SNRPD1

Summary

SNRPD1 (small nuclear ribonucleoprotein D1 polypeptide, HGNC:11158) is a protein-coding gene on chromosome 18q11.2, encoding Small nuclear ribonucleoprotein Sm D1 (P62314). Plays a role in pre-mRNA splicing as a core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. It is a common-essential gene (DepMap: required in 100.0% of cancer cell lines).

This gene encodes a small nuclear ribonucleoprotein that belongs to the SNRNP core protein family. The protein may act as a charged protein scaffold to promote SNRNP assembly or strengthen SNRNP-SNRNP interactions through nonspecific electrostatic contacts with RNA. Two transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 6632 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 10 total
• Druggable target: yes
• Cancer dependency (DepMap): dependent in 100.0% of screened cell lines (common-essential)
• MANE Select transcript: NM_006938

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11158
Approved symbol	SNRPD1
Name	small nuclear ribonucleoprotein D1 polypeptide
Location	18q11.2
Locus type	gene with protein product
Status	Approved
Aliases	HsT2456, Sm-D1
Ensembl gene	ENSG00000167088
Ensembl biotype	protein_coding
OMIM	601063
Entrez	6632

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000300413, ENST00000577906, ENST00000579618, ENST00000582475, ENST00000920869, ENST00000920870, ENST00000956710

RefSeq mRNA: 2 — MANE Select: NM_006938 NM_001291916, NM_006938

CCDS: CCDS32801

Canonical transcript exons

ENST00000300413 — 4 exons

Exon	Start	End
ENSE00001109508	21629062	21633520
ENSE00001109516	21622725	21622801
ENSE00001137497	21612314	21612443
ENSE00003666946	21623748	21623939

Expression profiles

Bgee: expression breadth ubiquitous, 291 present calls, max score 98.94.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 179.7856 / max 4188.2014, expressed in 1825 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
169605	179.7856	1825

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ganglionic eminence	UBERON:0004023	98.94	gold quality
embryo	UBERON:0000922	98.87	gold quality
ventricular zone	UBERON:0003053	98.85	gold quality
oocyte	CL:0000023	98.26	gold quality
cortical plate	UBERON:0005343	98.14	gold quality
mucosa of sigmoid colon	UBERON:0004993	96.47	gold quality
pharyngeal mucosa	UBERON:0000355	96.40	gold quality
oral cavity	UBERON:0000167	96.27	gold quality
mucosa of transverse colon	UBERON:0004991	96.20	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	96.13	gold quality
islet of Langerhans	UBERON:0000006	95.81	gold quality
vermiform appendix	UBERON:0001154	95.78	gold quality
caecum	UBERON:0001153	95.71	gold quality
colonic mucosa	UBERON:0000317	95.57	gold quality
trabecular bone tissue	UBERON:0002483	95.41	gold quality
nasal cavity mucosa	UBERON:0001826	95.17	gold quality
bone marrow	UBERON:0002371	95.16	gold quality
superior surface of tongue	UBERON:0007371	95.12	gold quality
tendon of biceps brachii	UBERON:0008188	95.00	gold quality
penis	UBERON:0000989	94.90	gold quality
pylorus	UBERON:0001166	94.90	gold quality
esophagus mucosa	UBERON:0002469	94.83	gold quality
pericardium	UBERON:0002407	94.79	gold quality
stromal cell of endometrium	CL:0002255	94.71	gold quality
bronchial epithelial cell	CL:0002328	94.69	gold quality
cartilage tissue	UBERON:0002418	94.54	gold quality
tendon	UBERON:0000043	94.47	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	94.45	gold quality
pons	UBERON:0000988	94.42	gold quality
mucosa of urinary bladder	UBERON:0001259	94.26	gold quality

Single-cell (SCXA)

Detected in 15 experiment(s), a significant marker in 10.

