SRSF10

Summary

SRSF10 (serine and arginine rich splicing factor 10, HGNC:16713) is a protein-coding gene on chromosome 1p36.11, encoding Serine/arginine-rich splicing factor 10 (O75494). Splicing factor that in its dephosphorylated form acts as a general repressor of pre-mRNA splicing. It is a selective cancer dependency (DepMap: 77.5% of cell lines).

This gene product is a member of the serine-arginine (SR) family of proteins, which are involved in constitutive and regulated RNA splicing. Members of this family are characterized by N-terminal RNP1 and RNP2 motifs, which are required for binding to RNA, and multiple C-terminal SR/RS repeats, which are important in mediating association with other cellular proteins. This protein interacts with the oncoprotein TLS, and abrogates the influence of TLS on adenovirus E1A pre-mRNA splicing. This gene has pseudogenes on chromosomes 4, 9, 14, 18, and 20. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 10772 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 6 total
• Cancer dependency (DepMap): dependent in 77.5% of screened cell lines
• MANE Select transcript: NM_054016

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16713
Approved symbol	SRSF10
Name	serine and arginine rich splicing factor 10
Location	1p36.11
Locus type	gene with protein product
Status	Approved
Aliases	TASR1, TASR2, SRp38, SRrp40, SFRS13, PPP1R149
Ensembl gene	ENSG00000188529
Ensembl biotype	protein_coding
OMIM	605221
Entrez	10772

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 12 protein_coding, 5 protein_coding_CDS_not_defined, 2 retained_intron, 2 nonsense_mediated_decay

ENST00000338597, ENST00000341154, ENST00000343255, ENST00000344989, ENST00000374452, ENST00000374453, ENST00000453840, ENST00000469303, ENST00000473754, ENST00000473858, ENST00000484146, ENST00000485292, ENST00000485841, ENST00000492112, ENST00000495785, ENST00000497214, ENST00000927174, ENST00000927175, ENST00000927176, ENST00000945920, ENST00000945921

RefSeq mRNA: 8 — MANE Select: NM_054016 NM_001191005, NM_001191006, NM_001191007, NM_001191009, NM_001300936, NM_001300937, NM_006625, NM_054016

CCDS: CCDS30629, CCDS30630, CCDS53280, CCDS53281, CCDS53282, CCDS53283, CCDS72728

Canonical transcript exons

ENST00000492112 — 6 exons

Exon	Start	End
ENSE00001387453	23974974	23975077
ENSE00001754425	23978713	23978817
ENSE00001833394	23980191	23980327
ENSE00001918313	23964347	23971439
ENSE00003497985	23971850	23972012
ENSE00003648695	23971573	23971626

Expression profiles

Bgee: expression breadth ubiquitous, 293 present calls, max score 98.85.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 106.6664 / max 804.1776, expressed in 1826 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
11028	52.0880	1821
11029	48.5891	1826
11027	4.6166	1472
11024	0.4458	241
201408	0.3669	181
11025	0.3580	170
11023	0.1655	78
11026	0.0365	10

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	98.85	gold quality
calcaneal tendon	UBERON:0003701	98.71	gold quality
ganglionic eminence	UBERON:0004023	98.54	gold quality
adrenal tissue	UBERON:0018303	98.05	gold quality
embryo	UBERON:0000922	97.90	gold quality
sural nerve	UBERON:0015488	97.89	gold quality
tibia	UBERON:0000979	97.67	gold quality
mucosa of stomach	UBERON:0001199	97.42	gold quality
right uterine tube	UBERON:0001302	97.39	gold quality
left ovary	UBERON:0002119	97.25	gold quality
rectum	UBERON:0001052	97.23	gold quality
left lobe of thyroid gland	UBERON:0001120	97.19	gold quality
left uterine tube	UBERON:0001303	97.14	gold quality
body of uterus	UBERON:0009853	97.14	gold quality
mucosa of sigmoid colon	UBERON:0004993	97.10	gold quality
right ovary	UBERON:0002118	96.98	gold quality
thyroid gland	UBERON:0002046	96.95	gold quality
endometrium	UBERON:0001295	96.92	gold quality
descending thoracic aorta	UBERON:0002345	96.89	gold quality
endocervix	UBERON:0000458	96.88	gold quality
cortical plate	UBERON:0005343	96.87	gold quality
right lobe of thyroid gland	UBERON:0001119	96.86	gold quality
body of pancreas	UBERON:0001150	96.84	gold quality
bone marrow cell	CL:0002092	96.57	gold quality
tendon	UBERON:0000043	96.52	gold quality
minor salivary gland	UBERON:0001830	96.50	gold quality
thoracic aorta	UBERON:0001515	96.49	gold quality
vermiform appendix	UBERON:0001154	96.47	gold quality
ascending aorta	UBERON:0001496	96.46	gold quality
small intestine Peyer’s patch	UBERON:0003454	96.44	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-CURD-112	yes	36.43
E-CURD-88	yes	5.47
E-MTAB-6386	no	507.16
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CREB1

