SNRNP40

Summary

SNRNP40 (small nuclear ribonucleoprotein U5 subunit 40, HGNC:30857) is a protein-coding gene on chromosome 1p35.2, encoding U5 small nuclear ribonucleoprotein 40 kDa protein (Q96DI7). Required for pre-mRNA splicing as component of the activated spliceosome. It is a selective cancer dependency (DepMap: 90.0% of cell lines).

This gene encodes a component of the U5 small nuclear ribonucleoprotein (snRNP) particle. The U5 snRNP is part of the spliceosome, a multiprotein complex that catalyzes the removal of introns from pre-messenger RNAs.

Source: NCBI Gene 9410 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 44 total
• Cancer dependency (DepMap): dependent in 90.0% of screened cell lines
• MANE Select transcript: NM_004814

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30857
Approved symbol	SNRNP40
Name	small nuclear ribonucleoprotein U5 subunit 40
Location	1p35.2
Locus type	gene with protein product
Status	Approved
Aliases	PRP8BP, SPF38, PRPF8BP, HPRP8BP
Ensembl gene	ENSG00000060688
Ensembl biotype	protein_coding
OMIM	607797
Entrez	9410

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding_CDS_not_defined, 4 protein_coding

ENST00000263694, ENST00000373720, ENST00000463988, ENST00000474025, ENST00000486941, ENST00000489853, ENST00000491106, ENST00000862789, ENST00000923594

RefSeq mRNA: 1 — MANE Select: NM_004814 NM_004814

CCDS: CCDS340

Canonical transcript exons

ENST00000263694 — 10 exons

Exon	Start	End
ENSE00000825236	31291913	31292006
ENSE00000825237	31293219	31293348
ENSE00001219703	31259568	31260121
ENSE00001830257	31296611	31296788
ENSE00003543542	31281374	31281496
ENSE00003547622	31269158	31269240
ENSE00003610168	31261529	31261632
ENSE00003662103	31289254	31289419
ENSE00003677573	31271379	31271499
ENSE00003681572	31267871	31267932

Expression profiles

Bgee: expression breadth ubiquitous, 257 present calls, max score 94.22.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 50.7187 / max 296.0451, expressed in 1822 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
11458	48.2766	1821
11459	2.2678	1236
11455	0.1743	59

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ganglionic eminence	UBERON:0004023	94.22	gold quality
ventricular zone	UBERON:0003053	93.43	gold quality
mucosa of transverse colon	UBERON:0004991	93.22	gold quality
cerebellar hemisphere	UBERON:0002245	92.89	gold quality
cerebellar cortex	UBERON:0002129	92.82	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	92.54	gold quality
embryo	UBERON:0000922	92.45	gold quality
adenohypophysis	UBERON:0002196	92.27	gold quality
right hemisphere of cerebellum	UBERON:0014890	92.20	gold quality
ectocervix	UBERON:0012249	91.93	gold quality
right ovary	UBERON:0002118	91.86	gold quality
tibial nerve	UBERON:0001323	91.84	gold quality
body of uterus	UBERON:0009853	91.71	gold quality
skin of abdomen	UBERON:0001416	91.60	gold quality
granulocyte	CL:0000094	91.59	gold quality
left uterine tube	UBERON:0001303	91.58	gold quality
skin of leg	UBERON:0001511	91.50	gold quality
endocervix	UBERON:0000458	91.40	gold quality
left ovary	UBERON:0002119	91.29	gold quality
right uterine tube	UBERON:0001302	91.27	gold quality
cerebellum	UBERON:0002037	91.18	gold quality
spleen	UBERON:0002106	91.15	gold quality
right testis	UBERON:0004534	91.10	gold quality
rectum	UBERON:0001052	91.09	gold quality
right lobe of thyroid gland	UBERON:0001119	91.05	gold quality
islet of Langerhans	UBERON:0000006	90.85	gold quality
spinal cord	UBERON:0002240	90.83	gold quality
left testis	UBERON:0004533	90.77	gold quality
pituitary gland	UBERON:0000007	90.63	gold quality
upper lobe of left lung	UBERON:0008952	90.61	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

