SNRPD3

Summary

SNRPD3 (small nuclear ribonucleoprotein D3 polypeptide, HGNC:11160) is a protein-coding gene on chromosome 22q11.23, encoding Small nuclear ribonucleoprotein Sm D3 (P62318). 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 core component of the spliceosome, which is a nuclear ribonucleoprotein complex that functions in pre-mRNA splicing. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 6634 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 9 total
• Druggable target: yes
• Cancer dependency (DepMap): dependent in 100.0% of screened cell lines (common-essential)
• MANE Select transcript: NM_004175

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11160
Approved symbol	SNRPD3
Name	small nuclear ribonucleoprotein D3 polypeptide
Location	22q11.23
Locus type	gene with protein product
Status	Approved
Aliases	SMD3, Sm-D3
Ensembl gene	ENSG00000100028
Ensembl biotype	protein_coding
OMIM	601062
Entrez	6634

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 11 protein_coding, 1 retained_intron

ENST00000215829, ENST00000402849, ENST00000468770, ENST00000865614, ENST00000865615, ENST00000865616, ENST00000865617, ENST00000865618, ENST00000940750, ENST00000940751, ENST00000940752, ENST00000972066

RefSeq mRNA: 2 — MANE Select: NM_004175 NM_001278656, NM_004175

CCDS: CCDS13828

Canonical transcript exons

ENST00000215829 — 4 exons

Exon	Start	End
ENSE00001402429	24571916	24574971
ENSE00001948969	24555999	24556071
ENSE00003846511	24567984	24568176
ENSE00003847767	24557657	24557800

Expression profiles

Bgee: expression breadth ubiquitous, 151 present calls, max score 96.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 186.5705 / max 3124.5312, expressed in 1826 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
191423	166.4727	1826
191422	18.1614	1799
191420	1.4144	890
191421	0.5220	331

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
embryo	UBERON:0000922	96.37	gold quality
ganglionic eminence	UBERON:0004023	96.37	gold quality
islet of Langerhans	UBERON:0000006	96.25	gold quality
ventricular zone	UBERON:0003053	95.41	gold quality
adrenal tissue	UBERON:0018303	95.32	gold quality
leukocyte	CL:0000738	95.25	gold quality
monocyte	CL:0000576	95.20	gold quality
vermiform appendix	UBERON:0001154	95.12	gold quality
hindlimb stylopod muscle	UBERON:0004252	95.10	gold quality
granulocyte	CL:0000094	95.04	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	94.98	gold quality
duodenum	UBERON:0002114	94.94	gold quality
cortical plate	UBERON:0005343	94.94	gold quality
rectum	UBERON:0001052	94.57	gold quality
skeletal muscle tissue	UBERON:0001134	94.56	gold quality
muscle of leg	UBERON:0001383	94.43	gold quality
gastrocnemius	UBERON:0001388	94.11	gold quality
mucosa of transverse colon	UBERON:0004991	94.09	gold quality
muscle tissue	UBERON:0002385	94.04	gold quality
smooth muscle tissue	UBERON:0001135	94.01	gold quality
lymph node	UBERON:0000029	93.76	gold quality
esophagus mucosa	UBERON:0002469	93.56	gold quality
endometrium	UBERON:0001295	93.11	gold quality
placenta	UBERON:0001987	93.11	gold quality
popliteal artery	UBERON:0002250	93.10	gold quality
tibial artery	UBERON:0007610	93.09	gold quality
fallopian tube	UBERON:0003889	93.05	gold quality
adult mammalian kidney	UBERON:0000082	93.03	gold quality
cortex of kidney	UBERON:0001225	92.88	gold quality
kidney	UBERON:0002113	92.81	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	14.27
E-MTAB-6524	no	286.54
E-MTAB-7303	no	80.36

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MYC

miRNA regulators (miRDB)

84 targeting SNRPD3, 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-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
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-8080	99.82	67.52	1342
HSA-MIR-548A-3P	99.76	70.58	3524
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-1283	99.69	72.42	3009

Functional genomics

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

Literature-anchored findings (GeneRIF, showing 4)