Experiment	Marker?	Max mean expression
E-HCAD-4	yes	136.41
E-HCAD-10	yes	34.69
E-GEOD-125970	yes	24.52
E-MTAB-9067	yes	22.97
E-HCAD-13	yes	20.57
E-CURD-122	yes	19.76
E-MTAB-10042	yes	13.51
E-MTAB-6678	yes	9.13
E-MTAB-10553	yes	7.29
E-MTAB-6379	no	1003.85
E-MTAB-7303	no	195.20
E-MTAB-9388	no	10.87
E-MTAB-8271	no	10.04
E-HCAD-5	no	2.24
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

69 targeting SNRPD1, 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-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-548J-3P	99.94	72.61	4881
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-552-5P	99.93	68.56	1583
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-548BC	99.82	70.61	3524
HSA-MIR-548E-3P	99.82	70.59	3514
HSA-MIR-548F-3P	99.82	70.59	3540
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-323A-3P	99.79	70.30	1739
HSA-MIR-548AJ-5P	99.78	71.12	3085

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 100.0% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 7)

• Overexpression of SNRPD1 is associated with highly aggressive breast cancers. (PMID:23358685)
• The interaction of SMN with the spliceosomal SmD1 (also known as SNRPD1), severely decreases SMN-coilin interaction and prevents Cajal body assembly. (PMID:24413165)
• Data show that the elevation of cerebrospinal fluid anti-Sm antibodies through transudation from systemic circulation due to damaged blood-brain barrier (BBB) plays a critical role in the pathogenesis of acute confusional state (ACS). (PMID:25273532)
• Data suggest that SNRPA1, SNRPD1, and PNN are key players in the regulation of pluripotency-specific spliceosome assembly and the acquisition and maintenance of pluripotency. (PMID:28595116)
• Anti-SmD1 antibodies are associated with renal disorder, seizures, and pulmonary arterial hypertension in Chinese patients with active systemic lupus erythematosus. (PMID:28790444)
• SNRPD1 inhibition suppresses the proliferation of hepatocellular carcinoma and promotes autophagy through the PI3K/AKT/mTOR/4EBP1 pathway. (PMID:37268273)
• Effect of E134K pathogenic mutation of SMN protein on SMN-SmD1 interaction, with implication in spinal muscular atrophy: A molecular dynamics study. (PMID:38969036)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	snrpd1	ENSDARG00000011648
mus_musculus	Snrpd1	ENSMUSG00000002477
rattus_norvegicus	Snrpd1	ENSRNOG00000013714
drosophila_melanogaster	SmD1	FBGN0261933
caenorhabditis_elegans		WBGENE00044916

Paralogs (2): SNRPD3 (ENSG00000100028), LSM4 (ENSG00000130520)

Protein

Protein identifiers

Small nuclear ribonucleoprotein Sm D1 — P62314 (reviewed: P62314)

Alternative names: Sm-D autoantigen, snRNP core protein D1

All UniProt accessions (3): P62314, J3QLI9, J3QLR7

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in pre-mRNA splicing as a core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Component of both the pre-catalytic spliceosome B complex and activated spliceosome C complexes. As a component of the minor spliceosome, involved in the splicing of U12-type introns in pre-mRNAs. May act as a charged protein scaffold to promote snRNP assembly or strengthen snRNP-snRNP interactions through non-specific electrostatic contacts with RNA.

Subunit / interactions. Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Most spliceosomal snRNPs contain a common set of Sm proteins, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. Component of the U1 snRNP. The U1 snRNP is composed of the U1 snRNA and the 7 core Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG, and at least three U1 snRNP-specific proteins SNRNP70/U1-70K, SNRPA/U1-A and SNRPC/U1-C. 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, SNRNP40, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39, plus LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8. Component of the minor spliceosome, which splices U12-type introns. Part of the SMN-Sm complex that contains SMN1, GEMIN2/SIP1, DDX20/GEMIN3, GEMIN4, GEMIN5, GEMIN6, GEMIN7, GEMIN8, STRAP/UNRIP and the Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG; catalyzes core snRNPs assembly. Forms a 6S pICln-Sm complex composed of CLNS1A/pICln, SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG; ring-like structure where CLNS1A/pICln mimics additional Sm proteins and which is unable to assemble into the core snRNP. Interacts (via C-terminus) with SMN1 (via Tudor domain); the interaction is direct. Interacts with GEMIN2; the interaction is direct. Interacts with SNRPD2; the interaction is direct.

Subcellular location. Cytoplasm. Cytosol. Nucleus.

Post-translational modifications. Methylated on arginine residues by PRMT5 and PRMT7; probable asymmetric dimethylation which is required for assembly and biogenesis of snRNPs.

Miscellaneous. In the autoimmune disease systemic lupus erythematosus, antinuclear antibodies are developed with Sm specificity.

Similarity. Belongs to the snRNP core protein family.