43 targeting SNRNP40, 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-3646	100.00	73.56	5283
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-345-3P	99.89	70.23	1421
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-374C-5P	99.80	72.06	2910
HSA-MIR-655-3P	99.80	72.19	2909
HSA-MIR-26A-1-3P	99.64	66.81	788
HSA-MIR-26A-2-3P	99.64	66.82	786
HSA-MIR-3120-3P	99.54	70.28	2669
HSA-MIR-154-3P	99.50	70.05	831
HSA-MIR-487A-3P	99.50	69.95	840
HSA-MIR-140-5P	99.44	67.20	792
HSA-MIR-29A-5P	99.08	68.59	1813
HSA-MIR-6868-5P	99.06	65.69	1284
HSA-MIR-452-3P	99.01	66.25	1241
HSA-MIR-605-5P	98.79	68.24	1161
HSA-MIR-876-3P	98.76	68.23	945
HSA-MIR-219A-2-3P	98.62	68.78	797

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 90.0% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 2)

• Clinically, low SNRNP40 expression is associated with metastatic relapse. (PMID:27138336)
• Novel genetic variants linked to prelabor rupture of membranes among Chinese pregnant women. (PMID:37054626)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	snrnp40	ENSDARG00000023160
mus_musculus	Snrnp40	ENSMUSG00000074088
rattus_norvegicus	Snrnp40	ENSRNOG00000012219
drosophila_melanogaster	CG3436	FBGN0031229
caenorhabditis_elegans		WBGENE00008586
caenorhabditis_elegans	snrp-40.2	WBGENE00015974

Paralogs (26): PAFAH1B1 (ENSG00000007168), WDR62 (ENSG00000075702), WDR7 (ENSG00000091157), TBL2 (ENSG00000106638), PAK1IP1 (ENSG00000111845), WDR75 (ENSG00000115368), DCAF4 (ENSG00000119599), DAW1 (ENSG00000123977), TEP1 (ENSG00000129566), AHI1 (ENSG00000135541), WDR38 (ENSG00000136918), MAPKBP1 (ENSG00000137802), POC1B (ENSG00000139323), NEDD1 (ENSG00000139350), COP1 (ENSG00000143207), WDR17 (ENSG00000150627), WDR43 (ENSG00000163811), POC1A (ENSG00000164087), WDR88 (ENSG00000166359), WDR81 (ENSG00000167716), DCAF4L2 (ENSG00000176566), DCAF4L1 (ENSG00000182308), WDR27 (ENSG00000184465), NWD1 (ENSG00000188039), WDR5 (ENSG00000196363), WDR5B (ENSG00000196981)

Protein

Protein identifiers

U5 small nuclear ribonucleoprotein 40 kDa protein — Q96DI7 (reviewed: Q96DI7)

Alternative names: 38 kDa-splicing factor, Prp8-binding protein, U5 snRNP-specific 40 kDa protein, WD repeat-containing protein 57

All UniProt accessions (3): Q96DI7, A0MNP2, Q9NSS8

UniProt curated annotations — full annotation on UniProt →

Function. Required for pre-mRNA splicing as component of the activated spliceosome. Component of the U5 small nuclear ribonucleoprotein (snRNP) complex and the U4/U6-U5 tri-snRNP complex, building blocks of the spliceosome. As a component of the minor spliceosome, involved in the splicing of U12-type introns in pre-mRNAs.

Subunit / interactions. Component of the pre-catalytic and catalytic spliceosome complexes. Component of the postcatalytic spliceosome P complex. Part of the U5 snRNP complex. Interacts with PRPF8. Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, WDR57, SNRNP40, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39. Component of the minor spliceosome, which splices U12-type introns.

