CIPC

Summary

CIPC (CLOCK interacting pacemaker, HGNC:20365) is a protein-coding gene on chromosome 14q24.3, encoding CLOCK-interacting pacemaker (Q9C0C6). Transcriptional repressor which may act as a negative-feedback regulator of CLOCK-BMAL1 transcriptional activity in the circadian-clock mechanism.

Predicted to be involved in negative regulation of DNA-templated transcription and negative regulation of circadian rhythm. Located in cytosol and nucleoplasm.

Source: NCBI Gene 85457 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 61 total
• GTEx eGene: eQTL in 15 tissues, sQTL in 15 (q < 0.05)
• Constraint (gnomAD): pLI 0.44 (intermediate), LOEUF 0.64 (unconstrained)
• MANE Select transcript: NM_033426
• Notable: 61 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20365
Approved symbol	CIPC
Name	CLOCK interacting pacemaker
Location	14q24.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000198894
Ensembl biotype	protein_coding
OMIM	616995
Entrez	85457

Gene structure

Transcript identifiers

Ensembl transcripts: 30 — 28 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay

MANE Select: ENST00000361786

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

ENST00000361786, ENST00000554447, ENST00000554658, ENST00000555200, ENST00000555437, ENST00000555611, ENST00000556863, ENST00000557115, ENST00000880022, ENST00000880023, ENST00000880024, ENST00000880025, ENST00000880026, ENST00000880027, ENST00000880028, ENST00000880029, ENST00000930386, ENST00000930387, ENST00000971302, ENST00000971303, ENST00000971304, ENST00000971305, ENST00001047262, ENST00001121553, ENST00001121554, ENST00001127132, ENST00001127133, ENST00001129491, ENST00001129492, ENST00001137530

RefSeq mRNA: 1 — MANE Select: NM_033426 NM_033426

CCDS: CCDS9855

Canonical transcript exons

ENST00000361786 — 4 exons

Exon	Start	End
ENSE00000911977	77109812	77109981
ENSE00000941065	77113425	77117287
ENSE00001240307	77098258	77098361
ENSE00003529256	77105657	77105844

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 97.84.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.0827 / max 215.5820, expressed in 1795 samples.

Highest expression (Bgee): skeletal muscle tissue of rectus abdominis, quadriceps femoris, vastus lateralis, tibialis anterior, deltoid.

Genetic regulation across tissues (GTEx eQTL / sQTL)

CIPC is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 15 tissues and its splicing (sQTL) in 15 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 30 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Muscle Skeletal	sqtl	9.0e-35	-1.61	14:77099904:G:A
Cells EBV-transformed lymphocytes	eqtl	2.5e-20	-0.58	14:77098635:G:C
Spleen	eqtl	2.0e-14	+0.51	14:77101076:C:T
Whole Blood	eqtl	2.5e-07	-0.14	14:77101322:G:C
Colon Transverse	sqtl	7.2e-07	-1.26	14:77099904:G:A
Cells Cultured fibroblasts	eqtl	6.5e-06	+0.15	14:77101076:C:T
Skin Sun Exposed Lower leg	eqtl	7.5e-06	+0.15	14:77104135:C:T
Esophagus Mucosa	eqtl	1.4e-04	-0.12	14:77122539:T:C
Lung	eqtl	1.8e-04	-0.19	14:77101322:G:C
Skin Sun Exposed Lower leg	sqtl	5.7e-04	-0.77	14:77066572:C:G
Artery Aorta	sqtl	2.2e-03	-0.92	14:77099904:G:A
Esophagus Mucosa	sqtl	3.9e-03	-0.80	14:77099904:G:A
Lung	sqtl	4.3e-03	-0.89	14:77099904:G:A
Nerve Tibial	eqtl	5.9e-03	+0.10	14:77134001:G:T
Esophagus Muscularis	sqtl	6.1e-03	-0.82	14:77099904:G:A
Skin Not Sun Exposed Suprapubic	sqtl	9.6e-03	-0.72	14:77099904:G:A
Thyroid	sqtl	1.3e-02	-0.71	14:77099904:G:A
Skin Not Sun Exposed Suprapubic	eqtl	1.4e-02	+0.14	14:77128571:T:A
Testis	sqtl	2.0e-02	-1.07	14:77099904:G:A
Artery Tibial	eqtl	2.1e-02	-0.10	14:77062352:G:C

