SNU13

Summary

SNU13 (small nuclear ribonucleoprotein 13, HGNC:7819) is a protein-coding gene on chromosome 22q13.2, encoding NHP2-like protein 1 (P55769). Part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit. It is a common-essential gene (DepMap: required in 99.9% of cancer cell lines).

Originally named because of its sequence similarity to the Saccharomyces cerevisiae NHP2 (non-histone protein 2), this protein appears to be a highly conserved nuclear protein that is a component of the [U4/U6.U5] tri-snRNP. It binds to the 5’ stem-loop of U4 snRNA. Two transcript variants encoding the same protein have been found for this gene.

Source: NCBI Gene 4809 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 6 total
• Druggable target: yes — 1 molecules with ChEMBL bioactivity
• Cancer dependency (DepMap): dependent in 99.9% of screened cell lines (common-essential)
• MANE Select transcript: NM_001003796

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:7819
Approved symbol	SNU13
Name	small nuclear ribonucleoprotein 13
Location	22q13.2
Locus type	gene with protein product
Status	Approved
Aliases	FA-1, SPAG12, SNRNP15-5, 15.5K
Ensembl gene	ENSG00000100138
Ensembl biotype	protein_coding
OMIM	601304
Entrez	4809

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 9 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000215956, ENST00000401959, ENST00000402458, ENST00000463675, ENST00000469028, ENST00000469522, ENST00000488571, ENST00000648161, ENST00000648350, ENST00000648674, ENST00000649479, ENST00000649722

RefSeq mRNA: 2 — MANE Select: NM_001003796 NM_001003796, NM_005008

CCDS: CCDS14022, CCDS33653

Canonical transcript exons

ENST00000401959 — 3 exons

Exon	Start	End
ENSE00001547860	41673933	41675195
ENSE00003679975	41680244	41680364
ENSE00003837536	41688794	41688867

Expression profiles

Bgee: expression breadth ubiquitous, 309 present calls, max score 98.96.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 136.7900 / max 914.1612, expressed in 1824 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
194378	50.2546	1819
194377	48.9969	1819
194376	36.4471	1783
194375	0.5826	292
194374	0.4792	256
194372	0.0213	9
194379	0.0083	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
adult organism	UBERON:0007023	98.96	gold quality
type B pancreatic cell	CL:0000169	98.73	gold quality
prefrontal cortex	UBERON:0000451	98.66	gold quality
hypothalamus	UBERON:0001898	98.51	gold quality
right frontal lobe	UBERON:0002810	98.47	gold quality
hindlimb stylopod muscle	UBERON:0004252	98.46	gold quality
heart right ventricle	UBERON:0002080	98.41	gold quality
stromal cell of endometrium	CL:0002255	98.40	gold quality
left testis	UBERON:0004533	98.35	gold quality
right atrium auricular region	UBERON:0006631	98.34	gold quality
Brodmann (1909) area 9	UBERON:0013540	98.34	gold quality
cerebellar hemisphere	UBERON:0002245	98.31	gold quality
nucleus accumbens	UBERON:0001882	98.30	gold quality
right testis	UBERON:0004534	98.29	gold quality
cerebellar cortex	UBERON:0002129	98.25	gold quality
amygdala	UBERON:0001876	98.24	gold quality
pituitary gland	UBERON:0000007	98.22	gold quality
biceps brachii	UBERON:0001507	98.21	gold quality
adenohypophysis	UBERON:0002196	98.21	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	98.21	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	98.16	gold quality
right hemisphere of cerebellum	UBERON:0014890	98.16	gold quality
cervix squamous epithelium	UBERON:0006922	98.15	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	98.13	gold quality
triceps brachii	UBERON:0001509	98.12	gold quality
diaphragm	UBERON:0001103	98.06	gold quality
cingulate cortex	UBERON:0003027	98.04	gold quality
cerebellum	UBERON:0002037	98.01	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	97.99	gold quality
putamen	UBERON:0001874	97.99	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-HCAD-9	yes	14.24
E-MTAB-6819	no	595.53
E-HCAD-5	no	2.19
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting SNU13, 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-6759-5P	99.99	66.54	785
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-1321	99.84	65.30	1811
HSA-MIR-4739	99.84	65.25	1832
HSA-MIR-4756-5P	99.84	64.98	1809
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-130B-5P	99.83	68.50	1888
HSA-MIR-4694-3P	99.79	69.53	2640
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-2392	99.43	67.50	708
HSA-MIR-542-3P	99.34	67.58	1270
HSA-MIR-3614-5P	99.30	65.25	837
HSA-MIR-4279	99.19	66.70	2437
HSA-MIR-10524-5P	99.05	66.08	963
HSA-MIR-5001-3P	98.91	67.28	1394
HSA-MIR-10A-5P	98.89	69.85	712
HSA-MIR-10B-5P	98.89	69.86	711
HSA-MIR-4755-3P	98.77	65.59	1915
HSA-MIR-1178-3P	98.57	67.09	890
HSA-MIR-7114-3P	98.42	66.53	569
HSA-MIR-1180-5P	98.16	65.32	460
HSA-MIR-3085-5P	97.72	65.43	544
HSA-MIR-6500-3P	97.42	67.20	867
HSA-MIR-1202	97.19	66.43	827

