SRSF9

Summary

SRSF9 (serine and arginine rich splicing factor 9, HGNC:10791) is a protein-coding gene on chromosome 12q24.31, encoding Serine/arginine-rich splicing factor 9 (Q13242). Plays a role in constitutive splicing and can modulate the selection of alternative splice sites.

The protein encoded by this gene is a member of the serine/arginine (SR)-rich family of pre-mRNA splicing factors, which constitute part of the spliceosome. Each of these factors contains an RNA recognition motif (RRM) for binding RNA and an RS domain for binding other proteins. The RS domain is rich in serine and arginine residues and facilitates interaction between different SR splicing factors. In addition to being critical for mRNA splicing, the SR proteins have also been shown to be involved in mRNA export from the nucleus and in translation. Two pseudogenes, one on chromosome 15 and the other on chromosome 21, have been found for this gene.

Source: NCBI Gene 8683 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 10 total
• Druggable target: yes
• MANE Select transcript: NM_003769

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:10791
Approved symbol	SRSF9
Name	serine and arginine rich splicing factor 9
Location	12q24.31
Locus type	gene with protein product
Status	Approved
Aliases	SRp30c
Ensembl gene	ENSG00000111786
Ensembl biotype	protein_coding
OMIM	601943
Entrez	8683

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 12 protein_coding, 5 nonsense_mediated_decay, 3 retained_intron

ENST00000229390, ENST00000546942, ENST00000548326, ENST00000548792, ENST00000550458, ENST00000603963, ENST00000706464, ENST00000706465, ENST00000706466, ENST00000706467, ENST00000706468, ENST00000706469, ENST00000706470, ENST00000863489, ENST00000863490, ENST00000914500, ENST00000914501, ENST00000957766, ENST00000957767, ENST00000957768

RefSeq mRNA: 1 — MANE Select: NM_003769 NM_003769

CCDS: CCDS9199

Canonical transcript exons

ENST00000229390 — 4 exons

Exon	Start	End
ENSE00002416829	120469422	120469748
ENSE00003995908	120463950	120464122
ENSE00003995910	120465627	120465787
ENSE00003995912	120461672	120462162

Expression profiles

Bgee: expression breadth ubiquitous, 302 present calls, max score 98.79.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 84.6333 / max 1338.7329, expressed in 1826 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
133663	82.5930	1826
133662	2.0402	1250

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endometrium epithelium	UBERON:0004811	98.79	gold quality
monocyte	CL:0000576	98.64	gold quality
body of pancreas	UBERON:0001150	98.64	gold quality
ventricular zone	UBERON:0003053	98.56	gold quality
mononuclear cell	CL:0000842	98.55	gold quality
buccal mucosa cell	CL:0002336	98.53	gold quality
leukocyte	CL:0000738	98.50	gold quality
right testis	UBERON:0004534	98.48	gold quality
ganglionic eminence	UBERON:0004023	98.46	gold quality
type B pancreatic cell	CL:0000169	98.44	gold quality
lower esophagus mucosa	UBERON:0035834	98.44	gold quality
palpebral conjunctiva	UBERON:0001812	98.43	gold quality
pharyngeal mucosa	UBERON:0000355	98.42	gold quality
embryo	UBERON:0000922	98.41	gold quality
right adrenal gland cortex	UBERON:0035827	98.39	gold quality
right adrenal gland	UBERON:0001233	98.37	gold quality
left testis	UBERON:0004533	98.37	gold quality
thymus	UBERON:0002370	98.36	gold quality
left adrenal gland	UBERON:0001234	98.33	gold quality
left adrenal gland cortex	UBERON:0035825	98.30	gold quality
adrenal cortex	UBERON:0001235	98.28	gold quality
granulocyte	CL:0000094	98.24	gold quality
esophagus mucosa	UBERON:0002469	98.22	gold quality
spleen	UBERON:0002106	98.21	gold quality
amniotic fluid	UBERON:0000173	98.20	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	98.20	gold quality
lymph node	UBERON:0000029	98.19	gold quality
mucosa of transverse colon	UBERON:0004991	98.17	gold quality
pancreas	UBERON:0001264	98.16	gold quality
adenohypophysis	UBERON:0002196	98.16	gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-MTAB-8205	yes	523.68
E-MTAB-7037	yes	182.13
E-GEOD-134144	yes	33.71
E-CURD-122	yes	5.49
E-CURD-79	no	493.30
E-GEOD-125970	no	3.15
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