FANTOM5 promoters

2 alternative TSS:

Promoter ID	TPM avg	Samples expressed
140756	16.9088	1794
140757	0.1739	70

Top tissues by expression

showing 100 of 256 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	97.84	gold quality
quadriceps femoris	UBERON:0001377	97.73	gold quality
vastus lateralis	UBERON:0001379	97.69	gold quality
tibialis anterior	UBERON:0001385	97.33	gold quality
deltoid	UBERON:0001476	97.25	gold quality
skeletal muscle tissue	UBERON:0001134	97.19	gold quality
left ventricle myocardium	UBERON:0006566	96.61	gold quality
biceps brachii	UBERON:0001507	96.55	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	96.44	gold quality
gastrocnemius	UBERON:0001388	96.07	gold quality
muscle tissue	UBERON:0002385	96.05	gold quality
cardiac muscle of right atrium	UBERON:0003379	95.62	gold quality
muscle of leg	UBERON:0001383	95.54	gold quality
hindlimb stylopod muscle	UBERON:0004252	95.36	gold quality
upper arm skin	UBERON:0004263	94.82	gold quality
bronchial epithelial cell	CL:0002328	94.71	gold quality
bronchus	UBERON:0002185	94.09	gold quality
lateral globus pallidus	UBERON:0002476	94.00	gold quality
corpus callosum	UBERON:0002336	93.84	gold quality
globus pallidus	UBERON:0001875	93.78	gold quality
inferior vagus X ganglion	UBERON:0005363	93.75	gold quality
medial globus pallidus	UBERON:0002477	93.74	gold quality
myocardium	UBERON:0002349	93.48	gold quality
lateral nuclear group of thalamus	UBERON:0002736	93.44	gold quality
subthalamic nucleus	UBERON:0001906	93.40	gold quality
mucosa of paranasal sinus	UBERON:0005030	93.38	gold quality
dorsal plus ventral thalamus	UBERON:0001897	93.35	gold quality
superior vestibular nucleus	UBERON:0007227	93.34	gold quality
cerebellum	UBERON:0002037	93.19	gold quality
cerebellar cortex	UBERON:0002129	93.09	gold quality
cerebellar hemisphere	UBERON:0002245	93.07	gold quality
substantia nigra	UBERON:0002038	93.03	gold quality
substantia nigra pars reticulata	UBERON:0001966	93.01	gold quality
midbrain	UBERON:0001891	92.88	gold quality
right hemisphere of cerebellum	UBERON:0014890	92.64	gold quality
postcentral gyrus	UBERON:0002581	92.62	gold quality
medulla oblongata	UBERON:0001896	92.61	gold quality
spinal cord	UBERON:0002240	92.58	gold quality
substantia nigra pars compacta	UBERON:0001965	92.53	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	92.48	gold quality
Ammon’s horn	UBERON:0001954	92.46	gold quality
Brodmann (1909) area 46	UBERON:0006483	92.41	gold quality
seminal vesicle	UBERON:0000998	92.37	gold quality
caudate nucleus	UBERON:0001873	92.10	gold quality
parietal lobe	UBERON:0001872	92.04	gold quality
body of tongue	UBERON:0011876	91.97	gold quality
amygdala	UBERON:0001876	91.96	gold quality
prefrontal cortex	UBERON:0000451	91.95	gold quality
hypothalamus	UBERON:0001898	91.43	gold quality
frontal cortex	UBERON:0001870	91.35	gold quality
nucleus accumbens	UBERON:0001882	91.34	gold quality
Brodmann (1909) area 9	UBERON:0013540	91.22	gold quality
anterior cingulate cortex	UBERON:0009835	91.21	gold quality
brain	UBERON:0000955	91.19	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	91.16	gold quality
putamen	UBERON:0001874	91.13	gold quality
cerebral cortex	UBERON:0000956	91.12	gold quality
neocortex	UBERON:0001950	91.10	gold quality
forebrain	UBERON:0001890	90.77	gold quality
superior frontal gyrus	UBERON:0002661	90.74	gold quality
temporal lobe	UBERON:0001871	90.73	gold quality
right frontal lobe	UBERON:0002810	90.71	gold quality
cerebellar vermis	UBERON:0004720	90.68	gold quality
cortical plate	UBERON:0005343	90.67	gold quality
pons	UBERON:0000988	90.56	gold quality
ganglionic eminence	UBERON:0004023	90.49	gold quality
right uterine tube	UBERON:0001302	90.42	gold quality
ventral tegmental area	UBERON:0002691	90.30	gold quality
muscle layer of sigmoid colon	UBERON:0035805	90.19	gold quality
lower esophagus mucosa	UBERON:0035834	89.31	gold quality
epithelium of nasopharynx	UBERON:0001951	89.07	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	89.06	gold quality
ileal mucosa	UBERON:0000331	89.05	gold quality
heart left ventricle	UBERON:0002084	88.99	gold quality
entorhinal cortex	UBERON:0002728	88.93	gold quality
cardiac ventricle	UBERON:0002082	88.87	gold quality
cardiac atrium	UBERON:0002081	88.73	gold quality
tongue	UBERON:0001723	88.66	gold quality
rectum	UBERON:0001052	88.63	gold quality
heart	UBERON:0000948	88.50	gold quality
right atrium auricular region	UBERON:0006631	88.35	gold quality
lower esophagus	UBERON:0013473	88.28	gold quality
lower esophagus muscularis layer	UBERON:0035833	88.26	gold quality
occipital lobe	UBERON:0002021	88.22	gold quality
palpebral conjunctiva	UBERON:0001812	88.20	gold quality
fallopian tube	UBERON:0003889	88.10	gold quality
tibial artery	UBERON:0007610	88.02	gold quality
popliteal artery	UBERON:0002250	88.01	gold quality
ventricular zone	UBERON:0003053	87.98	gold quality
colon	UBERON:0001155	87.92	gold quality
large intestine	UBERON:0000059	87.86	gold quality
prostate gland	UBERON:0002367	87.60	gold quality
oviduct epithelium	UBERON:0004804	87.59	gold quality
smooth muscle tissue	UBERON:0001135	87.56	gold quality
adrenal tissue	UBERON:0018303	87.34	gold quality
mucosa of transverse colon	UBERON:0004991	87.26	gold quality
transverse colon	UBERON:0001157	87.17	gold quality
primary visual cortex	UBERON:0002436	87.13	gold quality
esophagus	UBERON:0001043	86.93	gold quality
upper leg skin	UBERON:0004262	86.88	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.74