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.9% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 6)

• NHPX is specifically accumulated in both nucleoli and Cajal bodies (CBs) in vivo. The data show a specific temporal pathway involving the sequential and directed accumulation of NHPX in distinct subnuclear compartments (PMID:12011111)
• the testis-specific expression of FA-1 antigen at the mRNA level (PMID:12203836)
• Data show that binding of the 15.5 kD RNA binding protein to the box C/D motif of snoRNAs is essential for the association of other snoRNP-associated proteins. (PMID:12417735)
• describe the solution NMR structure of free 15.5K, as well as studies of conformational flexibility from 15N NMR relaxation and H/D exchange experiments (PMID:18044964)
• snoRNP assembly factor NUFIP can regulate the interactions between TIP48 and TIP49 and the core box C/D proteins. (PMID:19620283)
• Results solve the structure of a complex resulting from interaction between protein fragments of human NUFIP1 and its cofactor ZNHIT3, and emphasize their imbrication. Also, it seems that the complexes involving NUFIP1, ZNHIT3, and SNU13 share strong structural similarities between human and yeast, suggesting that the initial steps of the box C/D snoRNP assembly process are conserved among species. (PMID:27594683)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	snu13b	ENSDARG00000023299
danio_rerio	snu13a	ENSDARG00000069878
mus_musculus	Snu13	ENSMUSG00000063480
rattus_norvegicus	Snu13-ps5	ENSRNOG00000025154
drosophila_melanogaster	hoip	FBGN0286786
caenorhabditis_elegans		WBGENE00010896

Protein

Protein identifiers

NHP2-like protein 1 — P55769 (reviewed: P55769)

Alternative names: High mobility group-like nuclear protein 2 homolog 1, OTK27, SNU13 homolog, U4/U6.U5 small nuclear ribonucleoprotein SNU13, U4/U6.U5 tri-snRNP 15.5 kDa protein

All UniProt accessions (8): P55769, A0A3B3IRU2, A0A3B3ISH1, A0A3B3ISH9, A0A3B3ISK4, A0A3B3IUA2, B1AHD1, Q6FHM6

UniProt curated annotations — full annotation on UniProt →

Function. Part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit. During the assembly of the SSU processome in the nucleolus, many ribosome biogenesis factors, an RNA chaperone and ribosomal proteins associate with the nascent pre-rRNA and work in concert to generate RNA folding, modifications, rearrangements and cleavage as well as targeted degradation of pre-ribosomal RNA by the RNA exosome. Involved in pre-mRNA splicing as component of the spliceosome. Binds to the 5’-stem-loop of U4 snRNA and thereby contributes to spliceosome assembly. The protein undergoes a conformational change upon RNA-binding. Core component of box C/D small nucleolar ribonucleoprotein (snoRNP) complexes that function in methylation of multiple sites on ribosomal RNAs (rRNAs) and messenger RNAs (mRNAs).

Subunit / interactions. Identified in the spliceosome B complex. Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, WDR57, SNRNP40, DDX23, CD2BP2, PPIH, NHP2L1, EFTUD2, SART1 and USP39. Interacts with RAD17 and PRPF31. The complex formed by SNU13 and PRPF31 binds U4 snRNA. The complex formed by SNU13 and PRPF31 also binds U4atac snRNA, a characteristic component of specific, less abundant spliceosomal complexes. Part of the small subunit (SSU) processome, composed of more than 70 proteins and the RNA chaperone small nucleolar RNA (snoRNA) U3. Core component of box C/D small nucleolar ribonucleoprotein (snoRNP) particles; the core proteins SNU13, NOP56, NOP58 and FBL or FBLL1 assemble stepwise onto the snoRNA.

