RNPS1

Summary

RNPS1 (RNA binding protein with serine rich domain 1, HGNC:10080) is a protein-coding gene on chromosome 16p13.3, encoding RNA-binding protein with serine-rich domain 1 (Q15287). Part of pre- and post-splicing multiprotein mRNP complexes. It is a common-essential gene (DepMap: required in 98.0% of cancer cell lines).

This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. mRNA surveillance detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD). When translation ends upstream from the last exon-exon junction, this triggers NMD to degrade mRNAs containing premature stop codons. This protein binds to the mRNA and remains bound after nuclear export, acting as a nucleocytoplasmic shuttling protein. This protein contains many serine residues. Several transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 10921 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 58 total
• Cancer dependency (DepMap): dependent in 98.0% of screened cell lines (common-essential)
• MANE Select transcript: NM_080594

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:10080
Approved symbol	RNPS1
Name	RNA binding protein with serine rich domain 1
Location	16p13.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000205937
Ensembl biotype	protein_coding
OMIM	606447
Entrez	10921

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 20 protein_coding, 5 retained_intron, 1 nonsense_mediated_decay

ENST00000301730, ENST00000320225, ENST00000397086, ENST00000561518, ENST00000561718, ENST00000562205, ENST00000562690, ENST00000563857, ENST00000564311, ENST00000564601, ENST00000564764, ENST00000564822, ENST00000565243, ENST00000565333, ENST00000565589, ENST00000565678, ENST00000565870, ENST00000566180, ENST00000566397, ENST00000566458, ENST00000566783, ENST00000567147, ENST00000568631, ENST00000569598, ENST00000569709, ENST00000570051

RefSeq mRNA: 5 — MANE Select: NM_080594 NM_001286625, NM_001286626, NM_001286627, NM_006711, NM_080594

CCDS: CCDS10465, CCDS66907, CCDS73811

Canonical transcript exons

ENST00000320225 — 8 exons

Exon	Start	End
ENSE00001118819	2255585	2255726
ENSE00001389482	2264573	2264760
ENSE00002606093	2268055	2268126
ENSE00003499752	2262740	2262842
ENSE00003609811	2264176	2264331
ENSE00003650331	2262278	2262431
ENSE00003791132	2263096	2263287
ENSE00003843653	2253120	2254063

Expression profiles

Bgee: expression breadth ubiquitous, 253 present calls, max score 99.11.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.9844 / max 183.6214, expressed in 1768 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
155920	2.9168	1490
155919	2.1417	1281
155918	1.7886	946
155922	1.4723	913
155921	0.5377	308
155923	0.1274	14

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	99.11	gold quality
cerebellar hemisphere	UBERON:0002245	98.72	gold quality
right hemisphere of cerebellum	UBERON:0014890	98.71	gold quality
cerebellar cortex	UBERON:0002129	98.68	gold quality
endometrium epithelium	UBERON:0004811	98.47	gold quality
right frontal lobe	UBERON:0002810	98.34	gold quality
cortical plate	UBERON:0005343	98.29	gold quality
ganglionic eminence	UBERON:0004023	98.23	gold quality
paraflocculus	UBERON:0005351	98.17	gold quality
anterior cingulate cortex	UBERON:0009835	98.11	gold quality
cingulate cortex	UBERON:0003027	98.09	gold quality
ventricular zone	UBERON:0003053	98.06	gold quality
gastrocnemius	UBERON:0001388	98.03	gold quality
Brodmann (1909) area 10	UBERON:0013541	98.01	gold quality
adenohypophysis	UBERON:0002196	97.90	gold quality
lower esophagus muscularis layer	UBERON:0035833	97.90	gold quality
lower esophagus	UBERON:0013473	97.89	gold quality
body of uterus	UBERON:0009853	97.86	gold quality
muscle layer of sigmoid colon	UBERON:0035805	97.85	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	97.77	gold quality
hindlimb stylopod muscle	UBERON:0004252	97.76	gold quality
left uterine tube	UBERON:0001303	97.74	gold quality
cerebellum	UBERON:0002037	97.73	gold quality
muscle of leg	UBERON:0001383	97.70	gold quality
left ovary	UBERON:0002119	97.61	gold quality
right ovary	UBERON:0002118	97.59	gold quality
prefrontal cortex	UBERON:0000451	97.58	gold quality
granulocyte	CL:0000094	97.54	gold quality
endocervix	UBERON:0000458	97.49	gold quality
skin of abdomen	UBERON:0001416	97.49	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	26.89
E-MTAB-6911	no	2004.90
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