HPA expression

RNA tissue specificity: Tissue enhanced

showing 60 of 76 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM
Skeletal muscle	tissue	123.7
Hippocampus	tissue	98.5
Thalamus	tissue	85.5
Nucleus accumbens	tissue	82.7
Putamen	tissue	81.4
Locus coeruleus	tissue	79.4
Hippocampal formation	tissue	79.0
Cerebellum	tissue	77.6
Tongue	tissue	76.8
Midbrain	tissue	75.9
Corpus callosum	tissue	75.8
Ventral forebrain	tissue	74.7
Pons	tissue	71.6
Cerebral cortex	tissue	71.1
Superior colliculi	tissue	71.1
Somatosensory cortex	tissue	71.1
Postcentral gyrus	tissue	70.8
Periaqueductal gray	tissue	70.8
Basal ganglia	tissue	67.0
Septum	tissue	66.4
Motor cortex	tissue	65.9
Occipital cortex	tissue	65.4
Substantia nigra	tissue	63.7
Amygdala	tissue	62.6
Choroid plexus	tissue	62.6
Entorhinal cortex	tissue	62.6
Prefrontal cortex	tissue	61.9
Medulla oblongata	tissue	61.1
Temporal cortex	tissue	60.8
Retrosplenial cortex	tissue	59.3
Insular cortex	tissue	59.1
Hypothalamus	tissue	58.7
Retrosplenial and cingulate cortex	tissue	58.7
Caudate putamen	tissue	55.9
Spinal cord	tissue	54.9
Olfactory bulb	tissue	49.6
Frontal cortex	tissue	46.6
Retina	tissue	38.2
Heart muscle	tissue	37.3
Fallopian tube	tissue	28.6
Parathyroid gland	tissue	27.7
Prostate	tissue	23.9
Seminal vesicle	tissue	23.3
Esophagus	tissue	20.7
Salivary gland	tissue	19.3
Thyroid gland	tissue	19.1
Rectum	tissue	18.7
Colon	tissue	17.5
Cervix	tissue	15.8
Smooth muscle	tissue	15.4
Vagina	tissue	15.2
Breast	tissue	14.8
Liver	tissue	14.4
Endometrium 1	tissue	13.6
Kidney	tissue	13.3
Pituitary gland	tissue	13.2
Urinary bladder	tissue	12.7
Epididymis	tissue	12.7
Adipose tissue	tissue	12.4
Testis	tissue	10.9