Subcellular location. Nucleus. Nucleolus.

Tissue specificity. Ubiquitous.

Similarity. Belongs to the eukaryotic ribosomal protein eL8 family.

RefSeq proteins (2): NP_001003796, NP_004999 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002415	H/ACA_rnp_Nhp2-like	Family
IPR004037	Ribosomal_eL8-like_CS	Conserved_site
IPR004038	Ribosomal_eL8/eL30/eS12/Gad45	Domain
IPR018492	Ribosomal_eL8/Nhp2	Family
IPR029064	Ribosomal_eL30-like_sf	Homologous_superfamily
IPR050257	eL8/uL1-like	Family

Pfam: PF01248

UniProt features (27 total): helix 6, strand 5, modified residue 4, mutagenesis site 4, chain 2, region of interest 2, site 2, initiator methionine 1, sequence variant 1

Structure

Experimental structures (PDB)

32 structures, top 30 by resolution.

PDB	Method	Resolution (Å)
2OZB	X-RAY DIFFRACTION	2.6
8H6L	ELECTRON MICROSCOPY	2.6
3SIU	X-RAY DIFFRACTION	2.63
7MQA	ELECTRON MICROSCOPY	2.7
8H6K	ELECTRON MICROSCOPY	2.7
1E7K	X-RAY DIFFRACTION	2.9
6QW6	ELECTRON MICROSCOPY	2.92
8Q7N	ELECTRON MICROSCOPY	3.1
8QOZ	ELECTRON MICROSCOPY	3.1
8QPE	ELECTRON MICROSCOPY	3.1
8H6E	ELECTRON MICROSCOPY	3.2
8H6J	ELECTRON MICROSCOPY	3.25
6QX9	ELECTRON MICROSCOPY	3.28
3SIV	X-RAY DIFFRACTION	3.3
8Y6O	ELECTRON MICROSCOPY	3.38
7MQ8	ELECTRON MICROSCOPY	3.6
8QPA	ELECTRON MICROSCOPY	3.7
8QPB	ELECTRON MICROSCOPY	3.7
6AHD	ELECTRON MICROSCOPY	3.8
7MQ9	ELECTRON MICROSCOPY	3.87
8QZS	ELECTRON MICROSCOPY	4.1
8R09	ELECTRON MICROSCOPY	4.3
8R0B	ELECTRON MICROSCOPY	4.4
5O9Z	ELECTRON MICROSCOPY	4.5
8QO9	ELECTRON MICROSCOPY	5.29
6AH0	ELECTRON MICROSCOPY	5.7
8R0A	ELECTRON MICROSCOPY	5.8
8R08	ELECTRON MICROSCOPY	6.1
8RM5	ELECTRON MICROSCOPY	6.9
3JCR	ELECTRON MICROSCOPY	7

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P55769-F1	94.95	0.92

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (2): 61 (interaction with u4 snrna and u4atac snrna); 86 (interaction with u4 snrna and u4atac snrna)

Post-translational modifications (4): 122, 1, 2, 21

Mutagenesis-validated functional residues (4):

Position	Phenotype
38	abolishes u4 snrna-binding.
57	abolishes u4 snrna-binding.
80	reduces u4 snrna-binding by about 50%.
96–128	abolishes u4 snrna-binding.

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-6790901	rRNA modification in the nucleus and cytosol
R-HSA-6791226	Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-72163	mRNA Splicing - Major Pathway

MSigDB gene sets: 162 (showing top): GOBP_SINGLE_FERTILIZATION, GOBP_RIBOSOME_BIOGENESIS, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, KAAB_FAILED_HEART_ATRIUM_DN, GOBP_MATURATION_OF_SSU_RRNA, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, GOBP_NEUROGENESIS, GOBP_RNA_METHYLATION, GOBP_MRNA_MODIFICATION, GOLDRATH_ANTIGEN_RESPONSE, MODULE_388, GOBP_SPLICEOSOMAL_TRI_SNRNP_COMPLEX_ASSEMBLY, GOBP_RNA_MODIFICATION, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA

GO Biological Process (8): mRNA splicing, via spliceosome (GO:0000398), box C/D snoRNP assembly (GO:0000492), single fertilization (GO:0007338), maturation of SSU-rRNA (GO:0030490), ribosomal small subunit biogenesis (GO:0042274), mRNA processing (GO:0006397), RNA splicing (GO:0008380), ribosome biogenesis (GO:0042254)

