CLIP4

Summary

CLIP4 (CAP-Gly domain containing linker protein family member 4, HGNC:26108) is a protein-coding gene on chromosome 2p23.2, encoding CAP-Gly domain-containing linker protein 4 (Q8N3C7).

Predicted to enable microtubule plus-end binding activity. Predicted to be involved in cytoplasmic microtubule organization. Predicted to be active in cell cortex; microtubule plus-end; and nucleus.

Source: NCBI Gene 79745 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• Clinical variants (ClinVar): 104 total
• GTEx eGene: eQTL in 19 tissues, sQTL in 14 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 0.72 (unconstrained)
• MANE Select transcript: NM_024692
• Notable: 104 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26108
Approved symbol	CLIP4
Name	CAP-Gly domain containing linker protein family member 4
Location	2p23.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ21069
Ensembl gene	ENSG00000115295
Ensembl biotype	protein_coding
Entrez	79745

Gene structure

Transcript identifiers

Ensembl transcripts: 74 — 42 protein_coding, 22 nonsense_mediated_decay, 10 retained_intron

MANE Select: ENST00000320081

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 3, TSL 3: 3, TSL 4: 1, TSL 5: 4

ENST00000320081, ENST00000401605, ENST00000401617, ENST00000404424, ENST00000415891, ENST00000438819, ENST00000449202, ENST00000456385, ENST00000471165, ENST00000481628, ENST00000491701, ENST00000493551, ENST00000685126, ENST00000685829, ENST00000686125, ENST00000686470, ENST00000686848, ENST00000687104, ENST00000687166, ENST00000687450, ENST00000687506, ENST00000687889, ENST00000687915, ENST00000688337, ENST00000688724, ENST00000689017, ENST00000689045, ENST00000689070, ENST00000689605, ENST00000689687, ENST00000690063, ENST00000690615, ENST00000691129, ENST00000691341, ENST00000691509, ENST00000691585, ENST00000691796, ENST00000691852, ENST00000693041, ENST00000693232, ENST00000693264, ENST00000693446, ENST00000693482, ENST00000693513, ENST00000693694, ENST00000881705, ENST00000881706, ENST00000881707, ENST00000949173, ENST00000949174, ENST00000949175, ENST00000949176, ENST00000949177, ENST00000949178, ENST00000949179, ENST00000949180, ENST00000949181, ENST00000949182, ENST00000981336, ENST00000981337, ENST00001039587, ENST00001039590, ENST00001039591, ENST00001039593, ENST00001039596, ENST00001039597, ENST00001039598, ENST00001039599, ENST00001092041, ENST00001114131, ENST00001114132, ENST00001114133, ENST00001126024, ENST00001140106

RefSeq mRNA: 4 — MANE Select: NM_024692 NM_001287527, NM_001287528, NM_001410747, NM_024692

CCDS: CCDS1770, CCDS74502, CCDS92728

Canonical transcript exons

ENST00000320081 — 16 exons

Exon	Start	End
ENSE00001614395	29157204	29157347
ENSE00001735118	29174373	29174445
ENSE00001836545	29115415	29115665
ENSE00001955568	29181572	29183808
ENSE00002289868	29121374	29121521
ENSE00003485496	29145232	29145367
ENSE00003492604	29132152	29132245
ENSE00003495558	29133655	29133816
ENSE00003504495	29167476	29167540
ENSE00003505071	29131258	29131397
ENSE00003552762	29156354	29156443
ENSE00003561365	29163831	29163954
ENSE00003569398	29152685	29152828
ENSE00003603269	29143709	29143945
ENSE00003619527	29160333	29160467
ENSE00003636961	29135548	29135666

Expression profiles

Bgee: expression breadth ubiquitous, 269 present calls, max score 98.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 21.6450 / max 217.0966, expressed in 1628 samples.

Highest expression (Bgee): secondary oocyte, upper leg skin, skeletal muscle tissue of biceps brachii, skeletal muscle tissue of rectus abdominis, germinal epithelium of ovary.