miRNA regulators (miRDB)

145 targeting SRSF10, 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-3163	100.00	77.23	8605
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 77.5% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 18)

• found to be dephosphorylated specifically in mitotic cells; show that dephosphorylated SRp38 is required for the observed splicing repression (PMID:12419250)
• SRp38 plays a crucial role in cell survival under stress conditions by inhibiting the splicing machinery (PMID:14765198)
• SRp38 contains two arginine- and serine-rich domains (RS), one of which has a unique, second-step repression activity, while both function together as a splicing repression domain. (PMID:16135820)
• Data show that SFRS13A expression was significantly associated with LDLR splicing efficiency in vivo. (PMID:20232416)
• Splicing thermotolerance is acquired through maintenance of SRSF10 phosphorylation and that this is mediated at least in part by Hsp27. (PMID:21135127)
• In colorectal cancer, NSSR1 was highly expressed in the nucleus of tumor cells. (PMID:21984158)
• SRSF10 is a key regulator of BCLAF1 pre-mRNA splicing and the maintenance of oncogenic features in human colon cancer cells (PMID:25091051)
• Results show that YTHDC1 promotes exon inclusion in targeted mRNAs through recruiting pre-mRNA splicing factor SRSF3 while blocking SRSF10 mRNA binding. (PMID:26876937)
• DNA damage co-opts SRSF10 to control splicing decisions in transcripts encoding components involved in DNA repair, cell-cycle control, and apoptosis. (PMID:27851963)
• Moreover, SRSF10, hnRNP A1/A2 and Sam68 collaborate to drive the DNA damage-induced splicing response of several transcripts that produce components implicated in apoptosis, cell-cycle control and DNA repair. (PMID:29396485)
• Srsf10 and the minor spliceosome control tissue-specific and dynamic SR protein expression. (PMID:32338600)
• SRSF10 inhibits biogenesis of circ-ATXN1 to regulate glioma angiogenesis via miR-526b-3p/MMP2 pathway. (PMID:32600379)
• Hepatitis B virus Core protein nuclear interactome identifies SRSF10 as a host RNA-binding protein restricting HBV RNA production. (PMID:33180834)
• Identification of SRSF10 as a regulator of SMN2 ISS-N1. (PMID:33300159)
• The aberrant upregulation of exon 10-inclusive SREK1 through SRSF10 acts as an oncogenic driver in human hepatocellular carcinoma. (PMID:35296659)
• SRSF10 stabilizes CDC25A by triggering exon 6 skipping to promote hepatocarcinogenesis. (PMID:36539837)
• lncR-GAS5 upregulates the splicing factor SRSF10 to impair endothelial autophagy, leading to atherogenesis. (PMID:36645633)
• Identification of SRSF10 as a promising prognostic biomarker with functional significance among SRSFs for glioma. (PMID:38160788)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	srsf10b	ENSDARG00000086411
mus_musculus	Srsf10	ENSMUSG00000028676
rattus_norvegicus	Srsf10	ENSRNOG00000007992

Paralogs (3): SRSF12 (ENSG00000154548), SRSF2 (ENSG00000161547), SRSF8 (ENSG00000263465)

Protein

Protein identifiers

Serine/arginine-rich splicing factor 10 — O75494 (reviewed: O75494)