53 targeting RNPS1, 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-371B-5P	99.99	75.34	4759
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-10523-5P	99.91	69.22	2038
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-221-3P	99.86	71.56	1329
HSA-MIR-222-3P	99.86	71.35	1337
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-6756-5P	99.82	67.97	2466
HSA-MIR-548A-3P	99.76	70.58	3524
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-187-5P	99.74	70.26	1404
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-1287-3P	99.63	66.93	492
HSA-MIR-5003-5P	99.61	69.13	1624
HSA-MIR-7159-5P	99.53	72.12	2472
HSA-MIR-4480	99.42	66.02	735
HSA-MIR-6839-3P	99.39	68.86	1301
HSA-MIR-4311	99.31	70.47	3041
HSA-MIR-888-5P	99.30	70.15	1855
HSA-MIR-548V	99.29	69.47	1157
HSA-MIR-4504	99.10	69.14	1328

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 98.0% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 9)

• binds to Upf complexes which bind upstream of mRNA exon-exon junctions (PMID:11546873)
• has a role in mRNA surveillance (detecting mRNAs with truncated open reading frames and subjecting them to nonsense-mediated mRNA decay (NMD)) (PMID:11546874)
• The phosphorylation of RNPS1 at Ser-53 influences the efficiencies of both splicing and translation. (PMID:15684395)
• RNPS1 is able to function together with ASF/SF2 to form ribonucleoprotein complexes on nascent transcripts, and thereby prevent formation of transcriptional R-loops. (PMID:17959926)
• SRBD1 gene polymorphism is associated with the development of HTG as well as NTG, including late-onset NTG. (PMID:21508110)
• ubiquitin-specific protease 4 (USP4) is a binding partner of RNPS1. (PMID:27990632)
• RNA-binding protein with serine-rich domain 1 regulates microsatellite instability of uterine corpus endometrial adenocarcinoma. (PMID:34817046)
• RNPS1 functions as an oncogenic splicing factor in cervical cancer cells. (PMID:36300671)
• RNPS1 stabilizes NAT10 protein to facilitate translation in cancer via tRNA ac[4]C modification. (PMID:38246918)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
		ENSDARG00000100188
danio_rerio	rnps1	ENSDARG00000116743
mus_musculus	Rnps1	ENSMUSG00000034681
rattus_norvegicus	Rnps1	ENSRNOG00000008703
rattus_norvegicus	Rnps1-ps5	ENSRNOG00000065922
drosophila_melanogaster	CG34334	FBGN0263829
caenorhabditis_elegans		WBGENE00004388

Protein

Protein identifiers

RNA-binding protein with serine-rich domain 1 — Q15287 (reviewed: Q15287)

Alternative names: SR-related protein LDC2

All UniProt accessions (16): D3DU92, Q15287, H3BMM9, H3BMS0, H3BNI3, H3BNU7, H3BP82, H3BPG5, H3BRK4, H3BTC0, H3BTR6, H3BTV0, H3BTY0, H3BUG0, H3BUL0, H3BV80

