CWF19L2

Summary

CWF19L2 (CWF19 like cell cycle control factor 2, HGNC:26508) is a protein-coding gene on chromosome 11q22.3, encoding CWF19-like protein 2 (Q2TBE0). It is a selective cancer dependency (DepMap: 65.6% of cell lines).

Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be located in nucleoplasm. Predicted to be part of post-mRNA release spliceosomal complex.

Source: NCBI Gene 143884 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 171 total
• Cancer dependency (DepMap): dependent in 65.6% of screened cell lines
• MANE Select transcript: NM_152434

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26508
Approved symbol	CWF19L2
Name	CWF19 like cell cycle control factor 2
Location	11q22.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ32343
Ensembl gene	ENSG00000152404
Ensembl biotype	protein_coding
Entrez	143884

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 8 protein_coding, 2 nonsense_mediated_decay, 1 retained_intron

ENST00000282251, ENST00000431778, ENST00000462890, ENST00000532251, ENST00000897060, ENST00000897061, ENST00000897062, ENST00000897063, ENST00000931976, ENST00000942360, ENST00000942361

RefSeq mRNA: 1 — MANE Select: NM_152434 NM_152434

CCDS: CCDS8336

Canonical transcript exons

ENST00000282251 — 18 exons

Exon	Start	End
ENSE00001101377	107416209	107416298
ENSE00001101384	107392779	107392895
ENSE00001101388	107418194	107418287
ENSE00001101403	107390074	107390211
ENSE00001101408	107439090	107439183
ENSE00001101417	107433634	107433749
ENSE00001101420	107428799	107429451
ENSE00001244045	107353524	107353736
ENSE00001676981	107441503	107441622
ENSE00001698451	107455666	107455776
ENSE00001737636	107454450	107454572
ENSE00001778944	107442939	107443049
ENSE00001862353	107326360	107327053
ENSE00002146424	107457712	107457825
ENSE00003501553	107336558	107336713
ENSE00003614672	107329918	107330019
ENSE00003653729	107348937	107349053
ENSE00003689475	107334881	107334961

Expression profiles

Bgee: expression breadth ubiquitous, 243 present calls, max score 98.14.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 29.7981 / max 2956.8445, expressed in 1710 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
122116	29.7981	1710

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tendon of biceps brachii	UBERON:0008188	98.14	gold quality
oocyte	CL:0000023	95.37	gold quality
tendon	UBERON:0000043	95.00	gold quality
calcaneal tendon	UBERON:0003701	94.18	gold quality
secondary oocyte	CL:0000655	92.80	gold quality
sural nerve	UBERON:0015488	91.93	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.96	gold quality
medial globus pallidus	UBERON:0002477	87.53	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.02	gold quality
ventricular zone	UBERON:0003053	86.96	gold quality
amniotic fluid	UBERON:0000173	86.46	gold quality
epithelial cell of pancreas	CL:0000083	85.88	silver quality
monocyte	CL:0000576	84.48	gold quality
tibialis anterior	UBERON:0001385	84.33	gold quality
leukocyte	CL:0000738	84.31	gold quality
bone marrow cell	CL:0002092	83.76	gold quality
colonic epithelium	UBERON:0000397	83.70	gold quality
popliteal artery	UBERON:0002250	82.61	gold quality
tibial artery	UBERON:0007610	82.60	gold quality
ganglionic eminence	UBERON:0004023	82.54	gold quality
adrenal tissue	UBERON:0018303	82.01	gold quality
germinal epithelium of ovary	UBERON:0001304	81.96	gold quality
globus pallidus	UBERON:0001875	81.92	gold quality
ileal mucosa	UBERON:0000331	81.62	gold quality
epithelium of nasopharynx	UBERON:0001951	81.53	silver quality
nasopharynx	UBERON:0001728	81.51	silver quality
ovary	UBERON:0000992	81.29	gold quality
tonsil	UBERON:0002372	81.28	gold quality
left ovary	UBERON:0002119	81.19	gold quality
parietal pleura	UBERON:0002400	81.02	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.84
E-MTAB-4850	no	616.86

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

47 targeting CWF19L2, 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-4668-3P	100.00	68.74	2635
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-30A-3P	99.87	69.74	2928
HSA-MIR-30D-3P	99.87	69.92	2917
HSA-MIR-30E-3P	99.87	69.68	2942
HSA-MIR-5582-3P	99.86	72.48	4221
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-202-5P	99.78	67.65	991
HSA-MIR-548AJ-5P	99.78	71.12	3085
HSA-MIR-548F-5P	99.78	71.02	3093
HSA-MIR-548G-5P	99.78	71.12	3085
HSA-MIR-548X-5P	99.78	71.12	3085
HSA-MIR-548A-3P	99.76	70.58	3524

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 65.6% of screened cell lines.

