SNRPD2

Summary

SNRPD2 (small nuclear ribonucleoprotein D2 polypeptide, HGNC:11159) is a protein-coding gene on chromosome 19q13.2-q13.3, encoding Small nuclear ribonucleoprotein Sm D2 (P62316). 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).

The protein encoded by this gene belongs to the small nuclear ribonucleoprotein core protein family. It is required for pre-mRNA splicing and small nuclear ribonucleoprotein biogenesis. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 6633 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 10 total
• GTEx eGene: eQTL in 39 tissues, sQTL in 2 (q < 0.05)
• ChEMBL bioactivity: 1 clinical-phase molecule tested; no curated mechanism-of-action drug
• Cancer dependency (DepMap): dependent in 100.0% of screened cell lines (common-essential)
• Constraint (gnomAD): pLI 0.98 (loss-of-function intolerant), LOEUF 0.40 (moderately constrained)
• MANE Select transcript: NM_001384647

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11159
Approved symbol	SNRPD2
Name	small nuclear ribonucleoprotein D2 polypeptide
Location	19q13.2-q13.3
Locus type	gene with protein product
Status	Approved
Aliases	Sm-D2
Ensembl gene	ENSG00000125743
Ensembl biotype	protein_coding
OMIM	601061
Entrez	6633

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 15 protein_coding, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

MANE Select: ENST00000342669

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 1, TSL 3: 5, TSL 5: 1

ENST00000342669, ENST00000391932, ENST00000585392, ENST00000587367, ENST00000587579, ENST00000588301, ENST00000588599, ENST00000590212, ENST00001083716, ENST00001083720, ENST00001083721, ENST00001083723, ENST00001104193, ENST00001104194, ENST00001104195, ENST00001104196, ENST00001142732

RefSeq mRNA: 5 — MANE Select: NM_001384647 NM_001369751, NM_001369752, NM_001384647, NM_004597, NM_177542

CCDS: CCDS33053, CCDS54281, CCDS92646

Canonical transcript exons

ENST00000342669 — 3 exons

Exon	Start	End
ENSE00002778615	45687460	45687727
ENSE00002795847	45691887	45691953
ENSE00003548151	45688387	45688566

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 99.52.

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

Highest expression (Bgee): adult organism, type B pancreatic cell, embryo, oral cavity, corpus epididymis.

Genetic regulation across tissues (GTEx eQTL / sQTL)

SNRPD2 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 39 tissues and its splicing (sQTL) in 2 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 41 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Skin Sun Exposed Lower leg	eqtl	2.5e-59	-0.30	19:45691793:G:GC
Skin Not Sun Exposed Suprapubic	eqtl	3.0e-43	-0.30	19:45691793:G:GC
Adipose Subcutaneous	eqtl	2.4e-38	-0.27	19:45691793:G:GC
Esophagus Mucosa	eqtl	1.7e-34	-0.23	19:45686603:C:T
Cells Cultured fibroblasts	eqtl	4.7e-25	-0.17	19:45687273:A:G
Breast Mammary Tissue	eqtl	2.2e-24	-0.23	19:45691793:G:GC
Lung	eqtl	7.2e-21	-0.21	19:45697955:T:G
Adipose Visceral Omentum	eqtl	2.6e-17	-0.20	19:45691793:G:GC
Artery Tibial	eqtl	4.6e-15	-0.12	19:45691793:G:GC
Nerve Tibial	eqtl	2.2e-14	-0.14	19:45691793:G:GC
Artery Aorta	eqtl	5.4e-14	-0.17	19:45691793:G:GC
Thyroid	eqtl	2.3e-13	-0.15	19:45691793:G:GC
Pancreas	eqtl	1.5e-12	-0.24	19:45691793:G:GC
Cells EBV-transformed lymphocytes	eqtl	3.3e-12	-0.22	19:45675852:T:C
Colon Transverse	eqtl	1.8e-11	-0.17	19:45691793:G:GC
Stomach	eqtl	2.4e-11	-0.20	19:45675852:T:C
Colon Sigmoid	eqtl	2.2e-10	-0.20	19:45691793:G:GC
Whole Blood	eqtl	3.2e-09	-0.09	19:45691793:G:GC
Esophagus Muscularis	eqtl	3.3e-07	-0.15	19:45691793:G:GC
Prostate	eqtl	4.5e-07	-0.25	19:45691793:G:GC

FANTOM5 promoters

5 alternative TSS:

Promoter ID	TPM avg	Samples expressed
169605	179.7856	1825
181553	128.6987	1825
181552	0.3318	155
181554	0.2222	81
181555	0.2186	87