36 targeting SRSF9, 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-1277-5P	100.00	73.95	5056
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-613	99.91	71.50	1710
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-544A	99.84	68.66	1965
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-4799-5P	99.82	70.60	2663
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-1299	99.77	71.24	2389
HSA-MIR-646	99.68	67.84	1645
HSA-MIR-10394-5P	99.65	66.83	1852
HSA-MIR-1205	99.65	66.76	1826
HSA-MIR-3158-5P	99.65	67.51	1763
HSA-MIR-875-3P	99.63	69.47	2548
HSA-MIR-17-3P	99.55	66.77	1311
HSA-MIR-6128	99.33	67.83	1581
HSA-MIR-12113	99.32	67.54	1072
HSA-MIR-4263	99.18	69.25	2236
HSA-MIR-3117-5P	99.04	67.93	618
HSA-MIR-4650-3P	99.01	68.39	1062
HSA-MIR-4451	98.82	68.17	1455
HSA-MIR-4539	98.78	67.18	888
HSA-MIR-3668	98.52	68.76	951
HSA-MIR-7852-3P	98.37	67.98	823
HSA-MIR-4704-3P	98.28	69.33	1300
HSA-MIR-4303	98.01	68.13	2304
HSA-MIR-4660	97.79	67.44	1328

Literature-anchored findings (GeneRIF, showing 25)