Subcellular location. Nucleus.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96DI7-1	1	yes
Q96DI7-2	2

RefSeq proteins (1): NP_004805* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001680	WD40_rpt	Repeat
IPR015943	WD40/YVTN_repeat-like_dom_sf	Homologous_superfamily
IPR019775	WD40_repeat_CS	Conserved_site
IPR020472	WD40_PAC1	Repeat
IPR036322	WD40_repeat_dom_sf	Homologous_superfamily
IPR052234	U5_snRNP_Component	Family

Pfam: PF00400

UniProt features (56 total): strand 34, repeat 7, turn 6, sequence conflict 4, cross-link 2, chain 1, splice variant 1, modified residue 1

Structure

Experimental structures (PDB)

54 structures, top 30 by resolution.

PDB	Method	Resolution (Å)
8H6L	ELECTRON MICROSCOPY	2.6
8H6K	ELECTRON MICROSCOPY	2.7
8C6J	ELECTRON MICROSCOPY	2.8
6ID1	ELECTRON MICROSCOPY	2.86
7DVQ	ELECTRON MICROSCOPY	2.89
6ID0	ELECTRON MICROSCOPY	2.9
6QW6	ELECTRON MICROSCOPY	2.92
6ICZ	ELECTRON MICROSCOPY	3
8I0R	ELECTRON MICROSCOPY	3
8I0T	ELECTRON MICROSCOPY	3
8I0V	ELECTRON MICROSCOPY	3
8H6E	ELECTRON MICROSCOPY	3.2
8Q7Q	ELECTRON MICROSCOPY	3.2
8RC0	ELECTRON MICROSCOPY	3.2
8H6J	ELECTRON MICROSCOPY	3.25
6QX9	ELECTRON MICROSCOPY	3.28
6QDV	ELECTRON MICROSCOPY	3.3
8I0U	ELECTRON MICROSCOPY	3.3
9FMD	ELECTRON MICROSCOPY	3.3
8Y6O	ELECTRON MICROSCOPY	3.38
6ZYM	ELECTRON MICROSCOPY	3.4
8I0P	ELECTRON MICROSCOPY	3.4
8I0W	ELECTRON MICROSCOPY	3.4
8RO2	ELECTRON MICROSCOPY	3.5
5XJC	ELECTRON MICROSCOPY	3.6
7W59	ELECTRON MICROSCOPY	3.6
7W5A	ELECTRON MICROSCOPY	3.6
6AHD	ELECTRON MICROSCOPY	3.8
8Q7V	ELECTRON MICROSCOPY	3.8
8Q7W	ELECTRON MICROSCOPY	3.9

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96DI7-F1	85.70	0.75

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 (3): 270, 21, 18

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

ID	Pathway
R-HSA-72163	mRNA Splicing - Major Pathway
R-HSA-72165	mRNA Splicing - Minor Pathway
R-HSA-9918481	Dengue Virus-Host Interactions
R-HSA-72172	mRNA Splicing
R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854	Metabolism of RNA

MSigDB gene sets: 162 (showing top): ELVIDGE_HYPOXIA_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, PUJANA_CHEK2_PCC_NETWORK, GOBP_SPLICEOSOMAL_TRI_SNRNP_COMPLEX_ASSEMBLY, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_RNA_SPLICING, GENTILE_UV_HIGH_DOSE_DN, REACTOME_MRNA_SPLICING, ATF4_Q2, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP, FISCHER_DREAM_TARGETS, GTATGAT_MIR154_MIR487

GO Biological Process (5): RNA splicing, via transesterification reactions (GO:0000375), mRNA splicing, via spliceosome (GO:0000398), RNA processing (GO:0006396), RNA splicing (GO:0008380), mRNA processing (GO:0006397)

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (11): nucleus (GO:0005634), nucleoplasm (GO:0005654), spliceosomal complex (GO:0005681), U5 snRNP (GO:0005682), sno(s)RNA-containing ribonucleoprotein complex (GO:0005732), cytosol (GO:0005829), nuclear speck (GO:0016607), U4/U6 x U5 tri-snRNP complex (GO:0046540), U2-type catalytic step 2 spliceosome (GO:0071007), catalytic step 2 spliceosome (GO:0071013), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
mRNA Splicing	2
Dengue Virus Infection	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
cellular anatomical structure	3
RNA processing	2
ribonucleoprotein complex	2
U5 snRNP	2
RNA splicing	1
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
gene expression	1
RNA biosynthetic process	1
primary metabolic process	1
mRNA metabolic process	1
nucleic acid binding	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
nuclear protein-containing complex	1
spliceosomal snRNP complex	1
cytoplasm	1
nuclear ribonucleoprotein granule	1
U4/U6 snRNP	1
spliceosomal tri-snRNP complex	1
U2-type spliceosomal complex	1
U2 snRNP	1
U6 snRNP	1
catalytic step 2 spliceosome	1
Prp19 complex	1
spliceosomal complex	1
catalytic complex	1