Top tissues by expression

showing 100 of 295 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
adult organism	UBERON:0007023	99.52	gold quality
type B pancreatic cell	CL:0000169	99.46	gold quality
embryo	UBERON:0000922	99.38	gold quality
oral cavity	UBERON:0000167	99.33	gold quality
corpus epididymis	UBERON:0004359	99.33	gold quality
left ovary	UBERON:0002119	99.24	gold quality
ganglionic eminence	UBERON:0004023	99.21	gold quality
cauda epididymis	UBERON:0004360	99.20	gold quality
caput epididymis	UBERON:0004358	99.19	gold quality
islet of Langerhans	UBERON:0000006	99.17	gold quality
superficial temporal artery	UBERON:0001614	99.17	gold quality
mammalian vulva	UBERON:0000997	99.16	gold quality
right ovary	UBERON:0002118	99.15	gold quality
endocervix	UBERON:0000458	99.14	gold quality
pituitary gland	UBERON:0000007	99.12	gold quality
seminal vesicle	UBERON:0000998	99.12	gold quality
mucosa of sigmoid colon	UBERON:0004993	99.12	gold quality
adenohypophysis	UBERON:0002196	99.11	gold quality
lymph node	UBERON:0000029	99.07	gold quality
trabecular bone tissue	UBERON:0002483	99.07	gold quality
penis	UBERON:0000989	99.05	gold quality
right testis	UBERON:0004534	99.05	gold quality
upper arm skin	UBERON:0004263	99.04	gold quality
ectocervix	UBERON:0012249	99.04	gold quality
skin of abdomen	UBERON:0001416	99.03	gold quality
cartilage tissue	UBERON:0002418	99.03	gold quality
mammary duct	UBERON:0001765	99.02	gold quality
left testis	UBERON:0004533	99.02	gold quality
stromal cell of endometrium	CL:0002255	99.01	gold quality
upper leg skin	UBERON:0004262	99.00	gold quality
body of uterus	UBERON:0009853	99.00	gold quality
colonic mucosa	UBERON:0000317	98.99	gold quality
mucosa of transverse colon	UBERON:0004991	98.99	gold quality
zone of skin	UBERON:0000014	98.98	gold quality
ovary	UBERON:0000992	98.98	gold quality
skin of leg	UBERON:0001511	98.98	gold quality
right uterine tube	UBERON:0001302	98.97	gold quality
heart right ventricle	UBERON:0002080	98.95	gold quality
granulocyte	CL:0000094	98.94	gold quality
left uterine tube	UBERON:0001303	98.94	gold quality
thymus	UBERON:0002370	98.93	gold quality
ventricular zone	UBERON:0003053	98.93	gold quality
sigmoid colon	UBERON:0001159	98.90	gold quality
myometrium	UBERON:0001296	98.90	gold quality
nucleus accumbens	UBERON:0001882	98.90	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	98.89	gold quality
triceps brachii	UBERON:0001509	98.87	gold quality
skin of hip	UBERON:0001554	98.87	gold quality
Brodmann (1909) area 46	UBERON:0006483	98.87	gold quality
muscle layer of sigmoid colon	UBERON:0035805	98.87	gold quality
pigmented layer of retina	UBERON:0001782	98.86	gold quality
left adrenal gland cortex	UBERON:0035825	98.86	gold quality
lower esophagus mucosa	UBERON:0035834	98.86	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	98.86	gold quality
cortical plate	UBERON:0005343	98.85	gold quality
superior surface of tongue	UBERON:0007371	98.84	gold quality
gluteal muscle	UBERON:0002000	98.83	gold quality
spleen	UBERON:0002106	98.83	gold quality
right adrenal gland	UBERON:0001233	98.82	gold quality
left adrenal gland	UBERON:0001234	98.82	gold quality
lower esophagus	UBERON:0013473	98.82	gold quality
lower esophagus muscularis layer	UBERON:0035833	98.82	gold quality
mucosa of urinary bladder	UBERON:0001259	98.81	gold quality
urethra	UBERON:0000057	98.80	gold quality
adrenal cortex	UBERON:0001235	98.80	gold quality
nipple	UBERON:0002030	98.80	gold quality
left coronary artery	UBERON:0001626	98.78	gold quality
body of tongue	UBERON:0011876	98.78	gold quality
uterine cervix	UBERON:0000002	98.77	gold quality
prefrontal cortex	UBERON:0000451	98.77	gold quality
left lobe of thyroid gland	UBERON:0001120	98.77	gold quality
nasal cavity mucosa	UBERON:0001826	98.77	gold quality
layer of synovial tissue	UBERON:0007616	98.77	gold quality
pharyngeal mucosa	UBERON:0000355	98.76	gold quality
right lobe of thyroid gland	UBERON:0001119	98.76	gold quality
caudate nucleus	UBERON:0001873	98.76	gold quality
caecum	UBERON:0001153	98.75	gold quality
coronary artery	UBERON:0001621	98.75	gold quality
tongue	UBERON:0001723	98.75	gold quality
body of stomach	UBERON:0001161	98.74	gold quality
bone marrow	UBERON:0002371	98.73	gold quality
adipose tissue of abdominal region	UBERON:0007808	98.73	gold quality
right adrenal gland cortex	UBERON:0035827	98.72	gold quality
vermiform appendix	UBERON:0001154	98.71	gold quality
peritoneum	UBERON:0002358	98.71	gold quality
decidua	UBERON:0002450	98.71	gold quality
omental fat pad	UBERON:0010414	98.71	gold quality
olfactory bulb	UBERON:0002264	98.70	gold quality
smooth muscle tissue	UBERON:0001135	98.69	gold quality
ascending aorta	UBERON:0001496	98.68	gold quality
right coronary artery	UBERON:0001625	98.68	gold quality
amygdala	UBERON:0001876	98.68	gold quality
popliteal artery	UBERON:0002250	98.68	gold quality
pericardium	UBERON:0002407	98.68	gold quality
tibial artery	UBERON:0007610	98.68	gold quality
metanephros cortex	UBERON:0010533	98.68	gold quality
aorta	UBERON:0000947	98.67	gold quality
thoracic aorta	UBERON:0001515	98.67	gold quality
esophagus	UBERON:0001043	98.66	gold quality
body of pancreas	UBERON:0001150	98.66	gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-10042	yes	15.35
E-CURD-122	yes	11.87
E-MTAB-9388	no	3015.96
E-MTAB-7606	no	2031.13
E-GEOD-110499	no	941.21
E-ANND-3	no	0.00