• SRp30c can function as a repressor of 3’ splice site utilization and suggest that the SRp30c-CE9 interaction may contribute to the control of hnRNP A1 alternative splicing. (PMID:12024014)
• SRp30c protein is an interacting protein of YB-1 (PMID:12604611)
• Serine-arginine-rich protein p30 directs alternative splicing of glucocorticoid receptor pre-mRNA to glucocorticoid receptor beta in neutrophils. (PMID:12738786)
• Results suggest that bombesin-induced expression of SRp30c affects gllucorticoid receptor (GR) pre-mRNA splicing, leading to increased GR beta expression and contributing to glucocorticoid resistance in PC cells. (PMID:17540466)
• Study shows that PTB can function as an anti-repressor molecule to counteract the splicing inhibitory activity of SRp30c. (PMID:17548433)
• SRp30c stimulates splicing to the downstream 5’ splice site of Bcl-x(L), thereby attenuating the repressive effect of upstream U1 snRNP binding sit (PMID:18534987)
• findings indicate the importance of arginine methylation for the subnuclear localization of SFRS9. (PMID:19557313)
• These results suggest that SRp30c can activate human papillomavirus type 16 L1 mRNA expression via a bimodal mechanism: directly by stimulating splicing to late splice sites and indirectly by inhibiting competing early splice sites. (PMID:21697349)
• these data indicated that tumor suppressive miR-1 induces apoptosis through direct inhibition of SRSF9 in bladder cancer. (PMID:22178073)
• Relative levels of SRp20, SRp30c, and SRp40 in TM cells control differential expression of the two alternatively spliced isoforms of the GR and thereby regulate GC responsiveness. (PMID:22205602)
• Overexpression of SRSF9 and SRSF1 promote beta-catenin accumulation via the recruitment of beta-catenin mRNA and by enhancing its translation in an mTOR-dependent manner. (PMID:23592547)
• Report no correlation between expression of glucocorticoid receptor isoforms and SRp30c. (PMID:25665148)
• Dehydroepiandrosterone (DHEA) and cortisol modulate SRSF9 and SRSF3 in a different way and data suggest that the anti-glucocorticoid effect of DHEA, among other mechanisms, is also exerted by modulating the expression of proteins involved in the splicing of the GR pre-mRNA. (PMID:28373129)
• The splicing factor SRSF9 is a key factor that serves to restrict the editing of numerous protein-coding and non-coding sites to the brain. The results highlight the importance of SRSF9 as an editing regulator and suggest potential roles for other splicing factors. (PMID:29992293)
• Results identified SRSF9 protein as one of the factors involved in modulating the splicing of the DDC mutated (c.714+4A>T) transcript. (PMID:30260058)
• High SRSF9 expression is associated with cervical cancer. (PMID:30565744)
• LncRNA-dependent nuclear stress bodies promote intron retention through SR protein phosphorylation. (PMID:31782550)
• AMP-activated protein kinase regulates beta-catenin protein synthesis by phosphorylating serine/arginine-rich splicing factor 9. (PMID:33248688)
• SRSF9 Regulates Cassette Exon Splicing of Caspase-2 by Interacting with Its Downstream Exon. (PMID:33808656)
• SRSF9 promotes colorectal cancer progression via stabilizing DSN1 mRNA in an m6A-related manner. (PMID:35509101)
• High expression of serine and arginine-rich splicing factor 9 (SRSF9) is associated with hepatocellular carcinoma progression and a poor prognosis. (PMID:35971121)
• Investigation of the effect of SRSF9 overexpression on HIV-1 production. (PMID:36330710)
• EEF1D stabilized by SRSF9 promotes colorectal cancer via enhancing the proliferation and metastasis. (PMID:38771720)
• The m7G Methyltransferase Mettl1 Drives Cardiac Hypertrophy by Regulating SRSF9-Mediated Splicing of NFATc4. (PMID:38810124)
• SRSF9 promotes cell proliferation and migration of glioblastoma through enhancing CDK1 expression. (PMID:38842611)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	srsf9	ENSDARG00000008097
mus_musculus	Srsf9	ENSMUSG00000029538
rattus_norvegicus	Srsf9	ENSRNOG00000001163

Paralogs (8): SRSF5 (ENSG00000100650), RSRC2 (ENSG00000111011), SRSF3 (ENSG00000112081), SRSF7 (ENSG00000115875), SRSF4 (ENSG00000116350), RSRP1 (ENSG00000117616), SRSF6 (ENSG00000124193), SRSF1 (ENSG00000136450)

Protein

Protein identifiers

Serine/arginine-rich splicing factor 9 — Q13242 (reviewed: Q13242)

Alternative names: Pre-mRNA-splicing factor SRp30C, Splicing factor, arginine/serine-rich 9

All UniProt accessions (10): Q13242, A0A9L9PWX6, A0A9L9PWY3, A0A9L9PX63, A0A9L9PXI1, A0A9L9PXJ2, A0A9L9PXJ8, A0A9L9PY11, H0YIB4, S4R3G0

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in constitutive splicing and can modulate the selection of alternative splice sites. Represses the splicing of MAPT/Tau exon 10.

Subunit / interactions. Interacts with KHDRBS3. Interacts with HABP4. Interacts with NOL3/ARC/NOP30. Interacts with NSEP1/YB-1/YB1. Interacts with SAFB/SAFB1. Interacts with SRSF6/SFRS6. Interacts with TRA2B/SFRS10. Interacts with C1QBP. May also interact with DUSP11/PIR1.

Subcellular location. Nucleus.

Tissue specificity. Expressed at high levels in the heart, kidney, pancreas and placenta, and at lower levels in the brain, liver, lung and skeletal muscle.

Post-translational modifications. Extensively phosphorylated on serine residues in the RS domain.

Similarity. Belongs to the splicing factor SR family.