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	cwf19l2	ENSDARG00000091760
		ENSDARG00000111876
mus_musculus	Cwf19l2	ENSMUSG00000025898
rattus_norvegicus	Cwf19l2	ENSRNOG00000024372
drosophila_melanogaster	CG9213	FBGN0030655
caenorhabditis_elegans		WBGENE00015156

Paralogs (1): CWF19L1 (ENSG00000095485)

Protein

Protein identifiers

CWF19-like protein 2 — Q2TBE0 (reviewed: Q2TBE0)

All UniProt accessions (3): Q2TBE0, H0YE03, H7C3G7

UniProt curated annotations — full annotation on UniProt →

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. 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 CWF19 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q2TBE0-1	1	yes
Q2TBE0-2	2
Q2TBE0-3	3

RefSeq proteins (1): NP_689647* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006767	Cwf19-like_C_dom-2	Domain
IPR006768	Cwf19-like_C_dom-1	Domain
IPR036265	HIT-like_sf	Homologous_superfamily
IPR040194	Cwf19-like	Family

Pfam: PF04676, PF04677

UniProt features (65 total): strand 16, helix 10, compositionally biased region 8, modified residue 5, sequence variant 5, splice variant 4, turn 4, coiled-coil region 4, region of interest 3, sequence conflict 3, cross-link 2, chain 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
6ID1	ELECTRON MICROSCOPY	2.86
6ID0	ELECTRON MICROSCOPY	2.9
8RO2	ELECTRON MICROSCOPY	3.5

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q2TBE0-F1	66.67	0.21

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): 75, 360, 372, 479, 484, 171, 604

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

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

MSigDB gene sets: 57 (showing top): chr11q22, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, GOBP_RNA_SPLICING, REACTOME_MRNA_SPLICING, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, ACEVEDO_LIVER_CANCER_UP, YAMAZAKI_TCEB3_TARGETS_DN, YNGTTNNNATT_UNKNOWN, REACTOME_METABOLISM_OF_RNA, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, GOCC_SPLICEOSOMAL_COMPLEX, GOCC_RIBONUCLEOPROTEIN_COMPLEX, HAMAI_APOPTOSIS_VIA_TRAIL_UP, MIKKELSEN_ES_ICP_WITH_H3K4ME3, MIKKELSEN_NPC_ICP_WITH_H3K4ME3

GO Biological Process (1): mRNA splicing, via spliceosome (GO:0000398)

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

GO Cellular Component (2): nucleoplasm (GO:0005654), post-mRNA release spliceosomal complex (GO:0071014)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
mRNA Splicing	1
Processing of Capped Intron-Containing Pre-mRNA	1
Metabolism of RNA	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
binding	1
nuclear lumen	1
cellular anatomical structure	1
spliceosomal complex	1
U5 snRNP	1

Protein interactions and networks

STRING

914 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CWF19L2	RAB39A	Q14964	611
CWF19L2	YJU2	Q9BW85	565
CWF19L2	CEP170B	Q9Y4F5	557
CWF19L2	DBR1	Q9UK59	549
CWF19L2	ANKIB1	Q9P2G1	543
CWF19L2	ZFP62	Q8NB50	543
CWF19L2	INTS9	Q9NV88	515
CWF19L2	YEATS2	Q9ULM3	490
CWF19L2	FAM170B	A6NMN3	480
CWF19L2	ZNF491	Q8N8L2	479
CWF19L2	TAFA2	Q8N3H0	470
CWF19L2	STK35	Q8TDR2	453
CWF19L2	ZNF439	Q8NDP4	445
CWF19L2	CRYL1	Q9Y2S2	439
CWF19L2	ZNF440	Q8IYI8	432
CWF19L2	ZNF441	Q8N8Z8	432

IntAct

414 interactions, top by confidence:

A	B	Type	Score
CWF19L2	TRIM37	psi-mi:“MI:0915”(physical association)	0.720
CWF19L2	TRIM27	psi-mi:“MI:0915”(physical association)	0.720
MEOX1	CWF19L2	psi-mi:“MI:0915”(physical association)	0.720
CWF19L2	SF3B4	psi-mi:“MI:0915”(physical association)	0.720
CWF19L2	NAB2	psi-mi:“MI:0915”(physical association)	0.720
RINT1	CWF19L2	psi-mi:“MI:0915”(physical association)	0.720
TRIM54	CWF19L2	psi-mi:“MI:0915”(physical association)	0.720
TRIM9	CWF19L2	psi-mi:“MI:0915”(physical association)	0.720
CALCOCO1	CWF19L2	psi-mi:“MI:0915”(physical association)	0.720
MAD1L1	CWF19L2	psi-mi:“MI:0915”(physical association)	0.720
CWF19L2	MEOX1	psi-mi:“MI:0915”(physical association)	0.720
SF3B4	CWF19L2	psi-mi:“MI:0915”(physical association)	0.720
NAB2	CWF19L2	psi-mi:“MI:0915”(physical association)	0.720
CWF19L2	RINT1	psi-mi:“MI:0915”(physical association)	0.720
CWF19L2	TRIM54	psi-mi:“MI:0915”(physical association)	0.720
CWF19L2	CALCOCO1	psi-mi:“MI:0915”(physical association)	0.720
CWF19L2	MAD1L1	psi-mi:“MI:0915”(physical association)	0.720
CWF19L2	TRIM9	psi-mi:“MI:0915”(physical association)	0.720

BioGRID (224): CWF19L2 (Two-hybrid), CWF19L2 (Two-hybrid), CWF19L2 (Two-hybrid), CWF19L2 (Two-hybrid), CWF19L2 (Two-hybrid), CWF19L2 (Two-hybrid), CWF19L2 (Two-hybrid), CWF19L2 (Two-hybrid), CWF19L2 (Two-hybrid), CWF19L2 (Two-hybrid), CWF19L2 (Two-hybrid), CWF19L2 (Two-hybrid), CWF19L2 (Two-hybrid), CWF19L2 (Two-hybrid), CWF19L2 (Two-hybrid)

ESM2 similar proteins: A2RTL5, A6QLS2, B2RY56, O15042, P30189, P30640, P34433, P34594, P49756, Q10580, Q28C44, Q2TBE0, Q3LSS0, Q4V7C9, Q4X1D7, Q502P0, Q5M9I6, Q5M9Q1, Q5PQR4, Q5R7X2, Q5R814, Q5R8J6, Q5VTL8, Q5XHJ5, Q6AXY7, Q6DDA4, Q6DH74, Q6GLZ8, Q6NV83, Q6NWI1, Q6P7Y3, Q7L4I2, Q7SI59, Q7ZVW9, Q7ZYR8, Q80SY5, Q8GXN9, Q8IMP6, Q8N5F7, Q99LX5

Diamond homologs: Q09909, Q28C44, Q2TBE0, Q8BG79, Q10946, Q3LSS0, Q9VXT5, Q10414, Q5RGJ5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 118 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 Splicing	9	14.1×	1e-06
mRNA Splicing - Major Pathway	14	10.9×	8e-09
Processing of Capped Intron-Containing Pre-mRNA	9	10.6×	1e-05
Dengue Virus-Host Interactions	13	8.5×	5e-07
mRNA Polyadenylation	6	7.5×	8e-03
Metabolism of RNA	10	6.0×	4e-04

GO biological processes:

GO term	Partners	Fold	FDR
U2-type prespliceosome assembly	5	28.6×	3e-04
spliceosomal snRNP assembly	5	26.7×	3e-04
mRNA splicing, via spliceosome	16	13.4×	4e-11

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	145
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3328 predictions. Top by Δscore:

Variant	Effect	Δscore
11:107334875:A:AC	donor_gain	1.0000
11:107334875:ACTT:A	donor_loss	1.0000
11:107334876:C:CC	donor_gain	1.0000
11:107334878:TA:T	donor_loss	1.0000
11:107334879:A:AC	donor_gain	1.0000
11:107334879:ACAG:A	donor_loss	1.0000
11:107334880:C:A	donor_loss	1.0000
11:107334880:C:CA	donor_gain	1.0000
11:107334880:CAG:C	donor_gain	1.0000
11:107334880:CAGA:C	donor_gain	1.0000
11:107334958:CTTT:C	acceptor_gain	1.0000
11:107334962:C:CC	acceptor_gain	1.0000
11:107334973:CCA:C	acceptor_gain	1.0000
11:107334974:C:T	acceptor_gain	1.0000
11:107334974:CATT:C	acceptor_gain	1.0000
11:107334977:T:C	acceptor_gain	1.0000
11:107334977:T:TC	acceptor_gain	1.0000
11:107334980:T:C	acceptor_gain	1.0000
11:107334980:T:TC	acceptor_gain	1.0000
11:107334984:G:C	acceptor_gain	1.0000
11:107334984:G:GC	acceptor_gain	1.0000
11:107334997:A:C	acceptor_gain	1.0000
11:107336551:T:C	donor_gain	1.0000
11:107336586:ACTT:A	donor_gain	1.0000
11:107336587:CTTC:C	donor_gain	1.0000
11:107336589:T:TA	donor_gain	1.0000
11:107336590:C:A	donor_gain	1.0000
11:107348932:CTGA:C	donor_loss	1.0000
11:107348933:TGACC:T	donor_loss	1.0000
11:107348934:GACCT:G	donor_loss	1.0000

