CLASRP

Summary

CLASRP (CLK4 associating serine/arginine rich protein, HGNC:17731) is a protein-coding gene on chromosome 19q13.32, encoding CLK4-associating serine/arginine rich protein (Q8N2M8). Probably functions as an alternative splicing regulator. It is a selective cancer dependency (DepMap: 38.3% of cell lines).

Predicted to be involved in RNA splicing and mRNA processing. Located in nucleoplasm.

Source: NCBI Gene 11129 — RefSeq curated summary.

At a glance

• GWAS associations: 11
• Clinical variants (ClinVar): 153 total
• Cancer dependency (DepMap): dependent in 38.3% of screened cell lines
• MANE Select transcript: NM_007056

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17731
Approved symbol	CLASRP
Name	CLK4 associating serine/arginine rich protein
Location	19q13.32
Locus type	gene with protein product
Status	Approved
Aliases	SWAP2, CLASP
Ensembl gene	ENSG00000104859
Ensembl biotype	protein_coding
OMIM	618532
Entrez	11129

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 11 protein_coding, 8 retained_intron, 3 nonsense_mediated_decay

ENST00000221455, ENST00000391952, ENST00000391953, ENST00000544944, ENST00000585432, ENST00000585615, ENST00000587112, ENST00000587472, ENST00000588016, ENST00000588070, ENST00000588247, ENST00000588936, ENST00000591410, ENST00000591904, ENST00000592056, ENST00000592876, ENST00000867419, ENST00000867420, ENST00000917334, ENST00000917335, ENST00000917336, ENST00000962231

RefSeq mRNA: 2 — MANE Select: NM_007056 NM_001278439, NM_007056

CCDS: CCDS12652, CCDS62710

Canonical transcript exons

ENST00000221455 — 21 exons

Exon	Start	End
ENSE00000712245	45064012	45064227
ENSE00000712254	45064343	45064630
ENSE00000861665	45052791	45052892
ENSE00001048638	45039045	45039108
ENSE00001159121	45067337	45067594
ENSE00001209790	45068015	45068054
ENSE00001225437	45053098	45053177
ENSE00003464422	45057750	45057898
ENSE00003484779	45069202	45069248
ENSE00003486463	45059268	45059364
ENSE00003509856	45062154	45062195
ENSE00003529192	45052071	45052168
ENSE00003536101	45040184	45040311
ENSE00003545023	45068420	45068480
ENSE00003553615	45069066	45069124
ENSE00003592336	45070803	45070956
ENSE00003592825	45060554	45060627
ENSE00003598991	45070537	45070561
ENSE00003610064	45056450	45056534
ENSE00003642074	45060389	45060467
ENSE00003665096	45070022	45070104

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 98.48.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 30.4221 / max 325.6449, expressed in 1820 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
176374	29.1421	1820
176376	0.9811	224
176375	0.2990	143

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
adenohypophysis	UBERON:0002196	98.48	gold quality
lower esophagus mucosa	UBERON:0035834	98.43	gold quality
sural nerve	UBERON:0015488	98.20	gold quality
left ovary	UBERON:0002119	98.18	gold quality
right ovary	UBERON:0002118	98.06	gold quality
right lobe of thyroid gland	UBERON:0001119	98.04	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	98.01	gold quality
right hemisphere of cerebellum	UBERON:0014890	98.01	gold quality
left lobe of thyroid gland	UBERON:0001120	98.00	gold quality
pituitary gland	UBERON:0000007	97.97	gold quality
granulocyte	CL:0000094	97.91	gold quality
body of uterus	UBERON:0009853	97.73	gold quality
small intestine Peyer’s patch	UBERON:0003454	97.72	gold quality
right lobe of liver	UBERON:0001114	97.71	gold quality
body of stomach	UBERON:0001161	97.69	gold quality
peripheral nervous system	UBERON:0000010	97.68	gold quality
endocervix	UBERON:0000458	97.68	gold quality
tibial nerve	UBERON:0001323	97.68	gold quality
skin of abdomen	UBERON:0001416	97.66	gold quality
cerebellar hemisphere	UBERON:0002245	97.66	gold quality
left uterine tube	UBERON:0001303	97.64	gold quality
muscle layer of sigmoid colon	UBERON:0035805	97.62	gold quality
tendon of biceps brachii	UBERON:0008188	97.61	gold quality
skin of leg	UBERON:0001511	97.60	gold quality
spleen	UBERON:0002106	97.58	gold quality
mucosa of stomach	UBERON:0001199	97.55	gold quality
cerebellar cortex	UBERON:0002129	97.50	gold quality
minor salivary gland	UBERON:0001830	97.46	gold quality
left testis	UBERON:0004533	97.44	gold quality
ectocervix	UBERON:0012249	97.44	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.64