Genetic regulation across tissues (GTEx eQTL / sQTL)

CLIP4 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 19 tissues and its splicing (sQTL) in 14 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 33 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Esophagus Mucosa	sqtl	3.3e-49	-0.87	2:29115150:G:T
Cells Cultured fibroblasts	sqtl	8.2e-40	-0.78	2:29112892:C:T
Skin Sun Exposed Lower leg	sqtl	2.7e-38	-0.61	2:29115150:G:T
Skin Not Sun Exposed Suprapubic	sqtl	6.5e-32	-0.71	2:29115150:G:T
Artery Tibial	eqtl	5.1e-10	-0.25	2:29116739:T:A
Nerve Tibial	sqtl	9.2e-10	-0.40	2:29063206:G:A
Lung	sqtl	1.8e-07	+0.93	2:29181575:G:A
Esophagus Mucosa	eqtl	2.1e-07	+0.33	2:29058343:G:C
Lung	eqtl	3.0e-07	-0.17	2:28952109:T:C
Brain Spinal cord cervical c-1	eqtl	2.1e-06	+0.28	2:29084824:C:CTGTT
Muscle Skeletal	sqtl	1.1e-05	+0.68	2:29181575:G:A
Thyroid	sqtl	2.9e-05	+0.79	2:29181575:G:A
Testis	sqtl	2.9e-05	-0.38	2:29153036:T:C
Whole Blood	eqtl	3.0e-05	+0.10	2:29002209:C:G
Esophagus Muscularis	sqtl	5.6e-05	+0.94	2:29181575:G:A
Artery Tibial	sqtl	3.8e-04	+0.79	2:29160999:A:C
Esophagus Gastroesophageal Junction	sqtl	1.1e-03	+1.04	2:29181575:G:A
Artery Aorta	eqtl	1.8e-03	+0.19	2:28992139:G:T
Breast Mammary Tissue	sqtl	5.7e-03	-1.06	2:29180535:C:T
Heart Atrial Appendage	eqtl	6.2e-03	+0.13	2:28995030:C:T

FANTOM5 promoters

showing 10 of 22 alternative TSS:

Promoter ID	TPM avg	Samples expressed
19533	13.6745	1543
19526	1.3984	421
19534	1.3430	649
19531	1.2687	597
19535	1.1068	607
19527	1.0260	283
19524	0.6676	256
19530	0.1932	56
19525	0.1395	69
19543	0.1252	32