RefSeq proteins (2): NP_001278845, NP_008869* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001163	Sm_dom_euk/arc	Domain
IPR010920	LSM_dom_sf	Homologous_superfamily
IPR027141	LSm4/Sm_D1/D3	Family
IPR034102	Sm_D1	Domain
IPR047575	Sm	Domain

Pfam: PF01423

UniProt features (20 total): strand 7, helix 3, region of interest 3, mutagenesis site 2, chain 1, domain 1, turn 1, compositionally biased region 1, cross-link 1

Structure

Experimental structures (PDB)

83 structures, top 30 by resolution.

PDB	Method	Resolution (Å)
4F7U	X-RAY DIFFRACTION	1.9
1B34	X-RAY DIFFRACTION	2.5
5XJL	X-RAY DIFFRACTION	2.5
7EVO	ELECTRON MICROSCOPY	2.5
5XJU	X-RAY DIFFRACTION	2.58
8H6L	ELECTRON MICROSCOPY	2.6
8H6K	ELECTRON MICROSCOPY	2.7
8HK1	ELECTRON MICROSCOPY	2.7
8C6J	ELECTRON MICROSCOPY	2.8
6ID1	ELECTRON MICROSCOPY	2.86
7DVQ	ELECTRON MICROSCOPY	2.89
6ID0	ELECTRON MICROSCOPY	2.9
5XJT	X-RAY DIFFRACTION	2.92
6QW6	ELECTRON MICROSCOPY	2.92
6ICZ	ELECTRON MICROSCOPY	3
7VPX	ELECTRON MICROSCOPY	3
8I0R	ELECTRON MICROSCOPY	3
8I0T	ELECTRON MICROSCOPY	3
8I0V	ELECTRON MICROSCOPY	3
9GCL	ELECTRON MICROSCOPY	3
9E3B	ELECTRON MICROSCOPY	3.06
4V98	X-RAY DIFFRACTION	3.1
7QTT	ELECTRON MICROSCOPY	3.1
8Q91	ELECTRON MICROSCOPY	3.1
5XJR	X-RAY DIFFRACTION	3.12
9E3C	ELECTRON MICROSCOPY	3.19
8H6E	ELECTRON MICROSCOPY	3.2
8Q7Q	ELECTRON MICROSCOPY	3.2
8RC0	ELECTRON MICROSCOPY	3.2
9GC0	ELECTRON MICROSCOPY	3.2

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P62314-F1	83.43	0.63

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 (1): 86

Mutagenesis-validated functional residues (2):

Position	Phenotype
58	loss of interaction with clns1a.
60	loss of interaction with clns1a.

Function

Pathways and Gene Ontology

Reactome pathways

17 pathways

ID	Pathway
R-HSA-191859	snRNP Assembly
R-HSA-72163	mRNA Splicing - Major Pathway
R-HSA-72165	mRNA Splicing - Minor Pathway
R-HSA-9754678	SARS-CoV-2 modulates host translation machinery
R-HSA-9770562	mRNA Polyadenylation
R-HSA-9918481	Dengue Virus-Host Interactions
R-HSA-9943411	CHD1 and CHD2 subfamily
R-HSA-1643685	Disease
R-HSA-194441	Metabolism of non-coding RNA
R-HSA-5663205	Infectious disease
R-HSA-72172	mRNA Splicing
R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854	Metabolism of RNA
R-HSA-9679506	SARS-CoV Infections
R-HSA-9694516	SARS-CoV-2 Infection
R-HSA-9705683	SARS-CoV-2-host interactions
R-HSA-9824446	Viral Infection Pathways

MSigDB gene sets: 312 (showing top): E2F_Q4, GNF2_MSH2, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, E2F4DP1_01, CMYB_01, CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN, GOBP_NEGATIVE_REGULATION_OF_RNA_SPLICING, GTACAGG_MIR486, SHIPP_DLBCL_CURED_VS_FATAL_DN, GOBP_RNA_METHYLATION, GNF2_RRM1, MODULE_388, WEI_MYCN_TARGETS_WITH_E_BOX, MUELLER_PLURINET, E2F1DP1_01

GO Biological Process (8): spliceosomal complex assembly (GO:0000245), spliceosomal snRNP assembly (GO:0000387), mRNA splicing, via spliceosome (GO:0000398), RNA splicing (GO:0008380), 7-methylguanosine cap hypermethylation (GO:0036261), U2-type prespliceosome assembly (GO:1903241), RNA processing (GO:0006396), mRNA processing (GO:0006397)

GO Molecular Function (3): RNA binding (GO:0003723), U1 snRNP binding (GO:1990446), protein binding (GO:0005515)