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 80 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Ovary	tissue	537.1	medium
Thymus	tissue	466.3
Bone marrow	tissue	450.5	high
Lymph node	tissue	413.2	medium
Tonsil	tissue	379.5	medium
Breast	tissue	365.4	high
Vagina	tissue	328.2	medium
Epididymis	tissue	312.7	high
Pituitary gland	tissue	304.6
Fallopian tube	tissue	298.7	high
Urinary bladder	tissue	291.3	high
Skeletal muscle	tissue	287.0	high
Tongue	tissue	285.4
Cervix	tissue	251.3	high
Heart muscle	tissue	248.3	medium
Parathyroid gland	tissue	247.0	high
Rectum	tissue	237.4	high
Colon	tissue	236.8	high
Appendix	tissue	223.9	high
Smooth muscle	tissue	219.3	medium
Esophagus	tissue	216.7	high
Endometrium 1	tissue	214.0	medium
Adrenal gland	tissue	202.4	high
Placenta	tissue	201.8	high
Thyroid gland	tissue	200.7	high
Skin 1	tissue	199.6	high
Seminal vesicle	tissue	197.2	medium
Spleen	tissue	186.5	high
Liver	tissue	186.3	medium
Salivary gland	tissue	185.5	medium
Gallbladder	tissue	183.4	high
Adipose tissue	tissue	178.9	high
Kidney	tissue	174.4	medium
Spinal cord	tissue	172.6
Prostate	tissue	172.5	high
Stomach 1	tissue	170.0	high
Duodenum	tissue	159.7	high
Small intestine	tissue	157.7	medium
Pancreas	tissue	156.9	high
Pons	tissue	155.7
Superior colliculi	tissue	154.2
Corpus callosum	tissue	153.2
Midbrain	tissue	150.7
Lung	tissue	146.0	high
Putamen	tissue	145.9
Thalamus	tissue	144.9
Substantia nigra	tissue	144.6
Medulla oblongata	tissue	144.1
Testis	tissue	143.3	high
Hippocampal formation	tissue	141.7
Hypothalamus	tissue	130.4
Nucleus accumbens	tissue	128.6
Septum	tissue	127.2
Locus coeruleus	tissue	122.6
Ventral forebrain	tissue	117.0
Basal ganglia	tissue	115.3	high
Cerebral cortex	tissue	114.0	high
Somatosensory cortex	tissue	114.0
Retina	tissue	112.0
Motor cortex	tissue	110.7

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — Blood vessel (333.2), Dorsal spinal cord (172.6), Ventral spinal cord (159.3), White matter (153.2), Dorsal hippocampus (141.7).

Regulation

Is transcription factor: no

Functional genomics

gnomAD constraint: pLI 0.983, LOEUF 0.396, missense Z 2.46 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000342669 — one region, missense o/e 0.50. DepMap (CRISPR cell-line fitness): dependent in 100.0% of screened cell lines, common-essential.

Most-dependent cell lines (DepMap gene-effect, lower = stronger; ≤ −0.5 shown): S-117 (-3.444), CAL-29 (-3.237), NB-4 (-3.206), Capan-1 (-3.177), KP-2 (-3.174), Calu-6 (-3.156), CAL-120 (-3.092), NCI-H522 (-3.062), PA-TU-8988T (-3.05), NCI-H1693 (-3.048), JHOC-5 (-3.033), JH-EsoAd1 (-3.022), SIMA (-3.005), HCC1937 (-3.0), SLR 23 (-2.984).

Literature-anchored findings (GeneRIF, showing 2)

• Screen using siRNA revealed depletion of U1 snRNP components SNRPA, SNRNP70 or SNRPD2 caused significant cytoplasmic localization of MEG3 reporter transcripts. (PMID:31107149)
• Intron Retention of DDX39A Driven by SNRPD2 is a Crucial Splicing Axis for Oncogenic MYC/Spliceosome Program in Hepatocellular Carcinoma. (PMID:39018261)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	snrpd2	ENSDARG00000040440
mus_musculus	Snrpd2	ENSMUSG00000040824
rattus_norvegicus	Snrpd2	ENSRNOG00000015844
drosophila_melanogaster	SmD2	FBGN0261789
caenorhabditis_elegans		WBGENE00004917

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Bos taurus	Q32PE9	100.0%	Diamond
Arabidopsis thaliana	Q9C6K5	91.7%	Diamond
Sus scrofa	Q29329	90.0%	Diamond
Dictyostelium discoideum	Q54NC5	86.4%	Diamond
Schizosaccharomyces pombe 972h-	O14036	75.5%	Diamond
Saccharomyces cerevisiae S288C	Q06217	59.1%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
EML2-AS1	ncRNA	100287177
EML2	protein-coding	24139
GIPR	protein-coding	2696
QPCTL	protein-coding	54814
MIR642A	ncRNA	693227
MIR642B	ncRNA	100500845
MIR330	ncRNA	442902
DM1-AS	ncRNA	109729182
SIX5	protein-coding	147912
FBXO46	protein-coding	23403
MEIOSIN	protein-coding	388553

Protein

Protein identifiers

Small nuclear ribonucleoprotein Sm D2 — P62316 (reviewed: P62316)

Alternative names: snRNP core protein D2

All UniProt accessions (3): K7EJB5, K7ERG4, P62316

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.