Top tissues by expression

showing 100 of 286 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	98.37	gold quality
upper leg skin	UBERON:0004262	97.07	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	96.74	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	96.73	gold quality
germinal epithelium of ovary	UBERON:0001304	96.59	gold quality
oocyte	CL:0000023	96.52	gold quality
skin of hip	UBERON:0001554	96.49	gold quality
biceps brachii	UBERON:0001507	96.38	gold quality
gastrocnemius	UBERON:0001388	95.96	gold quality
sural nerve	UBERON:0015488	95.65	gold quality
skin of leg	UBERON:0001511	95.41	gold quality
skin of abdomen	UBERON:0001416	95.40	gold quality
muscle of leg	UBERON:0001383	95.15	gold quality
lateral globus pallidus	UBERON:0002476	95.10	gold quality
tibial nerve	UBERON:0001323	95.07	gold quality
Brodmann (1909) area 23	UBERON:0013554	94.96	gold quality
substantia nigra pars reticulata	UBERON:0001966	94.50	gold quality
globus pallidus	UBERON:0001875	94.46	gold quality
medial globus pallidus	UBERON:0002477	94.46	gold quality
parietal pleura	UBERON:0002400	94.44	gold quality
zone of skin	UBERON:0000014	94.39	gold quality
left lobe of thyroid gland	UBERON:0001120	94.16	gold quality
substantia nigra pars compacta	UBERON:0001965	94.07	gold quality
right lobe of thyroid gland	UBERON:0001119	93.96	gold quality
left ovary	UBERON:0002119	93.91	gold quality
thyroid gland	UBERON:0002046	93.62	gold quality
hindlimb stylopod muscle	UBERON:0004252	93.57	gold quality
mucosa of stomach	UBERON:0001199	93.46	gold quality
postcentral gyrus	UBERON:0002581	93.27	gold quality
muscle organ	UBERON:0001630	93.19	gold quality
right lung	UBERON:0002167	93.18	gold quality
corpus callosum	UBERON:0002336	93.14	gold quality
vagina	UBERON:0000996	92.78	gold quality
ovary	UBERON:0000992	92.73	gold quality
endothelial cell	CL:0000115	92.72	gold quality
visceral pleura	UBERON:0002401	92.71	gold quality
lateral nuclear group of thalamus	UBERON:0002736	92.67	gold quality
sperm	CL:0000019	92.56	gold quality
right ovary	UBERON:0002118	92.50	gold quality
primary visual cortex	UBERON:0002436	92.36	gold quality
adenohypophysis	UBERON:0002196	92.12	gold quality
pleura	UBERON:0000977	92.04	gold quality
entorhinal cortex	UBERON:0002728	91.92	gold quality
parietal lobe	UBERON:0001872	91.90	gold quality
esophagus mucosa	UBERON:0002469	91.79	gold quality
superior frontal gyrus	UBERON:0002661	91.74	gold quality
pigmented layer of retina	UBERON:0001782	91.66	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	91.61	gold quality
right atrium auricular region	UBERON:0006631	91.57	gold quality
cauda epididymis	UBERON:0004360	91.55	gold quality
middle temporal gyrus	UBERON:0002771	91.49	gold quality
heart right ventricle	UBERON:0002080	91.48	gold quality
palpebral conjunctiva	UBERON:0001812	91.47	gold quality
subthalamic nucleus	UBERON:0001906	91.46	gold quality
pituitary gland	UBERON:0000007	91.41	gold quality
gingiva	UBERON:0001828	91.32	gold quality
esophagus	UBERON:0001043	91.27	gold quality
cardiac atrium	UBERON:0002081	91.27	gold quality
mammalian vulva	UBERON:0000997	91.26	gold quality
adipose tissue	UBERON:0001013	91.18	gold quality
islet of Langerhans	UBERON:0000006	91.17	gold quality
seminal vesicle	UBERON:0000998	91.17	gold quality
esophagus squamous epithelium	UBERON:0006920	91.16	gold quality
skeletal muscle tissue	UBERON:0001134	90.98	gold quality
buccal mucosa cell	CL:0002336	90.91	gold quality
muscle layer of sigmoid colon	UBERON:0035805	90.89	gold quality
spinal cord	UBERON:0002240	90.84	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	90.74	gold quality
placenta	UBERON:0001987	90.69	gold quality
tibia	UBERON:0000979	90.64	gold quality
connective tissue	UBERON:0002384	90.63	gold quality
lower esophagus	UBERON:0013473	90.60	gold quality
lower esophagus muscularis layer	UBERON:0035833	90.60	gold quality
nucleus accumbens	UBERON:0001882	90.48	gold quality
caudate nucleus	UBERON:0001873	90.46	gold quality
oral cavity	UBERON:0000167	90.41	gold quality
monocyte	CL:0000576	90.35	gold quality
occipital lobe	UBERON:0002021	90.30	gold quality
ectocervix	UBERON:0012249	90.28	gold quality
subcutaneous adipose tissue	UBERON:0002190	90.27	gold quality
male germ cell	CL:0000015	90.24	gold quality
upper lobe of left lung	UBERON:0008952	90.24	gold quality
gingival epithelium	UBERON:0001949	90.21	gold quality
decidua	UBERON:0002450	90.19	gold quality
mononuclear cell	CL:0000842	90.13	gold quality
epithelium of nasopharynx	UBERON:0001951	90.13	gold quality
left coronary artery	UBERON:0001626	90.00	gold quality
amniotic fluid	UBERON:0000173	89.86	gold quality
myocardium	UBERON:0002349	89.81	gold quality
upper lobe of lung	UBERON:0008948	89.80	gold quality
adipose tissue of abdominal region	UBERON:0007808	89.76	gold quality
trigeminal ganglion	UBERON:0001675	89.73	gold quality
leukocyte	CL:0000738	89.72	gold quality
muscle tissue	UBERON:0002385	89.72	gold quality
penis	UBERON:0000989	89.53	gold quality
lower esophagus mucosa	UBERON:0035834	89.51	gold quality
coronary artery	UBERON:0001621	89.42	gold quality
omental fat pad	UBERON:0010414	89.42	gold quality
peritoneum	UBERON:0002358	89.40	gold quality
colonic epithelium	UBERON:0000397	89.37	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.41