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ESR1

miRNA regulators (miRDB)

5 targeting CLASRP, 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-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-1225-3P	97.29	64.60	876
HSA-MIR-4681	89.50	61.59	122

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 38.3% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

• Data identified a significantly differentially methylated cg26985354 near gene CLASRP to be associated with cleft lip and cleft palate. (PMID:30832715)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	clasrp	ENSDARG00000061742
mus_musculus	Clasrp	ENSMUSG00000061028
rattus_norvegicus	Clasrp	ENSRNOG00000046000
drosophila_melanogaster	CG6695	FBGN0039215
caenorhabditis_elegans		WBGENE00009200

Paralogs (1): SFSWAP (ENSG00000061936)

Protein

Protein identifiers

CLK4-associating serine/arginine rich protein — Q8N2M8 (reviewed: Q8N2M8)

Alternative names: Splicing factor, arginine/serine-rich 16, Suppressor of white-apricot homolog 2

All UniProt accessions (6): Q8N2M8, F5H0Q6, K7EKC9, K7EKR8, K7EM61, K7EP11

UniProt curated annotations — full annotation on UniProt →

Function. Probably functions as an alternative splicing regulator. May regulate the mRNA splicing of genes such as CLK1. May act by regulating members of the CLK kinase family.

Subunit / interactions. Probably interacts with CLK4.

Subcellular location. Nucleus.

Post-translational modifications. Phosphorylated in vitro by CLK4.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the splicing factor SR family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q8N2M8-1	1	yes
Q8N2M8-3	2
Q8N2M8-4	3

RefSeq proteins (2): NP_001265368, NP_008987* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR019147	SWAP_N_domain	Domain
IPR040397	SWAP	Family

Pfam: PF09750

UniProt features (29 total): compositionally biased region 13, modified residue 8, splice variant 3, region of interest 2, chain 1, sequence variant 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N2M8-F1	59.62	0.04

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 (8): 101, 285, 294, 327, 331, 335, 547, 573

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 93 (showing top): TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, ROVERSI_GLIOMA_COPY_NUMBER_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GGAANCGGAANY_UNKNOWN, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_RNA_SPLICING, IK2_01, IK3_01, AP2_Q6_01, GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN, SCGGAAGY_ELK1_02, HSF2_01, GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN, GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_DN, MTF1_Q4

GO Biological Process (2): mRNA processing (GO:0006397), RNA splicing (GO:0008380)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (2): nucleoplasm (GO:0005654), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
mRNA metabolic process	1
binding	1
nuclear lumen	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1096 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CLASRP	PHLDB2	Q86SQ0	989
CLASRP	CLIP2	Q9UDT6	974
CLASRP	CLIP1	P30622	973
CLASRP	CLASP2	O75122	959
CLASRP	CLASP1	Q7Z460	958
CLASRP	GCC2	Q8IWJ2	955
CLASRP	ERC1	Q8IUD2	864
CLASRP	PPFIA1	Q13136	788
CLASRP	PPFIA3	O75145	739
CLASRP	IQGAP1	P46940	730
CLASRP	CKAP5	Q14008	720
CLASRP	KIF2C	Q99661	708
CLASRP	DAB2	P98082	704
CLASRP	CENPE	Q02224	641
CLASRP	DCTN1	Q14203	634

IntAct

53 interactions, top by confidence:

A	B	Type	Score
CLASRP	CFAP20	psi-mi:“MI:0915”(physical association)	0.790
CLASRP	CLK3	psi-mi:“MI:0915”(physical association)	0.670
CLK2	CLASRP	psi-mi:“MI:0915”(physical association)	0.670
CFAP20	SFSWAP	psi-mi:“MI:0914”(association)	0.620
CLK1	CLASRP	psi-mi:“MI:0915”(physical association)	0.560
ANKEF1	CLASRP	psi-mi:“MI:0915”(physical association)	0.560
PIP4K2A	AP3B1	psi-mi:“MI:0914”(association)	0.530
SNIP1	CASC3	psi-mi:“MI:0914”(association)	0.530
TMEM184B	INPPL1	psi-mi:“MI:0914”(association)	0.530
SRPK2	RRP9	psi-mi:“MI:0914”(association)	0.530
WSB2	UBB	psi-mi:“MI:0914”(association)	0.530
CFAP20	KPNA4	psi-mi:“MI:0914”(association)	0.510
U2AF2	U2SURP	psi-mi:“MI:0914”(association)	0.480
CLASRP	CDK6	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
DAB1	CLASRP	psi-mi:“MI:0915”(physical association)	0.370
DAZAP2	CLASRP	psi-mi:“MI:0915”(physical association)	0.370
CLASRP	RHOXF2	psi-mi:“MI:0915”(physical association)	0.370
Snw1	AKR7A2	psi-mi:“MI:0914”(association)	0.350
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
CLK3	AIP	psi-mi:“MI:0914”(association)	0.350
DYRK2	ZSWIM8	psi-mi:“MI:0914”(association)	0.350
CEP135	MCRIP1	psi-mi:“MI:0914”(association)	0.350
CEP135	WWP2	psi-mi:“MI:0914”(association)	0.350
CEP135	WDR91	psi-mi:“MI:0914”(association)	0.350
CLASRP	RBBP4	psi-mi:“MI:0914”(association)	0.350
CLASRP	GAK	psi-mi:“MI:0914”(association)	0.350
SRSF6	U2SURP	psi-mi:“MI:0914”(association)	0.350