RefSeq proteins (1): NP_003760* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR034503	SRSF9_RRM1	Domain
IPR034995	SRSF9_RRM2	Domain
IPR035979	RBD_domain_sf	Homologous_superfamily
IPR050374	RRT5_SRSF_SR	Family

Pfam: PF00076

UniProt features (16 total): modified residue 9, domain 2, region of interest 2, chain 1, cross-link 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q13242-F1	69.97	0.10

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 (10): 204, 208, 211, 214, 216, 36, 189, 192, 193, 195

Function

Pathways and Gene Ontology

Reactome pathways

12 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-72203	Processing of Capped Intron-Containing Pre-mRNA
R-HSA-9770562	mRNA Polyadenylation
R-HSA-9918481	Dengue Virus-Host Interactions
R-HSA-73856	RNA Polymerase II Transcription Termination
R-HSA-72172	mRNA Splicing
R-HSA-72202	Transport of Mature Transcript to Cytoplasm
R-HSA-73857	RNA Polymerase II Transcription
R-HSA-74160	Gene expression (Transcription)
R-HSA-8953854	Metabolism of RNA

MSigDB gene sets: 240 (showing top): GSE45365_NK_CELL_VS_BCELL_UP, GCM_NPM1, GOBP_ALTERNATIVE_MRNA_SPLICING_VIA_SPLICEOSOME, MORF_UBE2I, GOBP_NEGATIVE_REGULATION_OF_RNA_SPLICING, MORF_HDAC1, MORF_UBE2N, MORF_RAD21, SHEPARD_BMYB_MORPHOLINO_DN, PUJANA_CHEK2_PCC_NETWORK, OUELLET_OVARIAN_CANCER_INVASIVE_VS_LMP_UP, MORF_SKP1A, GCM_PSME1, GCM_PPP1CC, MORF_CCNI

GO Biological Process (5): regulation of alternative mRNA splicing, via spliceosome (GO:0000381), mRNA splice site recognition (GO:0006376), mRNA processing (GO:0006397), negative regulation of mRNA splicing, via spliceosome (GO:0048025), RNA splicing (GO:0008380)

GO Molecular Function (5): RNA binding (GO:0003723), mRNA binding (GO:0003729), protein domain specific binding (GO:0019904), nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (4): nucleoplasm (GO:0005654), nucleolus (GO:0005730), nuclear speck (GO:0016607), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-8 pathways:

Category	Pathways
Processing of Capped Intron-Containing Pre-mRNA	3
Transport of Mature Transcript to Cytoplasm	1
mRNA Splicing	1
Metabolism of RNA	1
mRNA 3’-end processing	1
Dengue Virus Infection	1
RNA Polymerase II Transcription	1
Gene expression (Transcription)	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of mRNA splicing, via spliceosome	2
RNA processing	2
binding	2
nuclear lumen	2
alternative mRNA splicing, via spliceosome	1
spliceosomal complex assembly	1
protein-RNA complex assembly	1
mRNA metabolic process	1
mRNA splicing, via spliceosome	1
negative regulation of RNA splicing	1
negative regulation of mRNA processing	1
nucleic acid binding	1
RNA binding	1
protein binding	1
cellular anatomical structure	1
intracellular membraneless organelle	1
nuclear ribonucleoprotein granule	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

2516 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SRSF9	TRA2B	P62995	941
SRSF9	SRSF10	O75494	807
SRSF9	HNRNPH1	P31943	768
SRSF9	BEAN1	Q3B7T3	760
SRSF9	SMN1	Q16637	758
SRSF9	HNRNPA1	P09651	748
SRSF9	SRSF11	Q05519	728
SRSF9	YTHDC1	Q96MU7	711
SRSF9	SRSF2	Q01130	708
SRSF9	SRPK1	Q96SB4	701
SRSF9	U2AF2	P26368	678
SRSF9	HTRA2	O43464	669
SRSF9	YBX1	P16990	646
SRSF9	SRSF8	Q9BRL6	626
SRSF9	TRA2A	Q13595	613