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 146 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Caudate putamen	tissue	91.3
Cerebral cortex	tissue	39.5	not detected
Somatosensory cortex	tissue	39.5
Occipital cortex	tissue	37.4
Tongue	tissue	37.0
Motor cortex	tissue	35.6
Temporal cortex	tissue	34.4
Cerebellum	tissue	33.6	not detected
Skeletal muscle	tissue	33.4	medium
Hippocampal formation	tissue	33.3
Entorhinal cortex	tissue	33.3
Frontal cortex	tissue	33.1
Prefrontal cortex	tissue	32.9
Retrosplenial and cingulate cortex	tissue	32.7
Septum	tissue	32.6
Amygdala	tissue	31.9
Ventral forebrain	tissue	30.1
Insular cortex	tissue	30.1
Retrosplenial cortex	tissue	29.7
Choroid plexus	tissue	28.6
Basal ganglia	tissue	28.3	low
Heart muscle	tissue	26.9	medium
Nucleus accumbens	tissue	26.0
Thyroid gland	tissue	25.0	not detected
Putamen	tissue	24.6
Superior colliculi	tissue	23.9
Thalamus	tissue	22.3
Hypothalamus	tissue	21.9
Olfactory bulb	tissue	21.8
Spinal cord	tissue	21.4
Pons	tissue	20.9
Medulla oblongata	tissue	19.7
Locus coeruleus	tissue	19.7
Hippocampus	tissue	19.1	not detected
Midbrain	tissue	18.9
Esophagus	tissue	17.8	not detected
Periaqueductal gray	tissue	17.8
Thymus	tissue	17.6
Postcentral gyrus	tissue	17.5
Ovary	tissue	17.0	not detected
Substantia nigra	tissue	16.7
Smooth muscle	tissue	14.4	high
Testis	tissue	14.3	low
Adipose tissue	tissue	14.3	not detected
Lung	tissue	13.7	medium
Prostate	tissue	13.1	low
Parathyroid gland	tissue	11.9	low
Seminal vesicle	tissue	11.8	not detected
Placenta	tissue	10.9	low
Corpus callosum	tissue	10.6
Skin 1	tissue	10.3	not detected
Fallopian tube	tissue	10.3	not detected
Lymph node	tissue	10.3
Urinary bladder	tissue	10.2	not detected
Gallbladder	tissue	9.0	medium
Endometrium 1	tissue	8.7	not detected
Breast	tissue	6.9	low
Thymus	tissue	6.6
Retina	tissue	6.0
Kidney	tissue	5.6	low

Brain sub-regions (HPA Brain Atlas): detected in 227; highest nTPM — Parieto-temporal junction (white matter) (37.3), Corpus callosum, genu (white matter) (35.3), Corpus callosum, splenium (white matter) (33.6), Cerebellar white matter (30.7), Angular gyrus (white matter) (30.5).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting CLIP4 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 109 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-190A-3P	100.00	80.35	5520
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-3613-3P	100.00	76.36	7965
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488

Functional genomics

gnomAD constraint: pLI 9.25e-05, LOEUF 0.72, missense Z 0.334 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000320081 — one region, missense o/e 1.02.

Literature-anchored findings (GeneRIF, showing 2)

• FOXC2 and CLIP4 activity correlates to the presence of </=7-cm clear cell renal cell carcinomas (ccRCCs) with synchronous metastasis and may be potential molecular predictors of synchronous metastasis of </=7-cm ccRCCs. (PMID:27283491)
• miR-135b-5p promotes gastric carcinogenesis by targeting CLIP4-mediated JAK2/STAT3 signal pathway. (PMID:39121973)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:dkeyp-47f9.4	ENSDARG00000096961
mus_musculus	Clip4	ENSMUSG00000024059
rattus_norvegicus	Clip4	ENSRNOG00000008806

Paralogs (4): CLIP3 (ENSG00000105270), CLIP2 (ENSG00000106665), CLIP1 (ENSG00000130779), DCTN1 (ENSG00000204843)

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Pongo abelii	Q5R686	99.8%	Diamond
Sus scrofa	A0A287B8J2	97.3%	Diamond
Bos taurus	Q5E951	87.7%	Diamond
Xenopus laevis	Q5U243	80.2%	Diamond
Gallus gallus	P35458	73.0%	Diamond
Neurospora crassa OR74A	Q01397	61.5%	Diamond
Dictyostelium discoideum	Q54Z01	58.2%	Diamond
Drosophila melanogaster	Q9VJE5	57.6%	Diamond
Saccharomyces cerevisiae S288C	P33420	56.6%	Diamond
Schizosaccharomyces pombe 972h-	O42667	56.3%	Diamond
Caenorhabditis elegans	Q20728	56.3%	Diamond
Arabidopsis thaliana	Q67Z52	45.3%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
ALK	protein-coding	238
TOGARAM2	protein-coding	165186
PCARE	protein-coding	388939
SNORD53B	snoRNA	109617012
WDR43	protein-coding	23160
SNORD53	snoRNA	26796
SNORA10B	snoRNA	109616960
YPEL5	protein-coding	51646