Brain sub-regions (HPA Brain Atlas): detected in 189; highest nTPM — Posterior thalamic nucleus (125.6), Globus pallidus, externus (120.8), Ventral posteromedial thalamic nucleus (115.2), Lateral thalamic nuclei (114.1), Globus pallidus, internus (113.8).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

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

showing 30 of 171 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4745-5P	99.98	65.95	1028
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-3148	99.97	75.06	6478
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-3605-5P	99.96	67.12	932
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-590-3P	99.96	74.34	6478

Functional genomics

gnomAD constraint: pLI 0.438, LOEUF 0.64, missense Z 1.54 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000361786 — one region, missense o/e 0.86.

Literature-anchored findings (GeneRIF, showing 1)

• Since CAD and Erk have significant roles in cell proliferation and cell cycle, CIPC may work as a cell cycle regulator by interacting with these binding proteins. (PMID:26657846)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	cipca	ENSDARG00000075397
danio_rerio	cipcb	ENSDARG00000078095
mus_musculus	Cipc	ENSMUSG00000034157
rattus_norvegicus	Cipc	ENSRNOG00000011111

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	Q5R8C5	99.0%	Diamond
Xenopus laevis	Q6NRH7	35.0%	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
ZDHHC22	protein-coding	283576
TMEM63C	protein-coding	57156
LINC02288	ncRNA	283575
IRF2BPL	protein-coding	64207
LINC02289	ncRNA	102724190

Protein

Protein identifiers

CLOCK-interacting pacemaker — Q9C0C6 (reviewed: Q9C0C6)

Alternative names: CLOCK-interacting circadian protein

All UniProt accessions (7): G3V310, G3V3Y7, G3V405, G3V4V0, G3V5J4, G3V5Y7, Q9C0C6

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional repressor which may act as a negative-feedback regulator of CLOCK-BMAL1 transcriptional activity in the circadian-clock mechanism. May stimulate BMAL1-dependent phosphorylation of CLOCK. However, the physiological relevance of these observations is unsure, since experiments in an animal model showed that CIPC is not critially required for basic circadian clock.

Subunit / interactions. Interacts with CLOCK. Forms a ternary complex with the CLOCK-BMAL1 heterodimer. Interacts with CAD and HSPA5.

Subcellular location. Nucleus. Cytoplasm. Cytosol.

RefSeq proteins (1): NP_219494* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031602	CIPC	Family

Pfam: PF15800

UniProt features (13 total): region of interest 3, sequence variant 2, mutagenesis site 2, compositionally biased region 2, chain 1, coiled-coil region 1, short sequence motif 1, modified residue 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9C0C6-F1	58.88	0.16

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): cytosol; nucleoplasm; nucleoli

Antibody reliability (HPA): IF supported

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 (1)

Type	Positions
Phosphoserine	213

Mutagenesis-validated functional residues (2)

Position	Phenotype
186	loss of predominant localization in the nucleus; when associated with a-187. no effect on cad- and hspa5-binding; when associated with …
187	loss of predominant localization in the nucleus; when associated with a-186. no effect on cad- and hspa5-binding; when associated with …