UniProt curated annotations — full annotation on UniProt →

Function. Part of pre- and post-splicing multiprotein mRNP complexes. Auxiliary component of the splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of core proteins and several peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Component of the ASAP and PSAP complexes which bind RNA in a sequence-independent manner and are proposed to be recruited to the EJC prior to or during the splicing process and to regulate specific excision of introns in specific transcription subsets. The ASAP complex can inhibit RNA processing during in vitro splicing reactions. The ASAP complex promotes apoptosis and is disassembled after induction of apoptosis. Enhances the formation of the ATP-dependent A complex of the spliceosome. Involved in both constitutive splicing and, in association with SRP54 and TRA2B/SFRS10, in distinctive modulation of alternative splicing in a substrate-dependent manner. Involved in the splicing modulation of BCL2L1/Bcl-X (and probably other apoptotic genes); specifically inhibits formation of proapoptotic isoforms such as Bcl-X(S); the activity is different from the established EJC assembly and function. Participates in mRNA 3’-end cleavage. Involved in UPF2-dependent nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Also mediates increase of mRNA abundance and translational efficiency. Binds spliced mRNA 20-25 nt upstream of exon-exon junctions.

Subunit / interactions. Found in mRNA splicing-dependent exon junction complexes (EJC). Found in a post-splicing complex with NXF1, RBM8A, UPF1, UPF2, UPF3A, UPF3B and RNPS1. Component of the heterotrimeric ASAP (apoptosis- and splicing-associated protein) and PSAP complexes consisting of RNPS1, SAP18 and either ACIN1 or PNN, respectively; the ASAP and PSAP complexes probably are formed mutually exclusive. Component of the active spliceosome. Associates with polysomes. Interacts with the cleaved p110 isoform of CDC2L1, CSNK2A1, PNN, SART3, SRP54, SRRM1 and TRA2B/SFRS10.

Subcellular location. Nucleus. Nucleus speckle. Cytoplasm.

Tissue specificity. Ubiquitous.

Post-translational modifications. Phosphorylated on one or more of the four Ser/Thr residues (Ser-43, Thr-49, Ser-52 or Ser-53). Ser-53 phosphorylation site is important for splicing and translation stimulation activity in vitro.

Domain organisation. The RRM domain is required for the formation of the ASAP complex.

Similarity. Belongs to the splicing factor SR family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q15287-1	1	yes
Q15287-2	2
Q15287-3	3

RefSeq proteins (5): NP_001273554, NP_001273555, NP_001273556, NP_006702, NP_542161* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR034201	RNPS1_RRM	Domain
IPR035979	RBD_domain_sf	Homologous_superfamily

Pfam: PF00076

UniProt features (41 total): region of interest 8, compositionally biased region 7, modified residue 5, mutagenesis site 5, strand 5, sequence conflict 3, cross-link 2, splice variant 2, helix 2, chain 1, domain 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
4A8X	X-RAY DIFFRACTION	1.9

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q15287-F1	62.19	0.20

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 (7): 53, 155, 157, 161, 218, 7, 15

Mutagenesis-validated functional residues (5):

Position	Phenotype
53	abolishes phosphorylation by csnk2a1 and partially reduces splicing stimulation. does not abolish interaction with csnk2
53	partially reduces splicing stimulation. does not abolish interaction with csnk2a1 and subcellular localization.
171	impairs interaction with sap18.
205	abolishes exon-skipping.
207	abolishes exon-skipping.

Function

Pathways and Gene Ontology

Reactome pathways

18 pathways

ID	Pathway
R-HSA-159236	Transport of Mature mRNA derived from an Intron-Containing Transcript
R-HSA-72163	mRNA Splicing - Major Pathway
R-HSA-72187	mRNA 3’-end processing
R-HSA-9010553	Regulation of expression of SLITs and ROBOs
R-HSA-975957	Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
R-HSA-9918481	Dengue Virus-Host Interactions
R-HSA-73856	RNA Polymerase II Transcription Termination
R-HSA-1266738	Developmental Biology
R-HSA-376176	Signaling by ROBO receptors
R-HSA-422475	Axon guidance
R-HSA-72172	mRNA Splicing
R-HSA-72202	Transport of Mature Transcript to Cytoplasm
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-8953854	Metabolism of RNA
R-HSA-927802	Nonsense-Mediated Decay (NMD)
R-HSA-9675108	Nervous system development