Protein

Protein identifiers

CAP-Gly domain-containing linker protein 4 — Q8N3C7 (reviewed: Q8N3C7)

Alternative names: Restin-like protein 2

All UniProt accessions (27): A0A8I5KRC7, A0A8I5KRK9, A0A8I5KRT4, A0A8I5KS79, A0A8I5KSB1, A0A8I5KT47, A0A8I5KTC6, A0A8I5KTN3, A0A8I5KTX2, A0A8I5KUB8, A0A8I5KVT2, A0A8I5KW63, A0A8I5KX39, A0A8I5KXU9, A0A8I5KYN5, A0A8I5QJ97, A0A8I5QKL4, A0A8I5QKM8, A0A8I5QKP4, A0A8I5QKV0, A0A8I5QKZ2, B5MCH3, C9IYE4, E7EW06, E9PBB1, Q8N3C7, G3XAK3

Isoforms (4)

UniProt ID	Names	Canonical?
Q8N3C7-1	1	yes
Q8N3C7-2	2
Q8N3C7-3	3
Q8N3C7-4	4

RefSeq proteins (4): NP_001274456, NP_001274457, NP_001397676, NP_078968* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000938	CAP-Gly_domain	Domain
IPR002110	Ankyrin_rpt	Repeat
IPR036770	Ankyrin_rpt-contain_sf	Homologous_superfamily
IPR036859	CAP-Gly_dom_sf	Homologous_superfamily

Pfam: PF01302, PF12796

UniProt features (27 total): strand 6, splice variant 4, repeat 3, domain 3, compositionally biased region 2, modified residue 2, sequence variant 2, region of interest 2, chain 1, sequence conflict 1, helix 1

Structure

Experimental structures (PDB)

1 structures by resolution:

PDB	Title	Method	Resolution (Å)
2Z0W	Crystal structure of the 2nd CAP-Gly domain in human Restin-like protein 2 reveals a …	X-RAY DIFFRACTION	2.5

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N3C7-F1	72.24	0.46

Human Protein Atlas

Protein class: Predicted membrane proteins, Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): vesicles

Antibody reliability (HPA): IH uncertain · IF approved

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 (2)

Type	Positions
Phosphoserine	557, 609

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

MSigDB gene sets: 186 (showing top): WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN, GOBP_CYTOPLASMIC_MICROTUBULE_ORGANIZATION, BENPORATH_ES_WITH_H3K27ME3, TGCACTT_MIR519C_MIR519B_MIR519A, TATTATA_MIR374, DOANE_BREAST_CANCER_CLASSES_DN, VERNELL_RETINOBLASTOMA_PATHWAY_DN, MARTINEZ_RB1_TARGETS_DN, LASTOWSKA_COAMPLIFIED_WITH_MYCN, DOUGLAS_BMI1_TARGETS_DN, CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN, HUANG_FOXA2_TARGETS_UP, TTTGCAC_MIR19A_MIR19B, IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM, DURCHDEWALD_SKIN_CARCINOGENESIS_DN

GO Biological Process (1): cytoplasmic microtubule organization (GO:0031122)

GO Molecular Function (2): microtubule plus-end binding (GO:0051010), protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), cell cortex (GO:0005938), microtubule plus-end (GO:0035371)

GO top-level categories

8 GO namespaces:

Category	Terms
microtubule cytoskeleton organization	1
supramolecular fiber organization	1
microtubule binding	1
binding	1
intracellular membrane-bounded organelle	1
cytoplasm	1
cell periphery	1
microtubule end	1

Protein interactions and networks

STRING

showing 15 of 573 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CLIP4	MPG	P29372	555
CLIP4	C9orf50	Q5SZB4	451
CLIP4	SMAP2	Q8WU79	407
CLIP4	LYSMD4	Q5XG99	390
CLIP4	PHKB	Q93100	368
CLIP4	BCAS3	Q9H6U6	366
CLIP4	HSPH1	Q92598	363
CLIP4	APLP1	P51693	360
CLIP4	SMAP1	Q8IYB5	356
CLIP4	SNX31	Q8N9S9	354
CLIP4	SUCLG2	Q96I99	354
CLIP4	ZNF865	P0CJ78	351
CLIP4	RHBG	Q9H310	351
CLIP4	GARIN5A	Q6IPT2	332
CLIP4	RRP8	O43159	330

IntAct

Human interaction partners of CLIP4 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

showing 30 of 32 partners by confidence:

Partner	Interaction type	MIscore	Records
ZNF114	physical association	0.780	7
JAKMIP2	physical association	0.740	7
MAGEA12	physical association	0.720	6
TRIM32	physical association	0.720	6
KIFC3	physical association	0.560	6
HSF2BP	physical association	0.560	3
LZTS2	physical association	0.560	3
MAP7	physical association	0.560	3
MEOX2	physical association	0.560	3
SIX2	physical association	0.560	3
TRIP13	physical association	0.560	3
AMPH	association	0.530	2
TTN	physical association	0.000	2
TULP3	physical association	0.000	2
CDK5RAP2	physical association	0.000	1
CLIP1	physical association	0.000	1
CMYA5	physical association	0.000	1
DCAF6	physical association	0.000	1
DES	physical association	0.000	1
DST	physical association	0.000	1
KIF1B	physical association	0.000	1
MAP7D1	physical association	0.000	1
MYBPC1	physical association	0.000	1
MYH3	physical association	0.000	1
PDE4DIP	physical association	0.000	1
PEG10	physical association	0.000	1
RUNX1	physical association	0.000	1
SON	physical association	0.000	1
TAF1	physical association	0.000	1
TNNT1	physical association	0.000	1

BioGRID (60 interactions; top human partners by supporting records): AMPH (Affinity Capture-MS; 2 records), APP (Reconstituted Complex; 2 records), DCAF6 (Two-hybrid; 2 records), JAKMIP2 (Two-hybrid; 2 records), KIAA1161 (Affinity Capture-MS; 2 records), KIFC3 (Two-hybrid; 2 records), MAGEA12 (Two-hybrid; 2 records), TRIM32 (Two-hybrid; 2 records), ZNF114 (Two-hybrid; 2 records), CDK5RAP2 (Two-hybrid), CLASP1 (Affinity Capture-MS), CLASP2 (Affinity Capture-MS), CLIP1 (Two-hybrid), CMYA5 (Two-hybrid), DES (Two-hybrid)

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 32 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
Striated Muscle Contraction	7	108.0×	2e-11

GO biological processes:

GO term	Partners	Fold	FDR
sarcomere organization	6	76.6×	3e-08
microtubule cytoskeleton organization	5	20.2×	3e-04

Disease & clinical

Genetic variants

Variant evidence for CLIP4: 104 ClinVar records (0 pathogenic / likely pathogenic).

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	87
Likely benign	0
Benign	2

AlphaMissense

1,611 missense substitutions predicted likely pathogenic (of 4,603 scored), across 375 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
M108	9	0.988	0.999
M151	9	0.979	0.997
D103	8	0.997	0.999
F545	8	0.996	1.000
F509	8	0.994	1.000
F343	8	0.993	0.999
F536	8	0.989	0.999
F307	8	0.987	0.999
F160	8	0.985	0.999
F334	8	0.983	0.998
N526	8	0.979	0.998
F49	8	0.974	0.996
D107	8	0.973	0.997
H192	8	0.969	0.993
F48	8	0.966	0.998
F675	8	0.964	0.997
F71	8	0.958	0.994
N324	8	0.955	0.995
H155	8	0.954	0.989
H112	8	0.952	0.994

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

3 prognostic cancer types:

Cancer	Prognostic	p-value
Kidney Renal Clear Cell Carcinoma (TCGA)	unfavorable	0.000269
Stomach Adenocarcinoma (TCGA)	unfavorable	0.00032
Lung Adenocarcinoma (TCGA)	favorable	0.000464

Disease associations

OMIM: gene `` | disease phenotypes:

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	7
Cyclosporine	increases expression	3
Cadmium Chloride	increases abundance, increases expression	3
bisphenol A	increases expression	2
entinostat	decreases expression, affects cotreatment	2
Air Pollutants	affects cotreatment, increases abundance, increases oxidation, increases expression	2
Arsenic	increases abundance, increases expression, affects cotreatment	2
Benzo(a)pyrene	affects methylation, increases expression, increases methylation	2
Cadmium	increases expression, increases abundance	2
Calcitriol	increases expression, affects cotreatment	2
Estradiol	affects expression, affects cotreatment, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Tretinoin	increases expression	2
chloroacetaldehyde	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
tris(2-butoxyethyl) phosphate	affects expression	1
butyraldehyde	decreases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
perfluoro-n-nonanoic acid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression, increases expression	1
2,2’,4,4’,5-brominated diphenyl ether	increases expression	1
ICG 001	increases expression	1
abrine	increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	increases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.