Alternative names: 40 kDa SR-repressor protein, FUS-interacting serine-arginine-rich protein 1, Splicing factor SRp38, Splicing factor, arginine/serine-rich 13A, TLS-associated protein with Ser-Arg repeats, TLS-associated serine-arginine protein

All UniProt accessions (5): A0A0S2Z504, O75494, Q5JRI1, Q6IQ42, R4GMP8

UniProt curated annotations — full annotation on UniProt →

Function. Splicing factor that in its dephosphorylated form acts as a general repressor of pre-mRNA splicing. Seems to interfere with the U1 snRNP 5’-splice recognition of SNRNP70. Required for splicing repression in M-phase cells and after heat shock. Also acts as a splicing factor that specifically promotes exon skipping during alternative splicing. Interaction with YTHDC1, a RNA-binding protein that recognizes and binds N6-methyladenosine (m6A)-containing RNAs, prevents SRSF10 from binding to its mRNA-binding sites close to m6A-containing regions, leading to inhibit exon skipping during alternative splicing. May be involved in regulation of alternative splicing in neurons, with isoform 1 acting as a positive and isoform 3 as a negative regulator.

Subunit / interactions. The phosphorylated but not the dephosphorylated form interacts with TRA2B/SFRS10. The dephosphorylated form interacts with SNRNP70. Isoform 1 interacts with FUS C-terminus. Isoform 3 interacts with FUS C-terminus. Interacts with YTHDC1, leading to inhibit RNA-binding activity of SRSF10.

Subcellular location. Nucleus speckle. Cytoplasm.

Tissue specificity. Widely expressed.

Post-translational modifications. Phosphorylated. Fully dephosphorylated in mitosis and partially dephosphorylated on heat shock.

Similarity. Belongs to the splicing factor SR family.

Isoforms (6)

UniProt ID	Names	Canonical?
O75494-1	1, TASR-1	yes
O75494-2	2
O75494-3	3, TASR-2, SRp38-2
O75494-4	4
O75494-5	5
O75494-6	6

RefSeq proteins (8): NP_001177934, NP_001177935, NP_001177936, NP_001177938, NP_001287865, NP_001287866, NP_006616, NP_473357* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR035979	RBD_domain_sf	Homologous_superfamily
IPR050441	RBM	Family

Pfam: PF00076

UniProt features (27 total): modified residue 11, splice variant 7, compositionally biased region 6, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O75494-F1	60.65	0.12

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 (11): 106, 108, 129, 131, 133, 158, 160, 168, 158, 160, 23

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

ID	Pathway
R-HSA-72163	mRNA Splicing - Major Pathway
R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA
R-HSA-9770562	mRNA Polyadenylation
R-HSA-72172	mRNA Splicing
R-HSA-8953854	Metabolism of RNA

MSigDB gene sets: 307 (showing top): BORCZUK_MALIGNANT_MESOTHELIOMA_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GOBP_ALTERNATIVE_MRNA_SPLICING_VIA_SPLICEOSOME, GOBP_NEGATIVE_REGULATION_OF_RNA_SPLICING, ASTON_MAJOR_DEPRESSIVE_DISORDER_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, DITTMER_PTHLH_TARGETS_UP, BROWNE_HCMV_INFECTION_16HR_UP, CTATGCA_MIR153, PUJANA_CHEK2_PCC_NETWORK, CATTTCA_MIR203, GOBP_SPLICEOSOMAL_TRI_SNRNP_COMPLEX_ASSEMBLY, REACTOME_MRNA_3_END_PROCESSING, GROSS_HYPOXIA_VIA_ELK3_UP

GO Biological Process (11): spliceosomal tri-snRNP complex assembly (GO:0000244), RNA splicing, via transesterification reactions (GO:0000375), regulation of alternative mRNA splicing, via spliceosome (GO:0000381), mRNA splicing, via spliceosome (GO:0000398), regulation of DNA-templated transcription (GO:0006355), mRNA splice site recognition (GO:0006376), cytosolic transport (GO:0016482), regulation of mRNA splicing, via spliceosome (GO:0048024), negative regulation of mRNA splicing, via spliceosome (GO:0048025), mRNA processing (GO:0006397), RNA splicing (GO:0008380)