• The dimethylated arginine residues play an essential role in the formation of major SmD3 autoepitopes. 1 particular peptide of SmD3 represents a more sensitive and more reliable substrate for the detection of a subclass of anti-Sm antibodies. (PMID:15642139)
• Silencing Core Spliceosome Sm Gene Expression Induces a Cytotoxic Splicing Switch in the Proteasome Subunit Beta 3 mRNA in Non-Small Cell Lung Cancer Cells. (PMID:32545483)
• MYCN and SNRPD3 cooperate to maintain a balance of alternative splicing events that drives neuroblastoma progression. (PMID:38049564)
• Cancer-associated SNRPD3 mutation confers resistance to hypoxia, which is attenuated by DRP1 inhibition. (PMID:38241813)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	snrpd3l	ENSDARG00000076283
mus_musculus	Snrpd3	ENSMUSG00000020180
rattus_norvegicus	Snrpd3l1	ENSRNOG00000013839
rattus_norvegicus	Snrpd3	ENSRNOG00000050410
drosophila_melanogaster	SmD3	FBGN0023167
caenorhabditis_elegans		WBGENE00004914

Paralogs (2): LSM4 (ENSG00000130520), SNRPD1 (ENSG00000167088)

Protein

Protein identifiers

Small nuclear ribonucleoprotein Sm D3 — P62318 (reviewed: P62318)

Alternative names: snRNP core protein D3

All UniProt accessions (1): P62318

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. As part of the U7 snRNP it is involved in histone pre-mRNA 3’-end processing.

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 U7 snRNP complex, or U7 Sm protein core complex, that is composed of the U7 snRNA and at least LSM10, LSM11, SNRPB, SNRPD3, SNRPE, SNRPF and SNRPG; the complex does not contain SNRPD1 and SNRPD2. 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.

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.

Isoforms (2)

UniProt ID	Names	Canonical?
P62318-1	1	yes
P62318-2	2

RefSeq proteins (2): NP_001265585, NP_004166* (*=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
IPR034099	SmD3	Family
IPR047575	Sm	Domain

Pfam: PF01423

UniProt features (22 total): strand 7, repeat 5, helix 2, turn 2, initiator methionine 1, chain 1, splice variant 1, domain 1, region of interest 1, modified residue 1

Structure

Experimental structures (PDB)

79 structures, top 30 by resolution.

PDB	Method	Resolution (Å)
3VRI	X-RAY DIFFRACTION	1.6
1D3B	X-RAY DIFFRACTION	2
7EVO	ELECTRON MICROSCOPY	2.5
8H6L	ELECTRON MICROSCOPY	2.6
8H6K	ELECTRON MICROSCOPY	2.7
8HK1	ELECTRON MICROSCOPY	2.7
8C6J	ELECTRON MICROSCOPY	2.8
9NH5	ELECTRON MICROSCOPY	2.82
9NH6	ELECTRON MICROSCOPY	2.82
6ID1	ELECTRON MICROSCOPY	2.86
7DVQ	ELECTRON MICROSCOPY	2.89
6ID0	ELECTRON MICROSCOPY	2.9
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
7QTT	ELECTRON MICROSCOPY	3.1
8Q91	ELECTRON MICROSCOPY	3.1
9N96	ELECTRON MICROSCOPY	3.18
6V4X	ELECTRON MICROSCOPY	3.2
8H6E	ELECTRON MICROSCOPY	3.2
8Q7Q	ELECTRON MICROSCOPY	3.2
8RC0	ELECTRON MICROSCOPY	3.2
9GC0	ELECTRON MICROSCOPY	3.2
8H6J	ELECTRON MICROSCOPY	3.25
6QX9	ELECTRON MICROSCOPY	3.28
4PJO	X-RAY DIFFRACTION	3.3