MSigDB gene sets: 234 (showing top): GOBP_ALTERNATIVE_MRNA_SPLICING_VIA_SPLICEOSOME, MORF_SNRP70, MORF_UBE2I, GOBP_NEGATIVE_REGULATION_OF_RNA_SPLICING, MORF_HDAC1, DITTMER_PTHLH_TARGETS_UP, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, MORF_TERF1, GCM_RING1, MORF_CCNI, ATF1_Q6, MORF_CTBP1, REACTOME_MRNA_3_END_PROCESSING, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, SYED_ESTRADIOL_RESPONSE

GO Biological Process (8): nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184), regulation of alternative mRNA splicing, via spliceosome (GO:0000381), mRNA splicing, via spliceosome (GO:0000398), DNA-templated transcription (GO:0006351), RNA splicing (GO:0008380), positive regulation of apoptotic process (GO:0043065), negative regulation of mRNA splicing, via spliceosome (GO:0048025), mRNA processing (GO:0006397)

GO Molecular Function (4): RNA binding (GO:0003723), mRNA 3’-UTR binding (GO:0003730), nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (8): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), nuclear speck (GO:0016607), ASAP complex (GO:0061574), membrane (GO:0016020), exon-exon junction complex (GO:0035145)

Reactome top-level categories

Rollup of top-12 pathways:

Category	Pathways
Processing of Capped Intron-Containing Pre-mRNA	3
Metabolism of RNA	2
Transport of Mature Transcript to Cytoplasm	1
mRNA Splicing	1
Signaling by ROBO receptors	1
Nonsense-Mediated Decay (NMD)	1
Dengue Virus Infection	1
RNA Polymerase II Transcription	1
Axon guidance	1
Nervous system development	1
Gene expression (Transcription)	1
Developmental Biology	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
regulation of mRNA splicing, via spliceosome	2
RNA processing	2
binding	2
nuclear-transcribed mRNA catabolic process	1
alternative mRNA splicing, via spliceosome	1
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
gene expression	1
RNA biosynthetic process	1
apoptotic process	1
regulation of apoptotic process	1
positive regulation of programmed cell death	1
mRNA splicing, via spliceosome	1
negative regulation of RNA splicing	1
negative regulation of mRNA processing	1
mRNA metabolic process	1
nucleic acid binding	1
mRNA binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular anatomical structure	1
cytoplasm	1
nuclear ribonucleoprotein granule	1
protein-containing complex	1
nuclear protein-containing complex	1

Protein interactions and networks

STRING

2442 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RNPS1	SAP18	O00422	996
RNPS1	SRRM1	Q8IYB3	994
RNPS1	ACIN1	Q9UKV3	992
RNPS1	PNN	Q9H307	978
RNPS1	DEK	P35659	972
RNPS1	ALYREF	Q86V81	970
RNPS1	MAGOHB	Q96A72	960
RNPS1	EIF4A3	P38919	954
RNPS1	SRSF11	Q05519	935
RNPS1	MAGOH	P50606	934
RNPS1	UPF3B	Q9BZI7	922
RNPS1	UPF1	Q92900	897
RNPS1	UPF3A	Q9H1J1	886
RNPS1	UPF2	Q9HAU5	881
RNPS1	CASC3	O15234	843

IntAct

410 interactions, top by confidence:

A	B	Type	Score
RNPS1	SDCBP2	psi-mi:“MI:0915”(physical association)	0.670
RNPS1	SART3	psi-mi:“MI:0915”(physical association)	0.610
SART3	RNPS1	psi-mi:“MI:0915”(physical association)	0.610
RNPS1	ZNF286A	psi-mi:“MI:0915”(physical association)	0.560
RNPS1	SRSF6	psi-mi:“MI:0915”(physical association)	0.370
RNPS1	ZNF473	psi-mi:“MI:0915”(physical association)	0.370
JAK3	BAG2	psi-mi:“MI:0914”(association)	0.350
RNPS1	CSNK2A1	psi-mi:“MI:0914”(association)	0.350
JUN		psi-mi:“MI:0914”(association)	0.350
DDX41	DDX39A	psi-mi:“MI:0914”(association)	0.350
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
CDK1	RBMXL2	psi-mi:“MI:0914”(association)	0.350
COQ2	SNRPGP15	psi-mi:“MI:0914”(association)	0.350
COX15	SNRPGP15	psi-mi:“MI:0914”(association)	0.350
DLST		psi-mi:“MI:0914”(association)	0.350
DNM1L		psi-mi:“MI:0914”(association)	0.350
HSD17B10	HMGB1P1	psi-mi:“MI:0914”(association)	0.350
PARK7	SAP18	psi-mi:“MI:0914”(association)	0.350
VDAC1	SNRPGP15	psi-mi:“MI:0914”(association)	0.350
HSD17B10	HNRNPDL	psi-mi:“MI:0914”(association)	0.350

BioGRID (614): RNPS1 (Two-hybrid), RNPS1 (Two-hybrid), RNPS1 (Two-hybrid), RNPS1 (Two-hybrid), ZNF473 (Two-hybrid), SDCBP2 (Two-hybrid), TRIM41 (Two-hybrid), HEXIM2 (Two-hybrid), RNPS1 (Affinity Capture-MS), RNPS1 (Affinity Capture-MS), RNPS1 (Affinity Capture-MS), RNPS1 (Affinity Capture-MS), RNPS1 (Affinity Capture-MS), RNPS1 (Affinity Capture-MS), RNPS1 (Affinity Capture-MS)

ESM2 similar proteins: A2RVS6, A6QR16, O02008, O22315, O75494, P19018, P26686, P30352, P62995, P62996, P62997, Q01130, Q06A98, Q08170, Q10021, Q13595, Q15287, Q16629, Q1PDV2, Q28E41, Q3KPW1, Q3MHR5, Q3T106, Q3ZBT6, Q4R5N1, Q52KI8, Q5NVM8, Q5R1W5, Q5R5Q2, Q5XG24, Q5ZMJ9, Q62093, Q6AYK1, Q6PDU1, Q6PFR5, Q6PG31, Q84TH4, Q8BL97, Q8IYB3, Q8RWY7

Diamond homologs: A2A5N3, A2RVS6, A5A6M3, A6NDE4, A6NEQ0, A6QR16, D4AE41, F4JHI7, O22315, O35326, O93235, O94359, P0C7P1, P0DJD3, P0DJD4, P27476, P38159, P40561, P42731, P60824, P60825, P60826, P62995, P62996, P62997, P70318, P82277, P84586, Q01085, Q07955, Q09167, Q09511, Q0J9Y2, Q0VCY7, Q13243, Q13247, Q14011, Q15287, Q15415, Q16560

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 164 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
Transport of Mature Transcript to Cytoplasm	10	31.2×	2e-11
mRNA 3’-end processing	18	29.1×	3e-20
RNA Polymerase II Transcription Termination	16	28.8×	5e-18
Regulation of pyruvate metabolism	6	28.1×	2e-06
mRNA Splicing - Minor Pathway	12	22.0×	7e-12
mRNA Splicing	24	21.6×	9e-24
mRNA Polyadenylation	27	19.4×	2e-25
mRNA Splicing - Major Pathway	42	18.8×	2e-40

GO biological processes:

GO term	Partners	Fold	FDR
mRNA splice site recognition	9	46.9×	1e-11
negative regulation of mRNA splicing, via spliceosome	9	44.8×	2e-11
RNA splicing, via transesterification reactions	11	44.6×	5e-14
spliceosomal tri-snRNP complex assembly	6	43.8×	2e-07
spliceosomal snRNP assembly	10	37.7×	7e-12
regulation of mRNA splicing, via spliceosome	6	34.6×	8e-07
spliceosomal complex assembly	8	31.3×	8e-09
U2-type prespliceosome assembly	6	24.3×	8e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	43
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1759 predictions. Top by Δscore:

Variant	Effect	Δscore
16:2254062:ACC:A	acceptor_loss	1.0000
16:2255580:TTTA:T	donor_loss	1.0000
16:2255581:TTA:T	donor_loss	1.0000
16:2255583:A:T	donor_loss	1.0000
16:2255584:C:CA	donor_loss	1.0000
16:2255584:CCTT:C	donor_gain	1.0000
16:2255722:TTGTC:T	acceptor_gain	1.0000
16:2255723:TGTC:T	acceptor_gain	1.0000
16:2255724:GTC:G	acceptor_gain	1.0000
16:2255725:TC:T	acceptor_gain	1.0000
16:2255725:TCCT:T	acceptor_loss	1.0000
16:2255726:CC:C	acceptor_gain	1.0000
16:2255727:C:CC	acceptor_gain	1.0000
16:2255728:T:A	acceptor_loss	1.0000
16:2255730:T:TC	acceptor_gain	1.0000
16:2262273:CCCA:C	donor_loss	1.0000
16:2262275:CA:C	donor_loss	1.0000
16:2262276:A:C	donor_loss	1.0000
16:2262430:TC:T	acceptor_gain	1.0000
16:2262430:TCC:T	acceptor_loss	1.0000
16:2262431:CC:C	acceptor_gain	1.0000
16:2262432:C:CC	acceptor_gain	1.0000
16:2262432:C:CG	acceptor_loss	1.0000
16:2262433:T:G	acceptor_loss	1.0000
16:2262734:CCTCA:C	donor_loss	1.0000
16:2262735:CTCA:C	donor_loss	1.0000
16:2262736:TCA:T	donor_loss	1.0000
16:2262737:CAC:C	donor_loss	1.0000
16:2262738:A:AC	donor_gain	1.0000
16:2262739:C:CC	donor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000096797 (16:2256489 A>G), RS1000129287 (16:2256688 CA>C), RS1000153802 (16:2254640 C>A), RS1000745633 (16:2268920 C>CGT), RS1001118504 (16:2260284 T>A), RS1001347031 (16:2259437 T>G), RS1001404400 (16:2260066 G>C), RS1001550847 (16:2263926 T>A), RS1001568368 (16:2267018 C>G,T), RS1001600767 (16:2267247 G>C), RS1001784591 (16:2262553 GTGT>G), RS1002002977 (16:2263756 G>A), RS1002100391 (16:2255054 T>A,C), RS1002282928 (16:2265166 T>C), RS1002403636 (16:2252972 T>C)

Disease associations

OMIM: gene MIM:606447 | 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: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects expression, decreases expression, affects cotreatment, increases abundance	4
Arsenic	affects methylation, affects cotreatment, decreases expression, increases abundance	2
FR900359	increases phosphorylation	1
TAK-243	decreases sumoylation	1
bisphenol A	decreases methylation	1
sodium arsenate	decreases expression	1
beta-lapachone	decreases expression	1
fenpyroximate	decreases expression	1
picoxystrobin	decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Temozolomide	increases expression	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	affects methylation	1
Carbamazepine	affects expression	1
Doxorubicin	decreases expression	1
Gallic Acid	decreases expression, increases expression	1
Ivermectin	decreases expression	1
Rotenone	decreases expression	1
Selenium	increases expression	1
Smoke	decreases expression	1
Tetrachlorodibenzodioxin	affects expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Valproic Acid	increases methylation	1
Vitamin E	increases expression	1
Cyclosporine	increases expression	1

Clinical trials (associated diseases)

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