GO Molecular Function (6): RNA binding (GO:0003723), mRNA binding (GO:0003729), RS domain binding (GO:0050733), obsolete unfolded protein binding (GO:0051082), 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), dendrite (GO:0030425), neuronal cell body (GO:0043025), axon terminus (GO:0043679)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
mRNA Splicing	1
Metabolism of RNA	1
mRNA 3’-end processing	1
Processing of Capped Intron-Containing Pre-mRNA	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
regulation of mRNA splicing, via spliceosome	2
mRNA splicing, via spliceosome	2
RNA processing	2
binding	2
spliceosomal snRNP assembly	1
RNA splicing	1
alternative mRNA splicing, via spliceosome	1
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
spliceosomal complex assembly	1
protein-RNA complex assembly	1
cytosol	1
intracellular transport	1
regulation of RNA splicing	1
regulation of mRNA processing	1
negative regulation of RNA splicing	1
negative regulation of mRNA processing	1
mRNA metabolic process	1
nucleic acid binding	1
RNA binding	1
protein domain specific binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular anatomical structure	1
cytoplasm	1
nuclear ribonucleoprotein granule	1
neuron projection	1
dendritic tree	1
somatodendritic compartment	1
cell body	1
neuron projection terminus	1
presynapse	1
distal axon	1

Protein interactions and networks

STRING

2860 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SRSF10	YTHDC1	Q96MU7	979
SRSF10	FUS	P35637	951
SRSF10	SRSF1	Q07955	881
SRSF10	SRSF9	Q13242	807
SRSF10	ERG	P11308	760
SRSF10	HNRNPC	P07910	733
SRSF10	TRA2A	Q13595	699
SRSF10	SRSF11	Q05519	690
SRSF10	EWSR1	Q01844	687
SRSF10	HNRNPA1	P09651	680
SRSF10	PTBP1	P26599	653
SRSF10	KHDRBS1	Q07666	652
SRSF10	RBM4	Q9BWF3	652
SRSF10	HNRNPF	P52597	640
SRSF10	HNRNPL	P14866	612

IntAct

170 interactions, top by confidence:

A	B	Type	Score
SRSF10	YWHAG	psi-mi:“MI:0915”(physical association)	0.830
SRSF10	SRPK2	psi-mi:“MI:0217”(phosphorylation reaction)	0.690
SRSF10	RNPS1	psi-mi:“MI:0915”(physical association)	0.670
SRSF10	CLK3	psi-mi:“MI:0915”(physical association)	0.670
YWHAG	BLTP3B	psi-mi:“MI:2364”(proximity)	0.640
PNN	CASC3	psi-mi:“MI:0914”(association)	0.640
LIN28A	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
THOC1	DDX39A	psi-mi:“MI:0914”(association)	0.640
SRSF10	SRSF1	psi-mi:“MI:0915”(physical association)	0.640
SFN	SRSF10	psi-mi:“MI:0915”(physical association)	0.630
SRSF10	SFN	psi-mi:“MI:0915”(physical association)	0.630
YWHAH	PLEKHG3	psi-mi:“MI:0914”(association)	0.610
	SRSF10	psi-mi:“MI:0915”(physical association)	0.560
SRSF10	CLK1	psi-mi:“MI:0915”(physical association)	0.560
YWHAE	SRSF10	psi-mi:“MI:0914”(association)	0.560
SRSF10	YWHAE	psi-mi:“MI:0915”(physical association)	0.560
YWHAB	SRSF10	psi-mi:“MI:0915”(physical association)	0.540
NCBP3	SAP18	psi-mi:“MI:0914”(association)	0.530
N	NOP56	psi-mi:“MI:0914”(association)	0.530
SNRNP70	GTPBP1	psi-mi:“MI:0914”(association)	0.530
LUC7L2	CASC3	psi-mi:“MI:0914”(association)	0.530
SNIP1	CASC3	psi-mi:“MI:0914”(association)	0.530
SRPK2	RRP9	psi-mi:“MI:0914”(association)	0.530
ZC3H18	AQR	psi-mi:“MI:0914”(association)	0.530
SNRPC	SNRPGP15	psi-mi:“MI:0914”(association)	0.530
ILF2	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
GSPT2	IGF2BP3	psi-mi:“MI:0914”(association)	0.530