Protein interactions and networks

STRING

1576 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SNRNP40	PRPF8	Q6P2Q9	947
SNRNP40	EFTUD2	Q15029	834
SNRNP40	SNRNP200	O75643	682
SNRNP40	PRPF6	O94906	645
SNRNP40	DDX23	Q9BUQ8	620
SNRNP40	DDX49	Q9Y6V7	575
SNRNP40	SF3B6	Q9Y3B4	543
SNRNP40	SNRNP70	P08621	543
SNRNP40	INTS9	Q9NV88	543
SNRNP40	SF3A3	Q12874	541
SNRNP40	AAR2	Q9Y312	537
SNRNP40	SNRNP35	Q16560	533
SNRNP40	POLR2B	P30876	519
SNRNP40	SF3A1	Q15459	515
SNRNP40	ZNHIT2	Q9UHR6	498

IntAct

170 interactions, top by confidence:

A	B	Type	Score
SNRNP40	PRPF8	psi-mi:“MI:0915”(physical association)	0.860
EFTUD2	SNRNP40	psi-mi:“MI:0915”(physical association)	0.810
SNRNP200	SNRNP40	psi-mi:“MI:0915”(physical association)	0.810
SNRNP40	SNRNP200	psi-mi:“MI:0914”(association)	0.810
SNRPE	GEMIN2	psi-mi:“MI:0914”(association)	0.770
DDX23	SNRNP40	psi-mi:“MI:0915”(physical association)	0.740
PRPF8	SNRNP200	psi-mi:“MI:0915”(physical association)	0.740
CUL4B	CUL4A	psi-mi:“MI:0914”(association)	0.730
PRPF3	PRPF4	psi-mi:“MI:0914”(association)	0.730
SYF2	AQR	psi-mi:“MI:0914”(association)	0.730
SART1	PRPF3	psi-mi:“MI:0914”(association)	0.720
SNRPD2	GEMIN2	psi-mi:“MI:0914”(association)	0.710
SNRPB	PRMT5	psi-mi:“MI:0914”(association)	0.670
SNW1	AQR	psi-mi:“MI:0914”(association)	0.650
PRPF8	PRPF4	psi-mi:“MI:0914”(association)	0.640
SF3B1	SAP18	psi-mi:“MI:0914”(association)	0.640
SNRNP40	PRPF4	psi-mi:“MI:0914”(association)	0.640
PFDN1	PFDN6	psi-mi:“MI:0914”(association)	0.640
DDX23	PRPF4	psi-mi:“MI:0914”(association)	0.640
PRP4K	PRPF4	psi-mi:“MI:0914”(association)	0.640
SNRNP40	GFAP	psi-mi:“MI:0915”(physical association)	0.560
GRN	SNRNP40	psi-mi:“MI:0915”(physical association)	0.560
PRKN	SNRNP40	psi-mi:“MI:0915”(physical association)	0.560
SNRNP40	PMP22	psi-mi:“MI:0915”(physical association)	0.560
ATXN1	SNRNP40	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (1030): SNRNP40 (Affinity Capture-RNA), SNRNP40 (Affinity Capture-RNA), SNRNP40 (Affinity Capture-MS), SNRNP40 (Affinity Capture-MS), SNRNP40 (Affinity Capture-MS), SNRNP40 (Affinity Capture-MS), SNRNP40 (Affinity Capture-MS), SNRNP40 (Affinity Capture-MS), PRPF3 (Affinity Capture-MS), PRPF6 (Affinity Capture-MS), SNRNP200 (Affinity Capture-MS), PRPF8 (Affinity Capture-MS), TFIP11 (Affinity Capture-MS), EFTUD2 (Affinity Capture-MS), PAXBP1 (Affinity Capture-MS)