IntAct

126 interactions, top by confidence:

A	B	Type	Score
YBX1	SSB	psi-mi:“MI:0914”(association)	0.710
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
RBMX	SRSF9	psi-mi:“MI:0915”(physical association)	0.670
NCBP2	KPNA3	psi-mi:“MI:0914”(association)	0.640
THOC1	DDX39A	psi-mi:“MI:0914”(association)	0.640
SRSF9	RNPS1	psi-mi:“MI:0915”(physical association)	0.560
TRA2B	SRSF9	psi-mi:“MI:0915”(physical association)	0.560
SRSF9	FUS	psi-mi:“MI:0915”(physical association)	0.550
SNIP1	CASC3	psi-mi:“MI:0914”(association)	0.530
SRSF9	HABP4	psi-mi:“MI:0915”(physical association)	0.510
HABP4	SRSF9	psi-mi:“MI:0915”(physical association)	0.510
CPSF6	DDX39A	psi-mi:“MI:0914”(association)	0.480
DDX21	MED19	psi-mi:“MI:2364”(proximity)	0.480
SRSF9	SRPK2	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
LTK	PIK3R2	psi-mi:“MI:0914”(association)	0.420
SRSF9	DUX4	psi-mi:“MI:0915”(physical association)	0.400
SDC1	ILVBL	psi-mi:“MI:0915”(physical association)	0.400
SF3A2	SRSF9	psi-mi:“MI:0915”(physical association)	0.400
SRSF9	SHANK3	psi-mi:“MI:0915”(physical association)	0.370
SRSF9	ITGB5	psi-mi:“MI:0915”(physical association)	0.370
SRSF9	Dazl	psi-mi:“MI:0915”(physical association)	0.370
SRSF9	HNRNPUL1	psi-mi:“MI:0915”(physical association)	0.370
Spred2	TARS3	psi-mi:“MI:0914”(association)	0.350
MATR3	BCLAF3	psi-mi:“MI:0914”(association)	0.350
BCLAF1	PABPN1	psi-mi:“MI:0914”(association)	0.350

BioGRID (307): SRSF9 (Affinity Capture-MS), SRSF9 (Affinity Capture-MS), SRSF9 (Affinity Capture-MS), SRSF9 (Affinity Capture-MS), SRSF9 (Affinity Capture-MS), SRSF9 (Affinity Capture-MS), SRSF9 (Affinity Capture-MS), SRSF9 (Affinity Capture-MS), SRSF9 (Affinity Capture-MS), SRSF1 (Co-fractionation), SRSF6 (Co-fractionation), SRSF9 (Co-fractionation), SRSF9 (Co-fractionation), SRSF9 (Co-fractionation), SRSF9 (Co-fractionation)

ESM2 similar proteins: A2RVS6, F4JHI7, O22315, O75494, O81126, O81127, P30352, P84103, P84104, P92964, P92965, P92966, Q01130, Q06A98, Q07955, Q09511, Q0VCY7, Q10021, Q13242, Q13595, Q16629, Q18409, Q23120, Q23121, Q3MHR5, Q3SZR8, Q3T106, Q3YLA6, Q5PPI1, Q5R1W5, Q5R7H2, Q62093, Q69KL9, Q6DII2, Q6K4N0, Q6K9C3, Q6NYA0, Q6PDM2, Q6PDU1, Q6PFR5

Diamond homologs: A0A0D1C8Z4, A0A0D1DZT6, A2RVS6, A5DM21, A5DW14, B5FXN8, F1QB54, F4HT49, F4I3B3, F4JHI7, G3V6S8, O08583, O13845, O22315, O35326, O59670, O74400, P04147, P19682, P19683, P19684, P20965, P49313, P49314, P78814, P82277, P97855, Q04836, Q08170, Q08935, Q08937, Q09167, Q13242, Q13243, Q13247, Q13283, Q14498, Q1ZXC2, Q28FB9, Q32LC7