BioGRID (358): SRSF10 (Affinity Capture-MS), SRSF10 (Affinity Capture-MS), SRSF10 (Affinity Capture-MS), SRSF10 (Affinity Capture-MS), SRSF10 (Affinity Capture-MS), SRSF10 (Affinity Capture-MS), SRSF10 (Affinity Capture-MS), SRSF10 (Affinity Capture-MS), SRSF10 (Affinity Capture-MS), SRSF10 (Affinity Capture-MS), SRSF10 (Affinity Capture-MS), SRSF10 (Affinity Capture-MS), SRSF10 (Affinity Capture-MS), SRSF10 (Affinity Capture-MS), SRSF10 (Affinity Capture-MS)

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: A0A0D1DZT6, A2RVS6, A5A6M3, D4AE41, F4JHI7, G3V6S8, O22315, O22703, O35326, O75494, O81127, O93235, P19682, P26686, P28644, P30352, P33240, P38159, P60824, P60825, P60826, P78814, P84103, P84104, P84586, P92964, Q01130, Q02427, Q04836, Q06AT9, Q07955, Q08170, Q09167, Q0VCY7, Q10021, Q13242, Q13243, Q13247, Q14011, Q16629

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 174 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
Activation of BAD and translocation to mitochondria	6	37.8×	3e-07
Transport of Mature Transcript to Cytoplasm	11	34.6×	5e-13
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex	6	33.3×	6e-07
SARS-CoV-1 targets host intracellular signalling and regulatory pathways	6	33.3×	6e-07
mRNA 3’-end processing	16	26.0×	7e-17
Activation of BH3-only proteins	6	24.6×	4e-06
RNA Polymerase II Transcription Termination	12	21.8×	1e-11
Transport of Mature mRNA derived from an Intron-Containing Transcript	17	21.4×	2e-16

GO biological processes:

GO term	Partners	Fold	FDR
negative regulation of mRNA splicing, via spliceosome	9	45.1×	6e-11
mRNA splice site recognition	5	26.2×	1e-04
positive regulation of transcription by RNA polymerase I	5	21.2×	4e-04
regulation of alternative mRNA splicing, via spliceosome	13	20.8×	2e-11
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	5	15.3×	1e-03
mRNA export from nucleus	7	13.5×	1e-04
mRNA splicing, via spliceosome	20	12.0×	4e-13
protein targeting	5	12.0×	4e-03

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	3
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

829 predictions. Top by Δscore:

Variant	Effect	Δscore
1:23971568:TTTA:T	donor_loss	1.0000
1:23971569:TTACC:T	donor_loss	1.0000
1:23971570:TACC:T	donor_loss	1.0000
1:23971571:ACCTA:A	donor_loss	1.0000
1:23971572:C:A	donor_loss	1.0000
1:23971576:T:C	donor_gain	1.0000
1:23971624:CTG:C	acceptor_gain	1.0000
1:23971627:C:CC	acceptor_gain	1.0000
1:23971846:TTA:T	donor_loss	1.0000
1:23971847:TAC:T	donor_loss	1.0000
1:23971848:A:AC	donor_gain	1.0000
1:23971848:ACTTT:A	donor_gain	1.0000
1:23971849:C:CA	donor_gain	1.0000
1:23971849:CT:C	donor_gain	1.0000
1:23971849:CTT:C	donor_gain	1.0000
1:23971849:CTTT:C	donor_gain	1.0000
1:23971849:CTTTC:C	donor_gain	1.0000
1:23971864:CGAT:C	donor_gain	1.0000
1:23971897:T:TA	donor_gain	1.0000
1:23972008:TGGTG:T	acceptor_gain	1.0000
1:23972009:GGTG:G	acceptor_gain	1.0000
1:23972010:GTG:G	acceptor_gain	1.0000
1:23972011:TG:T	acceptor_gain	1.0000
1:23972013:C:CC	acceptor_gain	1.0000
1:23972020:A:AC	acceptor_gain	1.0000
1:23972020:A:C	acceptor_gain	1.0000
1:23972023:C:CT	acceptor_gain	1.0000
1:23972024:A:T	acceptor_gain	1.0000
1:23975115:T:C	acceptor_gain	1.0000
1:23980188:TACC:T	donor_loss	1.0000