AlphaMissense

5989 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:107334934:A:G	W796R	0.999
11:107334934:A:T	W796R	0.999
11:107329964:G:T	A832D	0.998
11:107418214:C:G	A503P	0.998
11:107334958:C:G	A788P	0.997
11:107327014:A:G	W861R	0.996
11:107327014:A:T	W861R	0.996
11:107327043:C:T	G851D	0.996
11:107334932:C:A	W796C	0.996
11:107334932:C:G	W796C	0.996
11:107336574:G:T	A781D	0.996
11:107326948:A:G	W883R	0.995
11:107326948:A:T	W883R	0.995
11:107329991:A:T	V823E	0.995
11:107336606:A:C	C770W	0.995
11:107336608:A:G	C770R	0.995
11:107441613:A:G	W154R	0.995
11:107441613:A:T	W154R	0.995
11:107329936:G:C	F841L	0.994
11:107329936:G:T	F841L	0.994
11:107329938:A:G	F841L	0.994
11:107334954:A:T	I789K	0.994
11:107353538:C:G	A691P	0.994
11:107433684:C:G	A244P	0.994
11:107329922:C:T	G846E	0.993
11:107336562:A:G	F785S	0.993
11:107455710:A:G	W58R	0.993
11:107455710:A:T	W58R	0.993
11:107334957:G:T	A788D	0.992
11:107336566:A:C	Y784D	0.992

dbSNP variants (sampled 300 via entrez): RS1000075441 (11:107410984 T>G), RS1000086449 (11:107331245 C>T), RS1000104854 (11:107451602 A>G), RS1000113584 (11:107458159 C>A,G), RS1000138188 (11:107415140 T>C), RS1000150538 (11:107421547 G>A,T), RS1000176173 (11:107457985 C>T), RS1000213308 (11:107328759 T>A,C), RS1000219343 (11:107416703 G>A,C,T), RS1000250528 (11:107416446 G>A,C), RS1000313976 (11:107359937 C>A,T), RS1000315207 (11:107380225 C>G), RS1000340305 (11:107379887 A>G), RS1000343533 (11:107381474 C>G,T), RS1000351259 (11:107427428 T>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST005196_56	Coronary artery disease	9.000000e-08
GCST007094_120	Diastolic blood pressure	2.000000e-07
GCST007096_57	Pulse pressure	1.000000e-06
GCST007099_15	Systolic blood pressure	4.000000e-11
GCST009193_10	Pars opercularis volume	8.000000e-07
GCST009197_7	Cortex volume	4.000000e-06
GCST009255_9	Fourth ventricle volume	9.000000e-06
GCST009439_4	Age-related cognitive decline (language) (slope of z-scores)	8.000000e-06
GCST011037_10	Parkinson’s disease progression (cognitive)	4.000000e-06

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0006336	diastolic blood pressure
EFO:0005763	pulse pressure measurement
EFO:0006335	systolic blood pressure
EFO:0007710	cognitive decline measurement
EFO:0008336	disease progression measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression	5
sodium arsenite	decreases expression, increases expression	2
aristolochic acid I	decreases expression	1
FR900359	decreases phosphorylation	1
TAK-243	increases sumoylation	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
deoxynivalenol	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
abrine	increases expression	1
MT19c compound	increases expression	1
Resveratrol	increases expression, affects cotreatment	1
Temozolomide	increases expression	1
Benzo(a)pyrene	increases methylation	1
Caffeine	decreases phosphorylation	1
Hydrogen Peroxide	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Ribonucleotides	affects binding	1
Urethane	decreases expression	1
Cyclosporine	increases expression	1
Antirheumatic Agents	increases expression	1
Cadmium Chloride	increases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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