GO Cellular Component (23): commitment complex (GO:0000243), nucleus (GO:0005634), nucleoplasm (GO:0005654), spliceosomal complex (GO:0005681), U5 snRNP (GO:0005682), U2-type spliceosomal complex (GO:0005684), U1 snRNP (GO:0005685), U2 snRNP (GO:0005686), U4 snRNP (GO:0005687), U12-type spliceosomal complex (GO:0005689), cytosol (GO:0005829), small nuclear ribonucleoprotein complex (GO:0030532), methylosome (GO:0034709), pICln-Sm protein complex (GO:0034715), SMN-Sm protein complex (GO:0034719), U4/U6 x U5 tri-snRNP complex (GO:0046540), U2-type precatalytic spliceosome (GO:0071005), U2-type catalytic step 2 spliceosome (GO:0071007), precatalytic spliceosome (GO:0071011), catalytic step 2 spliceosome (GO:0071013), spliceosomal tri-snRNP complex (GO:0097526), cytoplasm (GO:0005737), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-13 pathways:

Category	Pathways
mRNA Splicing	2
Metabolism of RNA	2
Metabolism of non-coding RNA	1
SARS-CoV-2-host interactions	1
mRNA 3’-end processing	1
Dengue Virus Infection	1
CHD chromatin remodelers	1
Disease	1
Processing of Capped Intron-Containing Pre-mRNA	1
Viral Infection Pathways	1
SARS-CoV Infections	1
SARS-CoV-2 Infection	1
Infectious disease	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
spliceosomal snRNP complex	4
spliceosomal complex	4
cytoplasm	4
U2-type spliceosomal complex	3
Sm-like protein family complex	3
mRNA splicing, via spliceosome	2
protein-RNA complex assembly	2
RNA processing	2
U1 snRNP	2
cellular anatomical structure	2
nuclear protein-containing complex	2
ribonucleoprotein complex	2
U5 snRNP	2
U2 snRNP	2
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
RNA methylation	1
RNA capping	1
spliceosomal complex assembly	1
gene expression	1
RNA biosynthetic process	1
primary metabolic process	1
mRNA metabolic process	1
nucleic acid binding	1
snRNP binding	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
methyltransferase complex	1
SMN complex	1
U4/U6 snRNP	1
spliceosomal tri-snRNP complex	1
U4/U6 x U5 tri-snRNP complex	1
precatalytic spliceosome	1
U6 snRNP	1
catalytic step 2 spliceosome	1
Prp19 complex	1
catalytic complex	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

253 interactions, top by confidence:

A	B	Type	Score
SMN1	GEMIN2	psi-mi:“MI:0914”(association)	0.960
LSM3	LSM1	psi-mi:“MI:0914”(association)	0.950
IFIT1	IFIT3	psi-mi:“MI:0914”(association)	0.920
SNRPF	GEMIN2	psi-mi:“MI:0914”(association)	0.910
MED29	MED19	psi-mi:“MI:0914”(association)	0.890
CLNS1A	SNRPD1	psi-mi:“MI:0915”(physical association)	0.880
SNRPD1	CLNS1A	psi-mi:“MI:0915”(physical association)	0.880
SNRPD1	SMN1	psi-mi:“MI:0915”(physical association)	0.840
SMN1	SNRPD1	psi-mi:“MI:0915”(physical association)	0.840
SNRPD1	SMN1	psi-mi:“MI:0407”(direct interaction)	0.840
SNRPB	SNRNP70	psi-mi:“MI:0915”(physical association)	0.830
CLNS1A	PRMT5	psi-mi:“MI:0914”(association)	0.830
CD2BP2	SNRNP200	psi-mi:“MI:0914”(association)	0.800
MED9	MED19	psi-mi:“MI:0914”(association)	0.790
IFIT2	IFIT3	psi-mi:“MI:0914”(association)	0.780
CLNS1A	SNRPE	psi-mi:“MI:0914”(association)	0.770
CLNS1A	SNRPE	psi-mi:“MI:0915”(physical association)	0.770
GEMIN2	SNRPE	psi-mi:“MI:0914”(association)	0.770
GEMIN2	SNRPE	psi-mi:“MI:0915”(physical association)	0.770
MED19	MED19	psi-mi:“MI:0914”(association)	0.730
GEMIN5	SNRPB	psi-mi:“MI:0914”(association)	0.730
PRPF3	PRPF4	psi-mi:“MI:0914”(association)	0.730