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 with SMN1; the interaction is direct. Interacts with GEMIN2; the interaction is direct. Interacts with SNRPD1; the interaction is direct. Interacts with SNRPF; the interaction is direct.

Subcellular location. Cytoplasm. Cytosol. Nucleus.

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?
P62316-1	1	yes
P62316-2	2

RefSeq proteins (5): NP_001356680, NP_001356681, NP_001371576, NP_004588, NP_808210 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001163	Sm_dom_euk/arc	Domain
IPR010920	LSM_dom_sf	Homologous_superfamily
IPR027248	Sm_D2	Family
IPR047575	Sm	Domain

Pfam: PF01423

UniProt features (28 total): strand 8, helix 5, turn 3, modified residue 3, cross-link 2, initiator methionine 1, chain 1, splice variant 1, sequence conflict 1, domain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

showing 30 of 85 structures by resolution:

PDB	Title	Method	Resolution (Å)
4F7U	The 6S snRNP assembly intermediate	X-RAY DIFFRACTION	1.9
9S2E	Human intron-lariat spliceosome-Aquarius (ILSaqr)	ELECTRON MICROSCOPY	2.4
1B34	CRYSTAL STRUCTURE OF THE D1D2 SUB-COMPLEX FROM THE HUMAN SNRNP CORE DOMAIN	X-RAY DIFFRACTION	2.5
5XJL	Crystal Structure of the Gemin2-binding domain of SMN, Gemin2 in Complex with …	X-RAY DIFFRACTION	2.5
7EVO	The cryo-EM structure of the human 17S U2 snRNP	ELECTRON MICROSCOPY	2.5
5XJU	Crystal Structure of the Gemin2-binding domain of SMN, Gemin2dN39 in Complex with …	X-RAY DIFFRACTION	2.58
8H6L	Cryo-EM structure of human exon-defined spliceosome in the early B state.	ELECTRON MICROSCOPY	2.6
8H6K	Cryo-EM structure of human exon-defined spliceosome in the mature B state.	ELECTRON MICROSCOPY	2.7
8HK1	The cryo-EM structure of human pre-17S U2 snRNP	ELECTRON MICROSCOPY	2.7
8C6J	Human spliceosomal PM5 C* complex	ELECTRON MICROSCOPY	2.8
6ID1	Cryo-EM structure of a human intron lariat spliceosome after Prp43 loaded (ILS2 complex) …	ELECTRON MICROSCOPY	2.86
7DVQ	Cryo-EM Structure of the Activated Human Minor Spliceosome (minor Bact Complex)	ELECTRON MICROSCOPY	2.89
6ID0	Cryo-EM structure of a human intron lariat spliceosome prior to Prp43 loaded (ILS1 …	ELECTRON MICROSCOPY	2.9
5XJT	Crystal Structure of the Gemin2-binding domain of SMN, Gemin2 in Complex with …	X-RAY DIFFRACTION	2.92
6QW6	Structure of the human U5.U4/U6 tri-snRNP at 2.9A resolution.	ELECTRON MICROSCOPY	2.92
9XTT	Human minor spliceosome branching-completed C complex (after step-I)	ELECTRON MICROSCOPY	2.92
6ICZ	Cryo-EM structure of a human post-catalytic spliceosome (P complex) at 3.0 angstrom	ELECTRON MICROSCOPY	3
7VPX	The cryo-EM structure of the human pre-A complex	ELECTRON MICROSCOPY	3
8I0R	The cryo-EM structure of human Bact-I complex	ELECTRON MICROSCOPY	3
8I0T	The cryo-EM structure of human Bact-III complex	ELECTRON MICROSCOPY	3
8I0V	The cryo-EM structure of human post-Bact complex	ELECTRON MICROSCOPY	3
9GCL	Structure of the U11 snRNP C-lobe	ELECTRON MICROSCOPY	3
9XU3	Human minor spliceosome exon-ligation-ready C* complex (prior to step-II)	ELECTRON MICROSCOPY	3
4V98	The 8S snRNP Assembly Intermediate	X-RAY DIFFRACTION	3.1
7QTT	Structural organization of a late activated human spliceosome (Baqr, core region)	ELECTRON MICROSCOPY	3.1
8Q91	Structure of the human 20S U5 snRNP core	ELECTRON MICROSCOPY	3.1
5XJR	Crystal Structure of the Gemin2-binding domain of SMN, Gemin2dN39 in Complex with …	X-RAY DIFFRACTION	3.12
9S2F	Human debranched intron spliceosome (DIS)	ELECTRON MICROSCOPY	3.14
8H6E	Cryo-EM structure of human exon-defined spliceosome in the late pre-B state.	ELECTRON MICROSCOPY	3.2
8Q7Q	Structure of the recycling U5 snRNP bound to chaperones CD2BP2 and TSSC4 (State 2)	ELECTRON MICROSCOPY	3.2

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P62316-F1	91.03	0.79

Human Protein Atlas

Protein class: Predicted intracellular proteins, Essential proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): cytosol