BioGRID (116): CLASRP (Two-hybrid), CLASRP (Two-hybrid), CLASRP (Affinity Capture-MS), CLASRP (Affinity Capture-MS), CLASRP (Affinity Capture-MS), RHOXF2 (Two-hybrid), CLASRP (Biochemical Activity), CLASRP (Biochemical Activity), CLASRP (Affinity Capture-MS), CLASRP (Affinity Capture-MS), CLASRP (Affinity Capture-MS), ATXN1L (Affinity Capture-MS), LUC7L2 (Affinity Capture-MS), CLASRP (Affinity Capture-MS), CLASRP (Affinity Capture-MS)

ESM2 similar proteins: A0JNI5, A2AJT4, A2AQ19, A4IFB1, B1H1X4, D3ZTQ1, O43290, P35269, Q05519, Q12872, Q13435, Q3THK3, Q3UJB0, Q3UQU0, Q3USH5, Q4V7C9, Q53F19, Q568R1, Q5EA53, Q5HZB6, Q5PQQ2, Q5R539, Q5RAD5, Q5XIW8, Q5ZM19, Q66I22, Q6AY96, Q6DDA4, Q6GLZ8, Q6INH5, Q6ZPZ3, Q8BZR9, Q8CFC7, Q8K194, Q8N2M8, Q8N5F7, Q8TF01, Q8VHI6, Q8WVK2, Q923D5

Diamond homologs: A0JNI5, D3ZTQ1, P12297, Q12872, Q3USH5, Q5HZB6, Q8CFC7, Q8N2M8, Q10580, A2VDN6, O13900, Q15459, Q8K4Z5

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
ABL1	“up-regulates activity”	CLASRP	phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 49 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 3’-end processing	5	31.8×	3e-05
Transport of Mature mRNA derived from an Intron-Containing Transcript	5	24.6×	9e-05
mRNA Splicing	6	21.2×	3e-05
mRNA Polyadenylation	7	19.8×	8e-06
Processing of Capped Intron-Containing Pre-mRNA	7	18.6×	8e-06
mRNA Splicing - Major Pathway	9	15.9×	1e-06
Metabolism of RNA	6	8.1×	4e-03

GO biological processes:

GO term	Partners	Fold	FDR
negative regulation of mRNA splicing, via spliceosome	5	87.0×	7e-07
mRNA splicing, via spliceosome	7	14.6×	7e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	121
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2689 predictions. Top by Δscore:

Variant	Effect	Δscore
19:45039105:GCCG:G	donor_gain	1.0000
19:45040293:G:GT	donor_gain	1.0000
19:45040293:G:T	donor_gain	1.0000
19:45040307:AGATC:A	donor_gain	1.0000
19:45040308:GATC:G	donor_gain	1.0000
19:45040308:GATCG:G	donor_gain	1.0000
19:45040309:ATC:A	donor_gain	1.0000
19:45040310:TC:T	donor_gain	1.0000
19:45040311:CGTG:C	donor_loss	1.0000
19:45040312:G:GG	donor_gain	1.0000
19:45040312:GTGA:G	donor_loss	1.0000
19:45040313:T:A	donor_loss	1.0000
19:45040316:G:GG	donor_gain	1.0000
19:45052069:A:AG	acceptor_gain	1.0000
19:45052070:G:GG	acceptor_gain	1.0000
19:45052169:G:GG	donor_gain	1.0000
19:45052893:G:GG	donor_gain	1.0000
19:45053095:A:G	acceptor_gain	1.0000
19:45053174:GGCA:G	donor_gain	1.0000
19:45053175:G:GT	donor_gain	1.0000
19:45053175:GCA:G	donor_gain	1.0000
19:45053178:G:GG	donor_gain	1.0000
19:45056442:T:A	acceptor_gain	1.0000
19:45056445:T:A	acceptor_gain	1.0000
19:45056448:A:AG	acceptor_gain	1.0000
19:45056449:G:GA	acceptor_gain	1.0000
19:45056449:GT:G	acceptor_gain	1.0000
19:45056449:GTC:G	acceptor_gain	1.0000
19:45056449:GTCT:G	acceptor_gain	1.0000
19:45056449:GTCTC:G	acceptor_gain	1.0000