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 145 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	9	33.9×	2e-10
RNA Polymerase II Transcription Termination	14	30.4×	1e-15
Processing of Intronless Pre-mRNAs	5	28.3×	3e-05
mRNA 3’-end processing	14	27.3×	5e-15
Processing of Capped Intron-Containing Pre-mRNA	27	22.0×	7e-27
mRNA Polyadenylation	25	21.7×	9e-25
mRNA Splicing	19	20.7×	5e-18
Transport of Mature mRNA derived from an Intron-Containing Transcript	12	18.1×	2e-10

GO biological processes:

GO term	Partners	Fold	FDR
negative regulation of mRNA splicing, via spliceosome	8	49.8×	6e-10
U2-type prespliceosome assembly	6	30.4×	5e-06
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	6	22.8×	2e-05
mRNA splicing, via spliceosome	27	20.1×	7e-25
mRNA export from nucleus	8	19.2×	1e-06
regulation of alternative mRNA splicing, via spliceosome	9	17.9×	3e-07
RNA splicing	18	12.9×	1e-12
positive regulation of transcription elongation by RNA polymerase II	5	12.2×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	4
Likely benign	0
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1734 predictions. Top by Δscore:

Variant	Effect	Δscore
12:120463945:CCCA:C	donor_loss	1.0000
12:120463946:CCA:C	donor_loss	1.0000
12:120463947:CACC:C	donor_loss	1.0000
12:120463949:C:CG	donor_loss	1.0000
12:120465703:T:TA	donor_gain	1.0000
12:120465708:AAGT:A	donor_gain	1.0000
12:120465783:CATCT:C	acceptor_gain	1.0000
12:120465786:CT:C	acceptor_gain	1.0000
12:120465788:C:CC	acceptor_gain	1.0000
12:120465788:CTAAA:C	acceptor_loss	1.0000
12:120465789:T:C	acceptor_loss	1.0000
12:120469419:CA:C	donor_loss	1.0000
12:120469420:A:AC	donor_gain	1.0000
12:120469421:C:CC	donor_gain	1.0000
12:120457075:GAT:G	acceptor_gain	0.9900
12:120459978:G:GT	donor_gain	0.9900
12:120463949:CCT:C	donor_gain	0.9900
12:120464122:CCTAG:C	acceptor_loss	0.9900
12:120464123:CT:C	acceptor_loss	0.9900
12:120464129:A:C	acceptor_gain	0.9900
12:120465622:CATA:C	donor_loss	0.9900
12:120465623:ATAC:A	donor_loss	0.9900
12:120465624:TACC:T	donor_loss	0.9900
12:120465711:T:TA	donor_gain	0.9900
12:120465784:ATCT:A	acceptor_gain	0.9900
12:120465799:A:T	acceptor_gain	0.9900
12:120469983:GACTT:G	donor_gain	0.9900
12:120457175:CCCAG:C	donor_loss	0.9800
12:120457176:CCAG:C	donor_loss	0.9800
12:120457177:CAGGT:C	donor_loss	0.9800

AlphaMissense

1422 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:120463955:G:C	H173D	1.000
12:120463963:A:G	F170S	1.000
12:120463978:A:G	L165P	1.000
12:120463990:G:T	A161D	1.000
12:120464017:T:G	Y152S	1.000
12:120464023:A:T	V150D	1.000
12:120464030:C:A	G148W	1.000
12:120464062:A:T	V137D	1.000
12:120464068:C:A	G135V	1.000
12:120464068:C:T	G135E	1.000
12:120464069:C:A	G135W	1.000
12:120464069:C:G	G135R	1.000
12:120464069:C:T	G135R	1.000
12:120464077:C:G	R132P	1.000
12:120464085:A:C	D129E	1.000
12:120464085:A:T	D129E	1.000
12:120464086:T:A	D129V	1.000
12:120464086:T:C	D129G	1.000
12:120464086:T:G	D129A	1.000
12:120464087:C:G	D129H	1.000
12:120464088:C:A	K128N	1.000
12:120464088:C:G	K128N	1.000
12:120464089:T:A	K128M	1.000
12:120464090:T:C	K128E	1.000
12:120464092:A:G	L127P	1.000
12:120464092:A:T	L127Q	1.000
12:120464095:T:A	D126V	1.000
12:120464095:T:C	D126G	1.000
12:120464095:T:G	D126A	1.000
12:120464097:C:A	Q125H	1.000