ESM2 similar proteins: A4QNE6, B0BNA7, B3MEY6, B3S4I5, B5FZ19, C4Q0P6, D3TLL6, D3Z7A5, O43172, O74184, P41318, Q13347, Q17N69, Q29RH4, Q2HJH6, Q2TBP4, Q32LN7, Q38884, Q3KQ62, Q3MHE2, Q4V7A0, Q54D08, Q5BK30, Q5BLX8, Q5E966, Q5EBE8, Q5IH81, Q5NVD0, Q5R7R2, Q5RF51, Q5XGI5, Q5ZJH5, Q66J51, Q6DH44, Q6GMD2, Q6PBD6, Q6PE01, Q8JZX3, Q8NBT0, Q8VE80

Diamond homologs: A1CTE6, A1DMI8, A2QVV2, B0Y7H6, B8N4F5, D9N129, P16649, P56094, Q08274, Q09019, Q0CKB1, Q10437, Q2HJH6, Q2UM42, Q4WN25, Q5RF51, Q5XIG8, Q6ZMW3, Q8TBZ3, Q96DI7, Q9P4R5, Q9VBC4, Q9Y3F4, Q9Z1Z2, O22469, Q5ZL33, C4R6H3, C4YFX2, P0CY34, P16371, Q00664, Q5M786, Q5RE95, Q5SQM0, Q6ED65, Q6PE01, Q86VZ2, Q9SY00, A1CF18, A4IIX9

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
SNRNP40	“form complex”	“U4/U6.U5 snRNP complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 159 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
Metabolism of non-coding RNA	6	32.5×	9e-07
mRNA Splicing - Minor Pathway	14	26.8×	5e-15
mRNA Splicing	27	25.3×	8e-29
mRNA Splicing - Major Pathway	49	22.9×	1e-52
Processing of Capped Intron-Containing Pre-mRNA	29	20.4×	3e-28
mRNA 3’-end processing	11	18.5×	9e-10
RNA Polymerase II Transcription Termination	9	16.9×	2e-07
Transport of Mature Transcript to Cytoplasm	5	16.3×	4e-04

GO biological processes:

GO term	Partners	Fold	FDR
spliceosomal complex assembly	12	51.2×	6e-16
spliceosomal tri-snRNP complex assembly	6	47.8×	2e-07
RNA splicing, via transesterification reactions	10	44.3×	2e-12
spliceosomal snRNP assembly	10	41.2×	4e-12
U2-type prespliceosome assembly	9	39.8×	9e-11
regulation of mRNA splicing, via spliceosome	6	37.7×	7e-07
mRNA splicing, via spliceosome	47	30.5×	3e-55
negative regulation of mRNA splicing, via spliceosome	5	27.2×	6e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	25
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1366 predictions. Top by Δscore:

Variant	Effect	Δscore
1:31261527:A:AC	donor_gain	1.0000
1:31261528:C:CA	donor_gain	1.0000
1:31261628:CAAAC:C	acceptor_gain	1.0000
1:31261633:C:T	acceptor_loss	1.0000
1:31261634:T:A	acceptor_loss	1.0000
1:31269237:CGAA:C	acceptor_gain	1.0000
1:31269241:C:CC	acceptor_gain	1.0000
1:31271425:TAA:T	donor_gain	1.0000
1:31271426:AAA:A	donor_gain	1.0000
1:31271432:AGG:A	donor_gain	1.0000
1:31271500:C:CA	acceptor_loss	1.0000
1:31281369:CATA:C	donor_loss	1.0000
1:31281370:ATAC:A	donor_loss	1.0000
1:31281371:TACCT:T	donor_loss	1.0000
1:31281372:A:AC	donor_gain	1.0000
1:31281372:A:T	donor_loss	1.0000
1:31281372:AC:A	donor_gain	1.0000
1:31281373:C:CC	donor_gain	1.0000
1:31281373:CC:C	donor_gain	1.0000
1:31281492:CAAAG:C	acceptor_gain	1.0000
1:31281493:AAAG:A	acceptor_gain	1.0000
1:31281494:AAG:A	acceptor_gain	1.0000
1:31281495:AG:A	acceptor_gain	1.0000
1:31281496:GC:G	acceptor_loss	1.0000
1:31281497:C:CC	acceptor_gain	1.0000
1:31281497:CTGA:C	acceptor_loss	1.0000
1:31281498:T:G	acceptor_loss	1.0000
1:31281503:C:CT	acceptor_gain	1.0000
1:31281504:A:T	acceptor_gain	1.0000
1:31289416:CATA:C	acceptor_gain	1.0000