AlphaMissense

4356 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:45040216:T:A	W2R	1.000
19:45040216:T:C	W2R	1.000
19:45040218:G:C	W2C	1.000
19:45040218:G:T	W2C	1.000
19:45040277:G:C	R22T	1.000
19:45040277:G:T	R22M	1.000
19:45040278:G:C	R22S	1.000
19:45040278:G:T	R22S	1.000
19:45040286:G:C	R25P	1.000
19:45040289:G:C	R26T	1.000
19:45040290:A:C	R26S	1.000
19:45040290:A:T	R26S	1.000
19:45040292:G:C	R27P	1.000
19:45040300:T:G	Y30D	1.000
19:45052081:C:A	P37Q	1.000
19:45052089:T:C	F40L	1.000
19:45052090:T:C	F40S	1.000
19:45052091:C:A	F40L	1.000
19:45052091:C:G	F40L	1.000
19:45052093:T:C	L41P	1.000
19:45052104:G:C	G45R	1.000
19:45052105:G:A	G45D	1.000
19:45052147:C:A	A59D	1.000
19:45052150:C:A	A60D	1.000
19:45052798:T:A	W69R	1.000
19:45052798:T:C	W69R	1.000
19:45052799:G:C	W69S	1.000
19:45052800:G:C	W69C	1.000
19:45052800:G:T	W69C	1.000
19:45052823:T:A	I77N	1.000

dbSNP variants (sampled 300 via entrez): RS1000040810 (19:45045290 A>G), RS1000053568 (19:45038792 G>A), RS1000123908 (19:45050637 T>C), RS1000209063 (19:45046160 A>G), RS1000307490 (19:45063010 C>T), RS1000399093 (19:45067687 C>A,G,T), RS1000500177 (19:45054191 C>T), RS1000568975 (19:45037644 G>A), RS1000616153 (19:45058534 C>T), RS1000731640 (19:45058825 G>A), RS1000890077 (19:45048186 C>T), RS1000967781 (19:45053361 G>A), RS1001000889 (19:45068819 C>G,T), RS1001087642 (19:45069266 C>T), RS1001128490 (19:45068678 G>A)

Disease associations

OMIM: gene MIM:618532 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

11 associations (top):

Study	Trait	p-value
GCST005950_15	Body mass index x sex x age interaction (4df test)	2.000000e-10
GCST005951_56	Body mass index	1.000000e-06
GCST005952_8	Body mass index (age>50)	9.000000e-12
GCST005954_4	Body mass index x age interaction	2.000000e-07
GCST007320_30	Alzheimer’s disease or family history of Alzheimer’s disease	1.000000e-17
GCST007320_33	Alzheimer’s disease or family history of Alzheimer’s disease	1.000000e-16
GCST007320_37	Alzheimer’s disease or family history of Alzheimer’s disease	3.000000e-14
GCST007827_13	Alzheimer’s disease or HDL levels (pleiotropy)	7.000000e-22
GCST007827_3	Alzheimer’s disease or HDL levels (pleiotropy)	1.000000e-97
GCST007827_5	Alzheimer’s disease or HDL levels (pleiotropy)	7.000000e-74
GCST007827_8	Alzheimer’s disease or HDL levels (pleiotropy)	3.000000e-36

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement
EFO:0009268	family history of Alzheimer’s disease
EFO:0004612	high density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Ozone	affects cotreatment, increases expression, increases oxidation, increases abundance, affects expression	3
methacrylaldehyde	affects cotreatment, increases expression, increases oxidation, increases abundance	2
Acrolein	affects cotreatment, increases expression, increases oxidation, increases abundance	2
Air Pollutants	affects cotreatment, increases abundance, increases expression, increases oxidation, affects expression	2
FR900359	affects phosphorylation	1
triphenyl phosphate	affects expression	1
alpha-pinene	increases expression, increases oxidation, increases abundance, affects cotreatment	1
pirinixic acid	increases expression, affects binding, increases activity	1
tris(2-butoxyethyl) phosphate	affects expression	1
beta-lapachone	increases expression	1
coumarin	increases phosphorylation	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	affects binding, increases reaction	1
perfluoro-n-nonanoic acid	decreases expression	1
abrine	increases expression	1
Leflunomide	increases expression	1
Cisplatin	decreases expression	1
Doxorubicin	decreases expression	1
Endosulfan	increases expression	1
Lead	increases expression	1
Smoke	decreases expression	1
Thiram	increases expression	1
Urethane	increases expression	1
Valproic Acid	increases methylation	1
Volatile Organic Compounds	affects cotreatment, increases expression, increases oxidation	1

Clinical trials (associated diseases)

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