AlphaMissense

1689 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:23971999:C:A	M96I	1.000
1:23971999:C:G	M96I	1.000
1:23971999:C:T	M96I	1.000
1:23972000:A:G	M96T	1.000
1:23974975:C:A	K91N	1.000
1:23974975:C:G	K91N	1.000
1:23974985:C:A	G88V	1.000
1:23974985:C:T	G88E	1.000
1:23974986:C:A	G88W	1.000
1:23974986:C:G	G88R	1.000
1:23974986:C:T	G88R	1.000
1:23974991:G:A	A86V	1.000
1:23974991:G:T	A86D	1.000
1:23974993:A:C	F85L	1.000
1:23974993:A:T	F85L	1.000
1:23974994:A:C	F85C	1.000
1:23974994:A:G	F85S	1.000
1:23974995:A:G	F85L	1.000
1:23975000:A:C	I83R	1.000
1:23975000:A:T	I83K	1.000
1:23975012:C:G	R79P	1.000
1:23975015:C:A	G78V	1.000
1:23975048:G:T	A67D	1.000
1:23975049:C:G	A67P	1.000
1:23975057:G:T	A64D	1.000
1:23975058:C:G	A64P	1.000
1:23975060:T:A	D63V	1.000
1:23975060:T:C	D63G	1.000
1:23975074:A:C	F58L	1.000
1:23975074:A:T	F58L	1.000

dbSNP variants (sampled 300 via entrez): RS1000291060 (1:23971102 A>C), RS1000327592 (1:23977741 A>G), RS1000378615 (1:23977409 T>C), RS1000385755 (1:23968608 A>G), RS1000997775 (1:23973004 C>T), RS1001513038 (1:23967764 A>G), RS1001879535 (1:23981544 C>T), RS1002000260 (1:23976371 G>A), RS1002004605 (1:23966132 A>C), RS1002049098 (1:23976162 T>A,C,G), RS1002460514 (1:23979932 G>A), RS1002563368 (1:23979619 G>A), RS1002687525 (1:23973991 T>C), RS1003190882 (1:23973600 C>T), RS1003276430 (1:23964908 G>A,C)

Disease associations

OMIM: gene MIM:605221 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST001762_851	Obesity-related traits	2.000000e-06
GCST007576_232	Chronotype	3.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0003940	physical activity
EFO:0008328	chronotype measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, affects cotreatment, increases methylation, decreases expression	3
Resveratrol	increases expression, affects cotreatment	2
Air Pollutants	affects cotreatment, increases abundance, increases expression, decreases expression	2
Tretinoin	decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
bisphenol F	increases expression	1
TAK-243	decreases sumoylation	1
graphene oxide	decreases expression	1
alpha-pinene	increases expression, increases abundance, affects cotreatment	1
sodium arsenate	decreases expression	1
pyrogallol 1,3-dimethyl ether	affects localization, increases expression, affects cotreatment	1
beta-lapachone	decreases expression	1
methylparaben	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	decreases expression	1
cobaltous chloride	decreases expression	1
coumarin	affects phosphorylation	1
methacrylaldehyde	affects cotreatment, increases expression, increases abundance	1
beta-methylcholine	affects expression	1
cyclic 3’,5’-uridine monophosphate	affects binding	1
pinosylvin	decreases expression	1
tamibarotene	affects expression, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
4-phenylbutyric acid	decreases expression	1
CGP 52608	affects binding, increases reaction	1
deguelin	increases expression	1
fenpyroximate	increases expression	1
4-chloro-N-((4-(1,1-dimethylethyl)phenyl)methyl)-3-ethyl-1-methyl-1H-pyrazole-5-carboxamide	increases expression	1
thifluzamide	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B3I7	Abcam HEK293T SRSF10 KO	Transformed cell line	Female

Clinical trials (associated diseases)

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