BioGRID (529): SNRPD1 (Two-hybrid), SNRPD1 (Affinity Capture-MS), SNRPD1 (Affinity Capture-MS), SNRPD1 (Affinity Capture-MS), SNRPD1 (Affinity Capture-MS), SNRPD1 (Affinity Capture-MS), SNRPD1 (Affinity Capture-MS), SNRPD1 (Affinity Capture-MS), SNRPD1 (Affinity Capture-MS), SNRPD1 (Affinity Capture-MS), SNRPD1 (Affinity Capture-MS), MCFD2 (Co-fractionation), PRPF31 (Co-fractionation), RCC2 (Co-fractionation), RUVBL1 (Co-fractionation)

ESM2 similar proteins: A5GFZ5, A8MWD9, C9WPN6, O35900, O60762, O70152, P02362, P50894, P62084, P62306, P62307, P62308, P62309, P62310, P62311, P62314, P62315, P62318, P62320, P62321, P62323, P62487, P62488, P62489, P82931, Q16576, Q1JQ93, Q24572, Q2TBV5, Q2VIR3, Q32PE9, Q3SWX8, Q3T0Z8, Q3ZBL0, Q3ZC10, Q4R304, Q4R5F6, Q5E9B8, Q5ZMS3, Q60973

Diamond homologs: O42661, P62314, P62315, Q02260, Q10013, Q1H595, Q3ZC10, Q4R5F6, Q54F84, Q9SSF1, Q9SY09, Q9UUC6, Q9VU02, O44437, P43321, P62318, P62320, P62323, Q17348, Q3ZBK6, Q9LM92, Q9QXA5, Q9S7E6, Q9Y4Z0, Q9ZRU9, Q969L4, Q19952, Q54KX4, O35900, Q9Y333, Q8QZX5, O14352, A1CE19, A1DM27, A4RQ29, A5DRQ6, A6R363, A6S5C9, A7F5M4, A7UXE4

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
SNRPD1	“form complex”	“U4/U6.U5 snRNP complex”	binding
SNRPD1	“form complex”	“U2 snRNP complex”	binding
SNRPD1	“form complex”	“U1 snRNP complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 171 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	8	36.5×	7e-10
mRNA Splicing	31	24.5×	5e-33
mRNA Splicing - Minor Pathway	15	24.2×	1e-15
snRNP Assembly	13	19.8×	3e-12
Processing of Capped Intron-Containing Pre-mRNA	33	19.5×	7e-32
SARS-CoV-2 modulates host translation machinery	12	19.3×	4e-11
mRNA Splicing - Major Pathway	49	19.3×	3e-48
CHD1 and CHD2 subfamily	22	17.2×	1e-19

GO biological processes:

GO term	Partners	Fold	FDR
U2-type prespliceosome assembly	17	69.8×	3e-26
spliceosomal snRNP assembly	16	61.2×	2e-23
RNA splicing, via transesterification reactions	10	41.1×	4e-12
spliceosomal tri-snRNP complex assembly	5	37.0×	2e-05
mRNA cis splicing, via spliceosome	5	32.6×	3e-05
spliceosomal complex assembly	8	31.7×	1e-08
mRNA splicing, via spliceosome	51	30.7×	2e-60
RNA splicing	24	13.9×	2e-18

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	4
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

673 predictions. Top by Δscore:

Variant	Effect	Δscore
18:21612435:GCTC:G	donor_gain	1.0000
18:21612441:GAGG:G	donor_loss	1.0000
18:21612442:AGGTG:A	donor_loss	1.0000
18:21612443:GGTG:G	donor_loss	1.0000
18:21612444:G:C	donor_loss	1.0000
18:21612445:T:G	donor_loss	1.0000
18:21612449:G:GT	donor_gain	1.0000
18:21622720:TATAG:T	acceptor_loss	1.0000
18:21622722:TA:T	acceptor_loss	1.0000
18:21622723:A:AC	acceptor_loss	1.0000
18:21622723:A:AG	acceptor_gain	1.0000
18:21622724:G:GA	acceptor_gain	1.0000
18:21622800:AG:A	donor_loss	1.0000
18:21622801:GGTA:G	donor_loss	1.0000
18:21622802:GTAC:G	donor_loss	1.0000
18:21623743:TTTA:T	acceptor_loss	1.0000
18:21623744:TTA:T	acceptor_loss	1.0000
18:21623744:TTAGG:T	acceptor_gain	1.0000
18:21623745:TAGG:T	acceptor_gain	1.0000
18:21623746:A:AG	acceptor_gain	1.0000
18:21623746:AG:A	acceptor_gain	1.0000
18:21623746:AGG:A	acceptor_loss	1.0000
18:21623746:AGGT:A	acceptor_gain	1.0000
18:21623746:AGGTG:A	acceptor_gain	1.0000
18:21623747:G:GG	acceptor_gain	1.0000
18:21623747:GG:G	acceptor_gain	1.0000
18:21623747:GGT:G	acceptor_gain	1.0000
18:21623747:GGTG:G	acceptor_gain	1.0000
18:21623747:GGTGT:G	acceptor_gain	1.0000
18:21623828:C:G	donor_gain	1.0000