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P62318-F1	83.33	0.61

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): 2

Function

Pathways and Gene Ontology

Reactome pathways

23 pathways

ID	Pathway
R-HSA-111367	SLBP independent Processing of Histone Pre-mRNAs
R-HSA-191859	snRNP Assembly
R-HSA-72163	mRNA Splicing - Major Pathway
R-HSA-72165	mRNA Splicing - Minor Pathway
R-HSA-73856	RNA Polymerase II Transcription Termination
R-HSA-77588	SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs
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-73857	RNA Polymerase II Transcription
R-HSA-74160	Gene expression (Transcription)
R-HSA-75067	Processing of Capped Intronless 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: 282 (showing top): CLAUS_PGR_POSITIVE_MENINGIOMA_UP, GCM_NPM1, MATTIOLI_MGUS_VS_PCL, GOBP_NEGATIVE_REGULATION_OF_RNA_SPLICING, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_RNA_METHYLATION, PUJANA_CHEK2_PCC_NETWORK, OUELLET_OVARIAN_CANCER_INVASIVE_VS_LMP_UP, MODULE_388, GCM_PSME1, GCM_PPP1CC, GOBP_SPLICEOSOMAL_TRI_SNRNP_COMPLEX_ASSEMBLY, GOBP_RNA_MODIFICATION, REACTOME_MRNA_3_END_PROCESSING, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA

GO Biological Process (8): spliceosomal snRNP assembly (GO:0000387), mRNA splicing, via spliceosome (GO:0000398), protein methylation (GO:0006479), 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 (6): RNA binding (GO:0003723), enzyme binding (GO:0019899), telomerase RNA binding (GO:0070034), histone pre-mRNA DCP binding (GO:0071208), U7 snRNA binding (GO:0071209), protein binding (GO:0005515)

GO Cellular Component (26): commitment complex (GO:0000243), nucleus (GO:0005634), nucleoplasm (GO:0005654), spliceosomal complex (GO:0005681), U5 snRNP (GO:0005682), U7 snRNP (GO:0005683), U2-type spliceosomal complex (GO:0005684), U1 snRNP (GO:0005685), U2 snRNP (GO:0005686), U4 snRNP (GO:0005687), U12-type spliceosomal complex (GO:0005689), telomerase holoenzyme complex (GO:0005697), cytosol (GO:0005829), nuclear body (GO:0016604), 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
Metabolism of RNA	3
Processing of Capped Intronless Pre-mRNA	2
mRNA Splicing	2
Metabolism of non-coding RNA	1
RNA Polymerase II Transcription	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
Gene expression (Transcription)	1
Viral Infection Pathways	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
spliceosomal snRNP complex	4
cytoplasm	4
nuclear protein-containing complex	3
ribonucleoprotein complex	3
Sm-like protein family complex	3
RNA processing	2
RNA binding	2
U2-type spliceosomal complex	2
U1 snRNP	2
cellular anatomical structure	2
spliceosomal complex	2
mRNA splicing, via spliceosome	1
protein-RNA complex assembly	1
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
protein alkylation	1
macromolecule methylation	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
protein binding	1
snRNA binding	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
small nuclear ribonucleoprotein complex	1
catalytic complex	1
nucleoplasm	1
intracellular membraneless organelle	1
methyltransferase complex	1
SMN complex	1
U5 snRNP	1
U4/U6 snRNP	1
spliceosomal tri-snRNP complex	1
U2 snRNP	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

260 interactions, top by confidence:

A	B	Type	Score
IFIT1	IFIT3	psi-mi:“MI:0914”(association)	0.920
CLNS1A	SNRPD3	psi-mi:“MI:0915”(physical association)	0.910
SNRPD3	CLNS1A	psi-mi:“MI:0915”(physical association)	0.910
PRPF4	PPIH	psi-mi:“MI:0914”(association)	0.910
SNRPB	SNRNP70	psi-mi:“MI:0915”(physical association)	0.830
SNRNP70	SNRPB	psi-mi:“MI:0914”(association)	0.830
CLNS1A	PRMT5	psi-mi:“MI:0914”(association)	0.830
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
CLNS1A	SNRPB	psi-mi:“MI:0914”(association)	0.770
LSM3	SNRPD3	psi-mi:“MI:0915”(physical association)	0.740
ISY1	AQR	psi-mi:“MI:0914”(association)	0.740
GEMIN5	SNRPB	psi-mi:“MI:0914”(association)	0.730
PRPF3	PRPF4	psi-mi:“MI:0914”(association)	0.730
SNRPD2	GEMIN2	psi-mi:“MI:0914”(association)	0.710
SNRPG	GEMIN2	psi-mi:“MI:0914”(association)	0.710
UBL5	SART1	psi-mi:“MI:0914”(association)	0.670
SNRPD3	LSM7	psi-mi:“MI:0915”(physical association)	0.670
SNRPB	PRMT5	psi-mi:“MI:0914”(association)	0.670
SNW1	AQR	psi-mi:“MI:0914”(association)	0.650
SNRNP70	GEMIN2	psi-mi:“MI:0914”(association)	0.640
SNRPA1	HTATSF1	psi-mi:“MI:0914”(association)	0.640
NCBP2	KPNA3	psi-mi:“MI:0914”(association)	0.640
LSM5	LSM1	psi-mi:“MI:0914”(association)	0.640
DDX23	PRPF4	psi-mi:“MI:0914”(association)	0.640
PRPF31	PRPF4	psi-mi:“MI:0914”(association)	0.640

