	421
SNRNP27	HOATZ	Q6PI97	400
SNRNP27	CIRSR	Q86X95	373
SNRNP27	SRRM1	Q8IYB3	373
SNRNP27	FAM13B	Q9NYF5	370
SNRNP27	CFAP92	Q9ULG3	360
SNRNP27	RSRC1	Q96IZ7	356
SNRNP27	EIF1AD	Q8N9N8	346
SNRNP27	ARRDC4	Q8NCT1	340
SNRNP27	GPN3	Q9UHW5	340

IntAct

86 interactions, top by confidence:

A	B	Type	Score
SNRPE	GEMIN2	psi-mi:“MI:0914”(association)	0.770
SNRNP27	SRPK2	psi-mi:“MI:0915”(physical association)	0.750
SNRNP27	SRPK2	psi-mi:“MI:0217”(phosphorylation reaction)	0.750
SRPK2	SNRNP27	psi-mi:“MI:0915”(physical association)	0.750
PRPF3	PRPF4	psi-mi:“MI:0914”(association)	0.730
SNRPG	GEMIN2	psi-mi:“MI:0914”(association)	0.710
SNRPA1	U2SURP	psi-mi:“MI:0914”(association)	0.640
SNRNP27	UBA6	psi-mi:“MI:0914”(association)	0.530
SNRPE	PRMT5	psi-mi:“MI:0914”(association)	0.530
SNRPN	PRMT5	psi-mi:“MI:0914”(association)	0.530
SNRPE	SNRPGP15	psi-mi:“MI:0914”(association)	0.530
KIF2C	KIF2A	psi-mi:“MI:0914”(association)	0.530
SNRNP40	AQR	psi-mi:“MI:0914”(association)	0.530
EZH1	EPOP	psi-mi:“MI:0914”(association)	0.530
DRG1	LRRC41	psi-mi:“MI:0914”(association)	0.530
SNRNP27	CHERP	psi-mi:“MI:0915”(physical association)	0.510
CHERP	SNRNP27	psi-mi:“MI:0915”(physical association)	0.510
Prpf8		psi-mi:“MI:0915”(physical association)	0.400
OTUB1		psi-mi:“MI:0914”(association)	0.350
ATL2	ACRBP	psi-mi:“MI:0914”(association)	0.350
LAMB3	MRPL58	psi-mi:“MI:0914”(association)	0.350
SNRPGP15	GEMIN2	psi-mi:“MI:0914”(association)	0.350
LSM5	LSM1	psi-mi:“MI:0914”(association)	0.350
PRPF3	PRPF4	psi-mi:“MI:0914”(association)	0.350
RBM42	SART1	psi-mi:“MI:0914”(association)	0.350

BioGRID (270): SNRNP27 (Two-hybrid), SNRNP27 (Affinity Capture-MS), SNRNP27 (Affinity Capture-MS), ARGLU1 (Co-fractionation), SNRNP27 (Affinity Capture-MS), SNRNP27 (Affinity Capture-MS), SNRNP27 (Affinity Capture-MS), SNRNP27 (Affinity Capture-MS), RECQL (Affinity Capture-MS), SNRNP27 (Affinity Capture-MS), WDR5B (Affinity Capture-MS), C9orf89 (Affinity Capture-MS), EIF2A (Affinity Capture-MS), SBDS (Affinity Capture-MS), SNRNP27 (Affinity Capture-MS)

ESM2 similar proteins: A0JNI5, A2AJT4, A2AQ19, A4IFB1, B1H1X4, D3ZTQ1, O43290, P35269, Q05519, Q12872, Q13435, Q3THK3, Q3UJB0, Q3UQU0, Q3USH5, Q4V7C9, Q53F19, Q568R1, Q5EA53, Q5HZB6, Q5PQQ2, Q5R539, Q5RAD5, Q5XIW8, Q5ZM19, Q66I22, Q6AY96, Q6DDA4, Q6GLZ8, Q6INH5, Q6ZPZ3, Q8BZR9, Q8CFC7, Q8K194, Q8N2M8, Q8N5F7, Q8TF01, Q8VHI6, Q8WVK2, Q923D5

Diamond homologs: O74418, Q6DDA4, Q6DH74, Q6GLZ8, Q8K194, Q8WVK2

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
SNRNP27	“form complex”	“U4/U6.U5 snRNP complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 117 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 Splicing	12	14.5×	1e-08
Processing of Capped Intron-Containing Pre-mRNA	12	10.8×	2e-07
mRNA Splicing - Major Pathway	18	10.8×	3e-11
CHD1 and CHD2 subfamily	7	8.4×	2e-03
Transcriptional regulation of granulopoiesis	6	8.3×	7e-03
Metabolism of RNA	15	6.9×	6e-07
Signaling by Interleukins	9	6.3×	2e-03
Dengue Virus-Host Interactions	10	5.0×	3e-03

GO biological processes:

GO term	Partners	Fold	FDR
RNA splicing, via transesterification reactions	6	33.7×	6e-06
spliceosomal complex assembly	5	27.1×	2e-04
spliceosomal snRNP assembly	5	26.2×	2e-04
mRNA splicing, via spliceosome	15	12.4×	9e-10
RNA splicing	15	11.9×	9e-10

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	16
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

656 predictions. Top by Δscore:

Variant	Effect	Δscore
2:69894016:GGG:G	donor_gain	1.0000
2:69894017:GGG:G	donor_gain	1.0000
2:69896427:A:AG	acceptor_gain	1.0000
2:69896428:A:G	acceptor_gain	1.0000
2:69896432:TTAG:T	acceptor_loss	1.0000
2:69896433:TAGAT:T	acceptor_loss	1.0000
2:69896434:A:AG	acceptor_gain	1.0000
2:69896434:AGATC:A	acceptor_loss	1.0000
2:69896435:G:GA	acceptor_gain	1.0000
2:69896545:ACTGG:A	donor_loss	1.0000
2:69896546:CTGGT:C	donor_loss	1.0000
2:69896547:TGGT:T	donor_loss	1.0000
2:69896548:GGTAA:G	donor_loss	1.0000
2:69896549:G:GG	donor_gain	1.0000
2:69896549:G:T	donor_loss	1.0000
2:69896550:T:A	donor_loss	1.0000
2:69897373:GCAGA:G	acceptor_loss	1.0000
2:69897374:CA:C	acceptor_loss	1.0000
2:69897375:A:AG	acceptor_gain	1.0000
2:69897375:AGAG:A	acceptor_gain	1.0000
2:69897376:G:GG	acceptor_gain	1.0000
2:69897376:GA:G	acceptor_gain	1.0000
2:69897376:GAGG:G	acceptor_gain	1.0000
2:69897376:GAGGA:G	acceptor_gain	1.0000
2:69897452:CAAAA:C	donor_gain	1.0000
2:69897453:AAAA:A	donor_gain	1.0000
2:69897453:AAAAG:A	donor_loss	1.0000
2:69897454:AAA:A	donor_gain	1.0000
2:69897455:AA:A	donor_gain	1.0000
2:69897455:AAGTA:A	donor_loss	1.0000

AlphaMissense

997 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:69897431:G:A	G108E	1.000
2:69903236:G:C	R135T	1.000
2:69903236:G:T	R135M	1.000
2:69903237:G:C	R135S	1.000
2:69903237:G:T	R135S	1.000
2:69903241:T:C	Y137H	1.000
2:69903241:T:G	Y137D	1.000
2:69903242:A:G	Y137C	1.000
2:69903244:A:G	R138G	1.000
2:69903244:A:T	R138W	1.000
2:69903245:G:C	R138T	1.000
2:69903245:G:T	R138M	1.000
2:69904254:G:C	R138S	1.000
2:69904254:G:T	R138S	1.000
2:69904257:G:C	Q139H	1.000
2:69904257:G:T	Q139H	1.000
2:69904258:T:A	Y140N	1.000
2:69904258:T:C	Y140H	1.000
2:69904258:T:G	Y140D	1.000
2:69904259:A:C	Y140S	1.000
2:69904259:A:G	Y140C	1.000
2:69904262:T:A	M141K	1.000
2:69904262:T:C	M141T	1.000
2:69904262:T:G	M141R	1.000
2:69904263:G:A	M141I	1.000
2:69904263:G:C	M141I	1.000
2:69904263:G:T	M141I	1.000
2:69904264:A:C	N142H	1.000
2:69904264:A:G	N142D	1.000
2:69904265:A:T	N142I	1.000

dbSNP variants (sampled 300 via entrez): RS1000133120 (2:69903229 C>G,T), RS1000133988 (2:69891962 G>A), RS1000861754 (2:69896320 C>A,G), RS1001291079 (2:69895980 T>G), RS1002246113 (2:69894105 G>A), RS1002400806 (2:69901490 T>A), RS1002601600 (2:69894639 G>T), RS1002632852 (2:69902766 T>C), RS1002934507 (2:69901643 C>T), RS1003065434 (2:69897672 G>A,C), RS1003197625 (2:69892607 A>G), RS1003476571 (2:69900149 G>A), RS1003824286 (2:69904082 T>C), RS1003913538 (2:69893159 A>G), RS1004030016 (2:69896679 T>G)

Disease associations

OMIM: gene MIM:619629 | 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
GCST006061_105	Atrial fibrillation	6.000000e-19
GCST009665_12	Breast cancer	4.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, increases expression	2
FR900359	increases phosphorylation	1
avobenzone	increases expression	1
di-n-butylphosphoric acid	affects expression	1
yessotoxin	decreases expression	1
abrine	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	decreases methylation	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Methyl Methanesulfonate	increases expression	1
Ribonucleotides	affects binding	1
Selenium	decreases expression	1
Tetrachlorodibenzodioxin	affects expression	1
Valproic Acid	decreases expression	1
Vitamin E	decreases expression	1
Aflatoxin B1	increases expression, increases methylation	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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