Antibody reliability (HPA): IH supported · IF supported

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)

Type	Positions
N-acetylserine	2
Phosphoserine	9
Phosphothreonine	12
Glycyl lysine isopeptide (lys-gly) (interchain with g-cter in sumo2)	6, 8

Function

Pathways and Gene Ontology

Reactome pathways

7 curated (TAS) of 17; 8 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

17 pathways:

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

MSigDB gene sets: 439 (showing top): E2F_Q4, GNF2_MSH2, TGCGCANK_UNKNOWN, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, E2F4DP1_01, MODULE_151, CMYB_01, GCM_NPM1, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN, GOBP_NEGATIVE_REGULATION_OF_RNA_SPLICING, MORF_HDAC1, HSIAO_HOUSEKEEPING_GENES, GTACAGG_MIR486, SHIPP_DLBCL_CURED_VS_FATAL_DN

GO Biological Process (10): spliceosomal tri-snRNP complex assembly (GO:0000244), spliceosomal complex assembly (GO:0000245), spliceosomal snRNP assembly (GO:0000387), spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) (GO:0000388), mRNA splicing, via spliceosome (GO:0000398), RNA splicing (GO:0008380), 7-methylguanosine cap hypermethylation (GO:0036261), negative regulation of mRNA splicing, via spliceosome (GO:0048025), U2-type prespliceosome assembly (GO:1903241), mRNA processing (GO:0006397)

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

GO Cellular Component (22): 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), extracellular exosome (GO:0070062), 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 snRNP complex (GO:0097525), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

13 top-level categories:

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

40 GO namespaces:

Category	Terms
spliceosomal snRNP complex	4
spliceosomal complex	4
cytoplasm	4
mRNA splicing, via spliceosome	3
protein-RNA complex assembly	3
Sm-like protein family complex	3
RNA processing	2
cellular anatomical structure	2
nuclear protein-containing complex	2
ribonucleoprotein complex	2
U5 snRNP	2
U2-type spliceosomal complex	2
U2 snRNP	2
spliceosomal snRNP assembly	1
spliceosomal conformational changes to generate catalytic conformation	1
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
RNA methylation	1
RNA capping	1
negative regulation of RNA splicing	1
regulation of mRNA splicing, via spliceosome	1
negative regulation of mRNA processing	1
spliceosomal complex assembly	1
mRNA metabolic process	1
nucleic acid 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
extracellular vesicle	1
U1 snRNP	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

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 17 of 34 annotations. The rest are phylogenetic / computational / electronic (IEA).

17 experimentally-supported GO terms:

GO term	NS	Evidence
mRNA splicing, via spliceosome	BP	direct assay
spliceosomal snRNP assembly	BP	direct assay
SMN-Sm protein complex	CC	direct assay
U1 snRNP	CC	direct assay
U12-type spliceosomal complex	CC	direct assay
U2-type catalytic step 2 spliceosome	CC	direct assay
U2-type precatalytic spliceosome	CC	direct assay
U2-type spliceosomal complex	CC	direct assay
U4 snRNP	CC	direct assay
U4/U6 x U5 tri-snRNP complex	CC	direct assay
catalytic step 2 spliceosome	CC	direct assay
cytosol	CC	direct assay
extracellular exosome	CC	high-throughput assay
methylosome	CC	direct assay
nucleus	CC	direct assay
pICln-Sm protein complex	CC	direct assay
RNA binding	MF	high-throughput assay

Protein interactions and networks

IntAct

Human interaction partners of SNRPD2 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

23 partners by confidence:

Partner	Interaction type	MIscore	Records
SNRPF	physical association	0.890	10
CLNS1A	physical association	0.880	7
LSM6	physical association	0.800	2
LSM2	physical association	0.750	3
GEMIN2	association	0.710	1
SNRPD1	physical association	0.680	3
GEMIN6	direct interaction	0.590	1
STRAP	direct interaction	0.590	1
ATXN1	physical association	0.560	3
CEP70	physical association	0.560	3
CINP	physical association	0.560	3
HTT	physical association	0.560	3
SPANXN2	physical association	0.560	3
SF3A2	physical association	0.560	1
H2BC9	physical association	0.400	1
OS9	physical association	0.370	1
ZCCHC10	physical association	0.370	1
CRLF3	association	0.350	1
PRDM7	association	0.350	1
DMTN	physical association	0.000	1
EEF1G	physical association	0.000	1
KAT5	physical association	0.000	1
PRPF31	physical association	0.000	1

BioGRID (688 interactions; top human partners by supporting records in a sample of 600 records): SNRPF (Co-fractionation; 12 records), SNRNP70 (Co-fractionation; 8 records), CLNS1A (Two-hybrid; 7 records), SNRPD1 (Co-fractionation; 7 records), SNRPE (Co-fractionation; 7 records), PRPF8 (Affinity Capture-MS; 6 records), SMN1 (Co-purification; 6 records), SNRNP40 (Affinity Capture-MS; 6 records), SNRPA1 (Affinity Capture-MS; 6 records), DDX23 (Affinity Capture-MS; 5 records), SNRPD3 (Co-fractionation; 5 records), SNRPG (Co-fractionation; 5 records), CD2BP2 (Affinity Capture-MS; 4 records), DDX20 (Affinity Capture-MS; 4 records), EFTUD2 (Affinity Capture-MS; 4 records)

SIGNOR signaling

3 signaling interactions:

A	Effect	B	Mechanism
SNRPD2	“form complex”	“U4/U6.U5 snRNP complex”	binding
SNRPD2	“form complex”	“U2 snRNP complex”	binding
SNRPD2	“form complex”	“U1 snRNP complex”	binding

Protein complexes (CORUM) (17)

Experimentally-characterized complexes this protein is a subunit of (★ = the complex contains a known drug target).