BioGRID (580): SNRPD3 (Affinity Capture-MS), SNRPD3 (Affinity Capture-MS), SNRPD3 (Affinity Capture-MS), SNRPD3 (Affinity Capture-MS), SNRPD3 (Affinity Capture-MS), SNRPD3 (Affinity Capture-MS), SNRPD3 (Affinity Capture-MS), SNRPD3 (Affinity Capture-MS), AIMP1 (Co-fractionation), DHX38 (Co-fractionation), HNRNPR (Co-fractionation), LSM2 (Co-fractionation), LSM3 (Co-fractionation), LSM6 (Co-fractionation), LSM7 (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: O44437, P43321, P62314, P62315, P62318, P62320, P62323, Q17348, Q3ZBK6, Q3ZC10, Q4R5F6, Q9LM92, Q9QXA5, Q9S7E6, Q9UUC6, Q9VU02, Q9Y4Z0, Q9ZRU9, O14352, Q54KX4, O42661, Q02260, Q10013, Q1H595, Q54F84, Q969L4, Q9SSF1, Q9SY09, Q19952, Q8QZX5, F4K4E3, P40070, Q43582, Q9LGE6, P38203, P62306, P62307, P62321, Q24297, Q3T0Z8

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
SNRPD3	“form complex”	“U4/U6.U5 snRNP complex”	binding
SNRPD3	“form complex”	“U2 snRNP complex”	binding
SNRPD3	“form complex”	“U1 snRNP complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 194 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	9	40.2×	2e-11
mRNA decay by 5’ to 3’ exoribonuclease	6	32.2×	8e-07
snRNP Assembly	14	20.9×	2e-13
SARS-CoV-2 modulates host translation machinery	12	18.9×	6e-11
mRNA Splicing	24	18.6×	5e-22
mRNA Splicing - Minor Pathway	11	17.4×	1e-09
Processing of Capped Intron-Containing Pre-mRNA	28	16.2×	5e-24
mRNA Splicing - Major Pathway	42	16.2×	4e-37

GO biological processes:

GO term	Partners	Fold	FDR
spliceosomal snRNP assembly	18	61.9×	6e-27
spliceosomal tri-snRNP complex assembly	5	33.2×	3e-05
spliceosomal complex assembly	9	32.0×	1e-09
RNA splicing, via transesterification reactions	8	29.6×	2e-08
U2-type prespliceosome assembly	8	29.6×	2e-08
mRNA splicing, via spliceosome	47	25.5×	6e-51
positive regulation of viral genome replication	6	20.6×	3e-05
mRNA stabilization	6	13.0×	5e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

9 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

725 predictions. Top by Δscore:

Variant	Effect	Δscore
22:24556053:GAAAA:G	donor_gain	1.0000
22:24557652:TGTA:T	acceptor_loss	1.0000
22:24557653:GTA:G	acceptor_loss	1.0000
22:24557654:TA:T	acceptor_loss	1.0000
22:24557655:A:AC	acceptor_loss	1.0000
22:24557655:A:AG	acceptor_gain	1.0000
22:24557656:G:GA	acceptor_gain	1.0000
22:24557656:GA:G	acceptor_gain	1.0000
22:24557656:GAA:G	acceptor_gain	1.0000
22:24557656:GAAC:G	acceptor_gain	1.0000
22:24557656:GAACT:G	acceptor_gain	1.0000
22:24557799:AG:A	donor_loss	1.0000
22:24567983:GAT:G	acceptor_gain	1.0000
22:24568177:GTA:G	donor_loss	1.0000
22:24571914:A:AG	acceptor_gain	1.0000
22:24571914:AGT:A	acceptor_gain	1.0000
22:24571915:G:GA	acceptor_gain	1.0000
22:24571915:GT:G	acceptor_gain	1.0000
22:24571915:GTG:G	acceptor_gain	1.0000
22:24556058:G:GG	donor_gain	0.9900
22:24557650:A:AG	acceptor_gain	0.9900
22:24557652:T:A	acceptor_gain	0.9900
22:24567979:TCCA:T	acceptor_loss	0.9900
22:24567980:CCA:C	acceptor_loss	0.9900
22:24567982:A:AC	acceptor_loss	0.9900
22:24571910:TTTCA:T	acceptor_loss	0.9900
22:24571911:TTCA:T	acceptor_loss	0.9900
22:24571912:TCAG:T	acceptor_loss	0.9900
22:24571913:CA:C	acceptor_loss	0.9900
22:24571915:G:GT	acceptor_loss	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000070163 (22:24555808 G>C), RS1000147489 (22:24564783 T>TC), RS1000351879 (22:24554766 C>G,T), RS1000384492 (22:24555086 T>C), RS1000490117 (22:24558930 C>G), RS1000499279 (22:24571749 A>AT), RS1000735400 (22:24558514 C>T), RS1000747705 (22:24567620 C>G), RS1000993989 (22:24561530 G>A), RS1001089781 (22:24573612 C>T), RS1001098701 (22:24570162 T>G), RS1001385860 (22:24556002 C>A,G,T), RS1001684815 (22:24574825 C>T), RS1001807717 (22:24566360 C>T), RS1001824963 (22:24568960 C>T)

Disease associations

OMIM: gene MIM:601062 | 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
GCST002481_6	Acne (severe)	6.000000e-07
GCST010045_1	Gamma glutamyl transferase levels	5.000000e-11

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004532	serum gamma-glutamyl transferase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5725034 (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
8.37	Kd	4.3	nM	CHEMBL5653589
8.37	ED50	4.3	nM	CHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 8 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	2149460: Binding affinity to human SNRPD3 incubated for 45 mins by Kinobead based pull down assay	kd	0.0043	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, decreases expression, increases expression	5
sodium arsenite	increases abundance, increases expression	3
dicrotophos	decreases expression	1
beauvericin	decreases expression, affects cotreatment	1
2,4,6-tribromophenol	increases expression	1
decabromobiphenyl ether	increases expression	1
arsenite	decreases reaction, affects binding	1
tetrabromobisphenol A	increases expression	1
perfluorooctanoic acid	decreases expression	1
aflatoxin B2	decreases methylation	1
lei gong teng	increases expression	1
epigallocatechin gallate	increases expression	1
yessotoxin	decreases expression	1
2,3,5-(triglutathion-S-yl)hydroquinone	increases ADP-ribosylation	1
CGP 52608	affects binding, increases reaction	1
enniatins	affects cotreatment, decreases expression	1
K 7174	decreases expression	1
fenpyroximate	increases expression	1
4-chloro-N-((4-(1,1-dimethylethyl)phenyl)methyl)-3-ethyl-1-methyl-1H-pyrazole-5-carboxamide	increases expression	1
pyrimidifen	increases expression	1
nutlin 3	affects cotreatment, increases secretion	1
2,2’,4,4’-tetrabromodiphenyl ether	increases expression	1
pentabrominated diphenyl ether 100	increases expression	1
PP242	increases expression	1
Resveratrol	increases expression, affects cotreatment	1
Arsenic Trioxide	increases expression	1
Antimycin A	increases expression	1
Arsenic	increases abundance, increases expression	1
Atrazine	decreases expression	1
Dactinomycin	affects cotreatment, increases secretion	1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652502	Binding	Binding affinity to human SNRPD3 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.