GO Molecular Function (8): RNA binding (GO:0003723), U4 snRNA binding (GO:0030621), U4atac snRNA binding (GO:0030622), U3 snoRNA binding (GO:0034511), box C/D sno(s)RNA binding (GO:0034512), ATPase binding (GO:0051117), protein binding (GO:0005515), snoRNA binding (GO:0030515)

GO Cellular Component (13): dense fibrillar component (GO:0001651), nucleus (GO:0005634), nucleoplasm (GO:0005654), spliceosomal complex (GO:0005681), U4atac snRNP (GO:0005690), nucleolus (GO:0005730), box C/D methylation guide snoRNP complex (GO:0031428), small-subunit processome (GO:0032040), protein-containing complex (GO:0032991), U4/U6 x U5 tri-snRNP complex (GO:0046540), U2-type precatalytic spliceosome (GO:0071005), precatalytic spliceosome (GO:0071011), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
rRNA processing in the nucleus and cytosol	2
mRNA Splicing	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
ribonucleoprotein complex biogenesis	2
RNA processing	2
snRNA binding	2
snoRNA binding	2
nucleolus	2
cellular anatomical structure	2
nuclear lumen	2
nuclear protein-containing complex	2
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
small nucleolar ribonucleoprotein complex assembly	1
fertilization	1
rRNA processing	1
ribosomal small subunit biogenesis	1
ribosome biogenesis	1
mRNA metabolic process	1
nucleic acid binding	1
enzyme binding	1
binding	1
RNA binding	1
intracellular membrane-bounded organelle	1
ribonucleoprotein complex	1
spliceosomal snRNP complex	1
intracellular membraneless organelle	1
box C/D RNP complex	1
preribosome	1
t-UTP complex	1
cellular_component	1
U5 snRNP	1
U4/U6 snRNP	1
spliceosomal tri-snRNP complex	1
U2-type spliceosomal complex	1
U1 snRNP	1
U2 snRNP	1
U4/U6 x U5 tri-snRNP complex	1
precatalytic spliceosome	1
spliceosomal complex	1
protein-containing complex	1

Protein interactions and networks

STRING

4668 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SNU13	NOP58	Q9Y2X3	998
SNU13	NOP56	O00567	998
SNU13	FBL	P22087	997
SNU13	PRPF31	Q8WWY3	993
SNU13	RRP9	O43818	941
SNU13	DKC1	O60832	874
SNU13	PRPF3	O43395	871
SNU13	NUFIP1	Q9UHK0	871
SNU13	PRPF6	O94906	855
SNU13	NOP10	Q9NPE3	810
SNU13	EFTUD2	Q15029	778
SNU13	RUVBL1	P82276	774
SNU13	RUVBL2	Q9Y230	771
SNU13	PIH1D1	Q9NWS0	770
SNU13	ZP3	P21754	763

IntAct

122 interactions, top by confidence:

A	B	Type	Score
LSM3	LSM1	psi-mi:“MI:0914”(association)	0.950
PRPF4	PPIH	psi-mi:“MI:0914”(association)	0.910
FBL	NOP56	psi-mi:“MI:0914”(association)	0.800
POLR2A	POLR2D	psi-mi:“MI:0914”(association)	0.730
PRPF3	PRPF4	psi-mi:“MI:0914”(association)	0.730
SART3	PRPF4	psi-mi:“MI:0914”(association)	0.730
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
SNRPD2	GEMIN2	psi-mi:“MI:0914”(association)	0.710
NOP58	SNU13	psi-mi:“MI:0915”(physical association)	0.560
SNU13	SMN1	psi-mi:“MI:0915”(physical association)	0.560
DLD	PDHB	psi-mi:“MI:0914”(association)	0.530
SNRPN	PRMT5	psi-mi:“MI:0914”(association)	0.530
LSM6	PRMT5	psi-mi:“MI:0914”(association)	0.530
VCAM1	PSMD11	psi-mi:“MI:0914”(association)	0.530
gag	SNU13	psi-mi:“MI:0915”(physical association)	0.500
SNU13	NUFIP1	psi-mi:“MI:0915”(physical association)	0.500
NUFIP1	SNU13	psi-mi:“MI:0914”(association)	0.500
CPSF6	DDX39A	psi-mi:“MI:0914”(association)	0.480
gag	RNH1	psi-mi:“MI:0914”(association)	0.460
CC2D2A	OFD1	psi-mi:“MI:2364”(proximity)	0.420
IL16	SNU13	psi-mi:“MI:0915”(physical association)	0.400
SNU13	NOP56	psi-mi:“MI:0915”(physical association)	0.400
MAP3K5	SNU13	psi-mi:“MI:0915”(physical association)	0.400
Prpf8		psi-mi:“MI:0915”(physical association)	0.400
Snu13		psi-mi:“MI:0915”(physical association)	0.400
SNU13	Ruvbl2	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (359): NHP2L1 (Affinity Capture-MS), NHP2L1 (Affinity Capture-MS), NHP2L1 (Affinity Capture-MS), NHP2L1 (Affinity Capture-MS), NHP2L1 (Affinity Capture-MS), NUFIP1 (Two-hybrid), CLVS2 (Co-fractionation), CORO1A (Co-fractionation), CORO1B (Co-fractionation), CORO1C (Co-fractionation), CUL4B (Co-fractionation), DDB1 (Co-fractionation), DDX56 (Co-fractionation), DKC1 (Co-fractionation), DPH2 (Co-fractionation)