17 complexes by size:

Complex	Subunits	Members
Spliceosome, E complex	129	RBM17, DDX39A, GEMIN2, NCBP2, PRPF31, SART3, SF3A2, SNRPA, SRSF7, DDX39B, DHX15, GEMIN5, SCAF4, SMARCB1, SNRPD3, SYNCRIP, U2AF2, HNRNPC, SF3B2, SMARCC2, SFSWAP, USP39, GEMIN6, HNRNPK, RBM42, SF3B1, SF3B4, SNRPG, SRSF6, BCAS2, SMN1, CPSF7, SMARCE1, SRSF8, ARID1A, LSM4, SNRPC, CHD8, FUS, SNRNP70, SRSF11, NUDT21, PBRM1, SNRPB2, SNRPD1, YBX1, SF1, SNRPD2, SRSF2, SRSF5, PPIH, SRSF3, DDX20, SART1, SRSF1, SRSF4, PRPF19, RBM39, RBMXL2, SREK1, PRPF3, SMARCA2, U2AF1, SF3B6, SMARCA1, CPSF1, DDX23, DHX9, RUVBL1, SNRPF, SRRM2, ALYREF, HNRNPA0, HNRNPH1, PCBP2, RBM10, SF3B3, STRAP, HNRNPR, RBM25, ACTBL2, CHERP, SNRPA1, ACTL6A, DDX46, HNRNPL, RBM7, CPSF6, ARID2, DNAJC8, EFTUD2, KHSRP, RUVBL2, SMARCA4, PCBP1, SNRNP40, SNRPE, PRPF4, PRPF8, SF3A1, SF3A3, SNRNP200, ZCCHC8, DDX5, LUC7L3, SMARCC1, HNRNPA2B1, HNRNPD, HTATSF1, LUC7L2, PHF5A, PRPF6, SMARCD1, SNRPB, GEMIN8, U2SURP, NCBP1, GEMIN4, HNRNPU, MTREX, ARID1B, CHD4, HNRNPM, PRPF40A, HNRNPF, SRRT, DDX17, HNRNPA1, PUF60
Spliceosome, A complex	112	RBM39, SAP30BP, CDK11A, CHERP, HNRNPA1, HNRNPK, HNRNPR, HNRNPU, RBM25, SF3A1, DDX46, HNRNPA3, RNPS1, SART1, SF1, SF3A2, SF3B4, SNRPB, ACIN1, CCAR2, DHX9, ELAVL1, ILF2, SF3B3, SRSF5, HNRNPA2B1, CD2BP2, DDX5, PUF60, RBM17, SNRPA1, TCERG1, ZC3H18, SNRPD1, SRSF2, SYNCRIP, ZNF207, CTNNBL1, HSPA8, NCBP2, SF3B2, TRA2B, YBX1, RBM10, SF3A3, SRRM1, SRSF6, SRSF7, SUGP1, DDX42, DNAJC8, EFTUD2, PRCC, SF3B5, SMNDC1, SNRNP200, WBP11, CDC5L, PPP1R8, PRPF6, BCAS2, NCBP1, PRPF19, PRPF3, SNRPD3, SRSF4, U2AF2, HNRNPUL1, NRIP2, PHF5A, RBM5, RBMX, SNRPA, SRRM2, U2AF1, CCAR1, CFAP20, CIRBP, DDX23, SF3B1, SF3B6, SNRPB2, SNRPE, BUB3, DHX15, PCBP1, PPP1CA, PQBP1, SNRNP70, SRSF1, U2SURP, DDX17, SNRPC, SNRPD2, SNRPF, SNRPG, SRRT, SRSF3, SRSF9, AGGF1, FUS, HNRNPC, HTATSF1, ILF3, PLRG1, SEC31B, TRIR, CWC15, HNRNPAB, PNN, PRPF40A, PRPF8
C complex spliceosome	80	RBM8A, ZCCHC8, EFTUD2, HNRNPK, PNN, SRSF1, CDC40, DHX35, HNRNPA2B1, HNRNPC, SF3B3, SYNCRIP, U2AF1, PLRG1, RBM22, SNRNP40, SNRPB2, EIF4A3, FRG1, GPATCH1, HNRNPA3, PPIL1, SF3B1, DHX38, HNRNPR, LSM2, LSM3, SNRPE, DDX23, HNRNPU, MTREX, SLU7, AQR, CWC15, CWC22, DDX41, PABPC1, SF3B2, SNRPD1, SNRPD2, DHX8, CWC27, HNRNPA1, HNRNPH1, MAGOH, SF3A1, PPIE, PPIL3, PRP4K, PRPF6, RALY, SNRPA1, SYF2, TFIP11, CACTIN, CRNKL1, DDX5, SF3A3, SNRNP200, SNRPD3, SNRPF, SRRM1, ALYREF, PPWD1, PRPF19, RBMX, SF3A2, SRRM2, WDR83, XAB2, CDC5L, HNRNPF, SART1, SNRPG, ESS2, ISY1, SNRPB, SNW1, HNRNPM, PRPF8
Spliceosome, B complex	43	EFTUD2, MFAP1, PRPF3, PRPF6, SF3B3, SF3B4, SF3B6, SNRNP40, LSM2, LSM4, LSM7, SF3B1, SNRPB, SNRPD1, SNRPD3, SNRPE, LSM6, SMU1, SNU13, PHF5A, SNRPB2, SNRPF, SF3A1, SNRPD2, TXNL4A, UBL5, WBP4, LSM3, PPIH, PRPF38A, SF3A3, LSM5, PRPF4, PRPF8, SF3A2, SF3B2, SNRNP200, SNRPA1, SNRPG, LSM8, PRPF31, SART1, ZMAT2