AlphaMissense

2327 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:31261619:A:G	W312R	1.000
1:31261619:A:T	W312R	1.000
1:31269232:A:G	W262R	1.000
1:31269232:A:T	W262R	1.000
1:31289272:A:C	S171R	1.000
1:31289272:A:T	S171R	1.000
1:31289274:T:G	S171R	1.000
1:31289379:A:G	W136R	1.000
1:31289379:A:T	W136R	1.000
1:31289396:T:A	D130V	1.000
1:31289397:C:G	D130H	1.000
1:31292001:A:G	W93R	1.000
1:31292001:A:T	W93R	1.000
1:31293236:C:T	G85E	1.000
1:31260085:C:T	G354E	0.999
1:31260086:C:G	G354R	0.999
1:31260086:C:T	G354R	0.999
1:31260103:T:A	D348V	0.999
1:31260104:C:G	D348H	0.999
1:31260109:G:C	S346W	0.999
1:31261579:C:T	G325D	0.999
1:31261580:C:G	G325R	0.999
1:31261585:A:G	L323P	0.999
1:31267874:T:A	D306V	0.999
1:31267875:C:G	D306H	0.999
1:31267883:C:T	G303D	0.999
1:31267892:A:T	I300K	0.999
1:31267914:A:G	W293R	0.999
1:31267914:A:T	W293R	0.999
1:31269215:A:C	F267L	0.999

dbSNP variants (sampled 300 via entrez): RS1000082214 (1:31288382 C>T), RS1000186113 (1:31281591 T>C), RS1000255569 (1:31264648 C>T), RS1000287439 (1:31293792 G>A,C), RS1000309872 (1:31277775 A>C), RS1000438363 (1:31283083 A>G), RS1000511552 (1:31298160 T>C), RS1000533732 (1:31259260 C>A,T), RS1000590629 (1:31292554 G>A), RS1000748807 (1:31297950 A>C), RS1000750258 (1:31272150 G>A,T), RS1000841800 (1:31288771 C>T), RS1000957601 (1:31276083 T>C), RS1000963899 (1:31262636 T>C), RS1001023410 (1:31292272 G>A)

Disease associations

OMIM: gene MIM:607797 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001874_1	Alcohol dependence	3.000000e-08
GCST005769_2	Body mass index	9.000000e-06
GCST005951_36	Body mass index	9.000000e-10

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

40 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects cotreatment, decreases expression, increases expression	3
bisphenol A	affects cotreatment, increases methylation, decreases expression	2
afuresertib	decreases expression	1
bisphenol F	affects cotreatment, increases expression	1
TAK-243	increases sumoylation	1
2,4,6-tribromophenol	decreases expression	1
decabromobiphenyl ether	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
tetrabromobisphenol A	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
K 7174	decreases expression	1
ICG 001	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	increases expression	1
pentabrominated diphenyl ether 100	increases expression	1
hexabrominated diphenyl ether 153	increases expression	1
bisphenol S	affects cotreatment, increases expression	1
jinfukang	affects cotreatment, decreases 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	decreases expression	1
Temozolomide	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Benzo(a)pyrene	increases methylation	1
Caffeine	decreases phosphorylation	1
Cisplatin	affects cotreatment, decreases expression	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	increases expression, affects cotreatment	1
Ivermectin	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B3HU	Abcam HEK293T SNRNP40 KO	Transformed cell line	Female

Clinical trials (associated diseases)

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