dbSNP variants (sampled 300 via entrez): RS1000172043 (12:120471504 A>G), RS1000204532 (12:120471138 T>A,C,G), RS1000479288 (12:120465871 A>C), RS1001055406 (12:120469239 G>A,T), RS1001077511 (12:120467369 C>A,T), RS1001109060 (12:120469056 A>G), RS1001240612 (12:120464823 C>G,T), RS1001241023 (12:120465137 T>G), RS1001310494 (12:120463670 T>C), RS1001743547 (12:120464227 T>C), RS1001872445 (12:120469920 C>T), RS1002076680 (12:120464522 G>C), RS1002857174 (12:120466402 A>G), RS1003188860 (12:120467559 C>T), RS1003243017 (12:120467397 A>T)

Disease associations

OMIM: gene MIM:601943 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST004401_6	Reading disability or specific language impairment (pleiotropy)	4.000000e-06
GCST004402_1	Reading disability or specific language impairment adjusted for intelligence quotient (pleiotropy)	1.000000e-06
GCST005312_3	Menopause (age at onset)	4.000000e-08
GCST90002385_4	High light scatter reticulocyte count	2.000000e-36
GCST90002386_337	High light scatter reticulocyte percentage of red cells	2.000000e-35
GCST90002406_348	Reticulocyte fraction of red cells	2.000000e-27

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004337	intelligence
EFO:0004704	age at menopause
EFO:0007986	reticulocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4295813 (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
8.14	Kd	7.313	nM	CHEMBL3752910
7.91	ED50	12.45	nM	CHEMBL3752910

PubChem BioAssay actives

1 with measured affinity, of 3 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-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149945: Binding affinity to human SRSF9 incubated for 45 mins by Kinobead based pull down assay	kd	0.0073	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, affects cotreatment, affects expression, increases abundance	2
chloropicrin	affects expression, decreases expression	2
FR900359	increases phosphorylation	1
ginger extract	affects cotreatment, affects expression, increases abundance	1
triphenyl phosphate	affects expression	1
hydroxyhydroquinone	decreases expression	1
beta-lapachone	decreases expression	1
arsenite	affects binding, increases reaction	1
sodium arsenite	decreases expression	1
perfluorooctanoic acid	decreases expression	1
coumarin	affects phosphorylation	1
cyclic 3’,5’-uridine monophosphate	affects binding	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	affects binding, increases reaction	1
K 7174	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1
ICG 001	decreases expression	1
LDN 193189	affects cotreatment, increases expression	1
Arsenic Trioxide	decreases expression	1
Benzo(a)pyrene	decreases expression	1
Dinitrochlorobenzene	affects binding	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Ivermectin	decreases expression	1
Lead	affects expression	1
Mustard Gas	increases phosphorylation	1
Oils, Volatile	affects cotreatment, affects expression, increases abundance	1
Ribonucleotides	affects binding	1
Rotenone	increases expression	1
Selenium	increases expression	1
Smoke	decreases expression	1

ChEMBL screening assays

2 unique, capped per target: 2 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL4155374	Binding	Binding affinity to serine/arginine-rich-splicing factor 9 in human A549 cells at 0.15 mM after 4 hrs by HPLC-MS based pull down assay relative to control	Synthesis, cytotoxic evaluation and target identification of thieno[2,3-d]pyrimidine derivatives with a dithiocarbamate side chain at C2 position. — Eur J Med Chem

Clinical trials (associated diseases)

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