Spliceosome, C complex	39	MAGOH, PPWD1, RBM8A, SNRPF, SNRPG, SYF2, PPIE, SNRPB2, SNRPA1, BCAS2, BUD31, CWC25, SNRPD2, SNRPD3, CASC3, EIF4A3, PRPF19, SNRPD1, SNRPE, YJU2, SRRM2, XAB2, CWC22, RBM22, SNRNP200, AQR, CWC15, EFTUD2, ISY1, PPIG, CDC40, CDC5L, DHX38, PLRG1, PPIL1, PRPF8, SNRPB, SNW1, CRNKL1
Spliceosome, pre-B complex	38	SF3A3, SF3B4, SNRPD1, EFTUD2, LSM8, PRPF8, PRPF31, SF3A1, SF3A2, LSM3, PHF5A, SF3B1, SF3B2, SNRPA1, SNRPD2, SNRPF, SNU13, PRPF4, SF3B6, SNRNP200, SNRPB2, SNRPE, USP39, LSM4, LSM5, PRPF3, PRPF6, SF3B3, SNRNP40, SNRPG, TXNL4A, DDX23, LSM6, LSM7, SF3B5, SNRPD3, SNRPB, LSM2
17S U2 snRNP	33	DHX15, PUF60, SF3A1, SNRPG, SF3B2, SF3B4, SF3B5, SNRPE, SNRPF, HMG20B, SNRPB, DDX46, SF3A3, SNRPB2, SNRPD1, SRSF1, U2AF1, CHERP, PHF5A, RBM17, SF3B6, SNRPD2, DNAJC8, SMNDC1, SF3B1, SNRPD3, U2AF2, HSPD1, SF3A2, SF3B3, SNRPA1, TRAP1, U2SURP
★ CDC5L complex	30	SRRM1, SF3B1, SRSF1, CDC5L, DYNC1H1, GCN1, HSPA8, PPP1CA, SF3B2, SCAF8, SNRPA, SRSF2, BZW1, RBMX, SFPQ, SNRPA1, SNRPD3, TCF4, PLRG1, SNRPD2, TOP2A, ILF2, SF3B4, SNRPD1, SFI1, BCAS2, CWC15, PPM1D, PRKDC, PRPF19
18S U11/U12 snRNP	24	PRPF8, RNPC3, SF3B2, SF3B4, SF3B5, SNRPD2, YBX1, SF3B1, SNRNP35, SNRNP48, SNRPE, ZCRB1, ZMAT5, ZRSR2, SNRPB, DHX15, PDCD7, SF3B3, SNRPD1, SNRPD3, SNRPF, SF3B6, SNRNP25, SNRPG
SMN complex (16 subunits)	16	SNRPD3, SNRPG, GEMIN4, GEMIN5, SNRPB, SNRPF, DDX20, GEMIN7, SMN1, STRAP, SNRPD1, SNRPD2, SNRPE, GEMIN2, GEMIN6, GEMIN8
12S U11 snRNP	15	SNRPD1, PRKRIP1, SNRNP35, SNRNP48, SNRPD3, SNRPE, YBX1, PDCD7, SNRNP25, TOE1, SNRPG, SRSF7, SNRPB, SNRPD2, SNRPF
SMN complex	15	SNRPE, GEMIN2, GEMIN5, SNRPD3, SNRPG, SNRPN, SNRPD2, DDX20, GEMIN4, GEMIN6, SNRPA, SNRPD1, SNRPF, GEMIN7, SNRPB
SMN complex (10 subunits)	10	SNRPB, SNRPD1, SNRPG, DDX20, GEMIN2, SMN1, SNRPD2, SNRPD3, SNRPE, SNRPF
SMN containing complex	8	GEMIN2, GEMIN4, LGALS1, LGALS3, SMN1, SNRPD1, SNRPD2, SNRPD3
6S methyltransferase and RG-containing Sm proteins complex	8	SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, CLNS1A
SMN complex (GEMIN2, SMN1, SNRPB, SNRPDs)	7	GEMIN2, SMN1, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE
20S methylosome and RG-containing Sm protein complex	6	SNRPD1, SNRPD2, SNRPD3, CLNS1A, PRMT5, SNRPB

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 23 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
snRNP Assembly	5	58.7×	3e-06
mRNA Splicing	5	30.5×	3e-05
Processing of Capped Intron-Containing Pre-mRNA	5	22.8×	6e-05
mRNA Splicing - Major Pathway	6	18.2×	3e-05
Metabolism of RNA	5	11.6×	1e-03

GO biological processes:

GO term	Partners	Fold	FDR
spliceosomal snRNP assembly	6	166.0×	1e-10
mRNA splicing, via spliceosome	7	30.5×	1e-07

Disease & clinical

Genetic variants

Variant evidence for SNRPD2: 10 ClinVar records (0 pathogenic / likely pathogenic); 5 GWAS associations.