ESM2 similar proteins: A6MZM2, B7F845, B8B9K6, C9WPN6, F1QGW6, G1SKZ8, G1SPK4, O48650, P05388, P14869, P19945, P20461, P41091, P41568, P47826, P50894, P53026, P53027, P55769, P55770, P56330, P59230, P59231, P62906, P62907, P81795, Q0D5W6, Q29214, Q2KHU8, Q2VIR3, Q3B8S0, Q4R5C6, Q4R5P3, Q5E9E6, Q5R797, Q5XH16, Q5ZMS3, Q6P8E9, Q6PC69, Q7ZYS8

Diamond homologs: A0A1D8PF11, A0B601, A0RUB4, A2BK92, A3DMR6, A3MTA9, A4YIL9, A5UJN3, A6UT51, A8A912, A9A2Z3, B0R4Z9, B1Y9V4, B6YWH9, B8D6E8, B9LPY2, C3MJN1, C3MYY9, C3N038, C3N8Q2, C3NMR6, C4KJ77, C5A1V9, O13672, O26355, O29494, O74690, O76732, P0CQ52, P0CQ53, P0DJ14, P0DKK7, P12743, P17076, P32429, P32495, P35685, P39990, P46223, P49692

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
SNU13	“form complex”	“U4/U6.U5 snRNP complex”	binding
SNU13	“form complex”	“U3 snoRNP”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 135 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
mRNA decay by 5’ to 3’ exoribonuclease	5	38.1×	9e-06
Metabolism of non-coding RNA	5	31.7×	2e-05
mRNA Splicing - Minor Pathway	9	20.1×	5e-08
mRNA Splicing	18	19.8×	1e-16
Processing of Capped Intron-Containing Pre-mRNA	20	16.4×	9e-17
mRNA Splicing - Major Pathway	27	14.8×	8e-22
SARS-CoV-2 modulates host translation machinery	6	13.4×	3e-04
mRNA Polyadenylation	15	13.2×	4e-11

GO biological processes:

GO term	Partners	Fold	FDR
spliceosomal snRNP assembly	9	44.3×	8e-11
RNA splicing, via transesterification reactions	7	37.0×	1e-07
U2-type prespliceosome assembly	5	26.4×	1e-04
spliceosomal complex assembly	5	25.5×	1e-04
mRNA splicing, via spliceosome	23	17.9×	1e-19
RNA splicing	16	12.0×	8e-11
ribosomal small subunit biogenesis	5	9.7×	1e-02
mRNA processing	13	8.7×	5e-07

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

735 predictions. Top by Δscore:

Variant	Effect	Δscore
22:41675191:GGTGG:G	acceptor_gain	1.0000
22:41675193:TGG:T	acceptor_gain	1.0000
22:41675194:GG:G	acceptor_gain	1.0000
22:41675194:GGC:G	acceptor_loss	1.0000
22:41675196:C:A	acceptor_loss	1.0000
22:41675196:C:CC	acceptor_gain	1.0000
22:41680238:CCTTA:C	donor_loss	1.0000
22:41680240:TTACC:T	donor_loss	1.0000
22:41680241:TA:T	donor_loss	1.0000
22:41680242:A:AC	donor_gain	1.0000
22:41680242:A:AG	donor_loss	1.0000
22:41680242:AC:A	donor_gain	1.0000
22:41680243:C:CA	donor_loss	1.0000
22:41680243:C:CC	donor_gain	1.0000
22:41680243:CC:C	donor_gain	1.0000
22:41680243:CCCT:C	donor_gain	1.0000
22:41680360:TCAGT:T	acceptor_gain	1.0000
22:41680361:CAGT:C	acceptor_gain	1.0000
22:41680361:CAGTC:C	acceptor_gain	1.0000
22:41680363:GT:G	acceptor_gain	1.0000
22:41680363:GTCTA:G	acceptor_loss	1.0000
22:41680364:TCTA:T	acceptor_loss	1.0000
22:41680365:C:CA	acceptor_loss	1.0000
22:41680365:C:CC	acceptor_gain	1.0000
22:41680367:A:C	acceptor_gain	1.0000
22:41688793:C:A	donor_loss	1.0000
22:41675192:GTGG:G	acceptor_gain	0.9900
22:41680275:G:C	donor_gain	0.9900
22:41680279:CATGA:C	donor_gain	0.9900
22:41680362:AGT:A	acceptor_gain	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000174801 (22:41688985 T>C), RS1000210108 (22:41685704 G>A,C,T), RS1000255517 (22:41677086 G>A), RS1000266051 (22:41691448 G>T), RS1000288149 (22:41677414 A>G), RS1000303155 (22:41688105 A>G), RS1000596713 (22:41680292 C>A,T), RS1000646939 (22:41673900 C>T), RS1000699223 (22:41673632 C>G,T), RS1001434220 (22:41681559 C>T), RS1001521493 (22:41681094 C>T), RS1001552569 (22:41680892 C>T), RS1001750295 (22:41686531 C>G), RS1001865414 (22:41681832 G>A), RS1001878226 (22:41685445 C>T)

Disease associations

OMIM: gene MIM:601304 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

Study	Trait	p-value
GCST003043_197	Inflammatory bowel disease	3.000000e-06
GCST003044_35	Crohn’s disease	2.000000e-10
GCST005232_52	Neuroticism	3.000000e-18
GCST008362_131	Birth weight	3.000000e-13
GCST010002_83	Refractive error	2.000000e-27
GCST010143_2	Meat-related diet	4.000000e-08
GCST90000025_889	Appendicular lean mass	5.000000e-24

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0007660	neuroticism measurement
EFO:0004344	birth weight
EFO:0008111	diet measurement
EFO:0004980	appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5725191 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 1,538 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

Molecule	Name	Phase	Patents
CHEMBL1232461	MOLIBRESIB	2	1,538

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs6519270	SNU13		0.00	0

ChEMBL bioactivities

3 potent at pChembl≥5 of 3 total, top 3 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
5.55	IC50	2840	nM	MOLIBRESIB
5.46	Kd	3499	nM	CHEMBL5653589
5.46	ED50	3499	nM	CHEMBL5653589

PubChem BioAssay actives

2 with measured affinity, of 8 total; 2 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	2179071: Inhibition of NHP2L1 (unknown origin) incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysis	ic50	2.8400	uM
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2148867: Binding affinity to human NHP2L1 incubated for 45 mins by Kinobead based pull down assay	kd	3.4994	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, increases methylation	3
sodium arsenite	affects cotreatment, increases expression, decreases expression	2
FR900359	increases phosphorylation	1
alpha-pinene	affects cotreatment, increases expression, increases abundance	1
bisphenol A	decreases expression	1
deoxynivalenol	increases expression	1
decabromobiphenyl ether	decreases expression	1
arsenite	affects binding, increases reaction	1
cobaltous chloride	decreases expression	1
methacrylaldehyde	affects cotreatment, increases expression, increases abundance	1
yessotoxin	decreases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
erucylphospho-N,N,N-trimethylpropylammonium	decreases expression	1
pentabrominated diphenyl ether 100	decreases expression	1
bisphenol S	increases expression	1
LDN 193189	affects cotreatment, decreases expression	1
PP242	increases expression	1
Arsenic Trioxide	decreases expression	1
Acrolein	affects cotreatment, increases expression, increases abundance	1
Air Pollutants	increases expression, affects cotreatment, increases abundance	1
Arsenic	affects expression	1
Azacitidine	increases expression	1
Benzo(a)pyrene	increases methylation	1
Dinitrochlorobenzene	affects binding	1
Ethyl Methanesulfonate	decreases expression	1
Gasoline	affects cotreatment, increases abundance, increases expression	1
Hydralazine	affects cotreatment, increases expression	1
Ivermectin	decreases expression	1
Lead	decreases expression	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
CHEMBL5651909	Binding	Binding affinity to human NHP2L1 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.