AlphaMissense

757 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
18:21622789:G:A	G27R	1.000
18:21622789:G:C	G27R	1.000
18:21622790:G:A	G27E	1.000
18:21623764:G:A	M36I	1.000
18:21623764:G:C	M36I	1.000
18:21623764:G:T	M36I	1.000
18:21623775:T:C	L40P	1.000
18:21623840:G:A	G62R	1.000
18:21623840:G:C	G62R	1.000
18:21623841:G:A	G62E	1.000
18:21623841:G:T	G62V	1.000
18:21622726:T:C	F6L	0.999
18:21622728:T:A	F6L	0.999
18:21622728:T:G	F6L	0.999
18:21622730:T:C	L7S	0.999
18:21622766:T:G	L19W	0.999
18:21622770:G:C	K20N	0.999
18:21622770:G:T	K20N	0.999
18:21622784:T:A	V25D	0.999
18:21622790:G:T	G27V	0.999
18:21623763:T:C	M36T	0.999
18:21623767:T:A	N37K	0.999
18:21623767:T:G	N37K	0.999
18:21623769:C:A	T38K	0.999
18:21623775:T:A	L40H	0.999
18:21623775:T:G	L40R	0.999
18:21623831:A:C	S59R	0.999
18:21623833:T:A	S59R	0.999
18:21623833:T:G	S59R	0.999
18:21623835:T:A	I60N	0.999

dbSNP variants (sampled 300 via entrez): RS1000424564 (18:21612083 C>A,T), RS1000594643 (18:21626963 T>A), RS1000667915 (18:21629329 C>A,T), RS1000718542 (18:21629599 C>G,T), RS1000775984 (18:21612355 C>G,T), RS1000894303 (18:21622410 A>G), RS1001122660 (18:21630102 T>A,C), RS1001182849 (18:21623102 T>C), RS1001399280 (18:21622753 G>A), RS1001501387 (18:21624043 A>C), RS1001594491 (18:21618068 T>C), RS1001716391 (18:21617488 T>C), RS1001842782 (18:21623509 T>G), RS1001953315 (18:21633953 C>T), RS1001993246 (18:21622708 T>C)

Disease associations

OMIM: gene MIM:601063 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066339 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
7.67	Kd	21.61	nM	CHEMBL5653589
7.67	ED50	21.61	nM	CHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149458: Binding affinity to human SNRPD1 incubated for 45 mins by Kinobead based pull down assay	kd	0.0216	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, decreases expression	3
sodium arsenite	decreases expression, increases expression	3
Cisplatin	decreases expression, increases expression, affects cotreatment	3
Particulate Matter	increases expression, decreases expression, increases abundance, affects expression	3
Benzo(a)pyrene	increases expression, increases methylation	2
bisphenol F	increases expression, affects cotreatment	1
dicrotophos	decreases expression	1
arsenite	affects binding, decreases reaction, increases reaction	1
afimoxifene	decreases reaction, increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
cupric chloride	increases expression	1
yessotoxin	decreases expression	1
2,3,5-(triglutathion-S-yl)hydroquinone	increases ADP-ribosylation	1
K 7174	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
bisphenol B	increases expression	1
pentabrominated diphenyl ether 100	decreases expression	1
jinfukang	affects cotreatment, decreases expression	1
LDN 193189	affects cotreatment, decreases expression	1
NSC 689534	affects binding, decreases expression	1
PP242	decreases expression	1
Sunitinib	decreases expression	1
Vorinostat	increases expression	1
Air Pollutants	increases abundance, decreases expression	1
Copper	affects binding, decreases expression	1
Coumestrol	increases expression	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Estrogens	decreases reaction, increases expression	1
Ethyl Methanesulfonate	decreases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652500	Binding	Binding affinity to human SNRPD1 incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Clinical trials (associated diseases)

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