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	3
Likely benign	0
Benign	0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 19 predictions of 182):

Position(s)	Effect	Δscore	Sites
19:45687728–45687729	acceptor_loss	1.0000	5
19:45688385–45688386	donor_loss	1.0000	4
19:45688567–45688568	acceptor_loss	1.0000	2
19:45688571	acceptor_gain	1.0000
19:45688577	acceptor_gain	1.0000
19:45688581	acceptor_gain	1.0000
19:45687740	acceptor_gain	0.9900
19:45688386	donor_loss	0.9900
19:45688568	acceptor_loss	0.9900	2
19:45691905	donor_gain	0.9900

AlphaMissense

616 missense substitutions predicted likely pathogenic (of 782 scored), across 115 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
M65	9	0.936	1.000
M73	9	0.895	0.996
D60	8	1.000	1.000
H62	8	0.999	1.000
D104	8	0.999	1.000
N64	8	0.997	1.000
F100	8	0.994	1.000
F59	8	0.992	1.000
D93	8	0.972	0.995
F24	8	0.970	0.998
N112	8	0.943	0.994
N49	8	0.936	0.997
N48	8	0.923	0.999
E72	7	0.998	1.000
W74	7	0.998	1.000
R61	7	0.997	1.000
C46	7	0.996	1.000
E20	7	0.980	0.995
E68	7	0.975	0.998
C63	7	0.972	1.000

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

4 prognostic cancer types:

Cancer	Prognostic	p-value
Liver Hepatocellular Carcinoma (validation)	unfavorable	8.95e-08
Kidney Renal Papillary Cell Carcinoma (TCGA)	unfavorable	2.65e-06
Liver Hepatocellular Carcinoma (TCGA)	unfavorable	2.83e-05
Lung Adenocarcinoma (TCGA)	unfavorable	0.00068

Disease associations

OMIM: gene MIM:601061 | disease phenotypes:

GWAS associations

5 associations:

Study	Trait	p-value
GCST010136_30	Fruit consumption	1e-11
GCST007612_3	Chronic obstructive pulmonary disease or coronary artery disease (pleiotropy)	1e-8
GCST004787_12	Coronary artery disease (myocardial infarction, percutaneous transluminal coronary angioplasty, coronary artery bypass grafting, angina or chromic ischemic heart disease)	3e-8
GCST001521_38	Subcutaneous adipose tissue	1e-6
GCST001521_8	Subcutaneous adipose tissue	2e-6

EFO canonical traits (from GWAS)

1 canonical traits:

EFO ID	Trait name
EFO:0008111	diet measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5725105 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

Phase ≥1, by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 1,601 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

1 molecules by phase:

Molecule	Name	Phase	Patents
CHEMBL1232461	MOLIBRESIB	2	1,601

PharmGKB: 1 entry (CPIC guideline: no)

Binding affinities (BindingDB)

1 measured of 1 human assays (3 total across all organisms); most potent 1 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value
CHEMBL5653589	KD	1440 nM

ChEMBL bioactivities

1 potent at pChembl≥5 of 4 total, top 1 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
7.13	Kd	74	nM	MOLIBRESIB

PubChem BioAssay actives

1 with measured affinity, of 11 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
2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide	2179142: Binding affinity against SNRPD2 (unknown origin) assessed as apparent dissociation constant incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysis	kd	0.0740	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	3
bisphenol A	affects expression, decreases expression	2
bisphenol S	affects expression, increases expression	2
Air Pollutants	affects cotreatment, increases abundance, increases expression, decreases expression	2
Valproic Acid	affects cotreatment, increases expression, increases methylation	2
Particulate Matter	decreases reaction, increases expression, decreases expression, increases abundance	2
FR900359	increases phosphorylation	1
TAK-243	decreases sumoylation	1
beauvericin	affects cotreatment, increases expression	1
alpha phellandrene	decreases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases expression, increases abundance	1
arsenite	affects binding, increases reaction	1
methylparaben	decreases expression	1
perfluorooctanoic acid	decreases expression	1
artenimol	affects binding	1
methacrylaldehyde	increases expression, increases abundance, affects cotreatment	1
hinokiflavone	increases sumoylation	1
CD 437	decreases expression	1
chloropicrin	increases expression	1
enniatins	affects cotreatment, increases expression	1
K 7174	decreases expression	1
3-(4’-hydroxy-3’-adamantylbiphenyl-4-yl)acrylic acid	decreases expression	1
nutlin 3	affects cotreatment, increases secretion	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases reaction, increases expression	1
Acrolein	affects cotreatment, increases expression, increases abundance	1
Vehicle Emissions	increases expression, decreases reaction	1
Benztropine	increases expression	1
Dactinomycin	affects cotreatment, increases secretion	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1

ChEMBL screening assays

8 unique, capped per target: 8 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652501	Binding	Binding affinity to human SNRPD2 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)

Via MONDO — disease-level, not drug-specific.

Predicted chemistry — Sugi Predict

The predicted patent-compound landscape for SNRPD2 across ~30M SureChEMBL compounds — explore on Sugi Predict.