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 2; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

2 pathways:

ID	Pathway	Evidence
R-HSA-9909396	Circadian clock	—
R-HSA-9931510	Phosphorylated BMAL1:CLOCK (ARNTL:CLOCK) activates expression of core clock genes	electronic

MSigDB gene sets: 205 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_DN, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_UP, GOBP_CIRCADIAN_RHYTHM, RNGTGGGC_UNKNOWN, GCM_PTPRD, GOLDRATH_IMMUNE_MEMORY, TGACCTY_ERR1_Q2, SRF_Q5_01, GOBP_REGULATION_OF_CIRCADIAN_RHYTHM, chr14q24, NF1_Q6_01, WCTCNATGGY_UNKNOWN, USF_01, GGCKCATGS_UNKNOWN, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN

GO Biological Process (4): DNA-templated transcription (GO:0006351), negative regulation of circadian rhythm (GO:0042754), negative regulation of DNA-templated transcription (GO:0045892), rhythmic process (GO:0048511)

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

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829)

Reactome top-level categories

1 top-level categories:

Category	Pathways
Circadian clock	1

GO top-level categories

14 GO namespaces:

Category	Terms
cellular anatomical structure	2
gene expression	1
RNA biosynthetic process	1
circadian rhythm	1
regulation of circadian rhythm	1
negative regulation of biological process	1
DNA-templated transcription	1
regulation of DNA-templated transcription	1
negative regulation of RNA biosynthetic process	1
biological_process	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cytoplasm	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 2 of 8 annotations. The rest are phylogenetic / computational / electronic (IEA).

2 experimentally-supported GO terms:

GO term	NS	Evidence
cytosol	CC	direct assay
nucleoplasm	CC	direct assay

Protein interactions and networks

STRING

showing 16 of 360 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CIPC	CIART	Q8N365	516
CIPC	NR1D2	Q14995	515
CIPC	CFAP77	Q6ZQR2	507
CIPC	BMAL2	Q8WYA1	475
CIPC	ITGB1BP1	O14713	442
CIPC	PER3	P56645	418
CIPC	ACTRT3	Q9BYD9	410
CIPC	BMAL1	O00327	410
CIPC	LCTL	Q6UWM7	402
CIPC	RPS19	P39019	396
CIPC	PER2	O15055	381
CIPC	ASZ1	Q8WWH4	370
CIPC	DBP	Q10586	364
CIPC	MSRA	Q9UJ68	361
CIPC	E2F6	O75461	361
CIPC	KCNJ1	P48048	361

IntAct

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

6 partners by confidence:

Partner	Interaction type	MIscore	Records
NCK2	physical association	0.560	3
RABGEF1	physical association	0.560	3
CLOCK	association	0.530	2
BMAL1	association	0.350	1
APPL1	physical association	0.000	1
VPS26C	physical association	0.000	1

BioGRID (28 interactions; top human partners by supporting records): CLOCK (Two-hybrid; 4 records), COPS5 (Affinity Capture-MS; 4 records), ZMYM4 (Affinity Capture-MS; 3 records), ARNTL2 (Affinity Capture-MS; 2 records), NPAS2 (Affinity Capture-MS; 2 records), APPL1 (Two-hybrid), ARNTL (Affinity Capture-MS), CSNK2B (Two-hybrid), DDX39A (Affinity Capture-RNA), DEC1 (Two-hybrid), DSCR3 (Two-hybrid), ELAVL1 (Affinity Capture-RNA), MOV10 (Affinity Capture-RNA), NCK2 (Two-hybrid), NXF1 (Affinity Capture-RNA)

Disease & clinical

Genetic variants

Variant evidence for CIPC: 61 ClinVar records (0 pathogenic / likely pathogenic); 3 GWAS associations.

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	59
Likely benign	2
Benign	0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 33 predictions of 316):

Position(s)	Effect	Δscore	Sites
14:77098362–77098363	donor_loss	0.9900	4
14:77105815	donor_gain	0.9900
14:77105845–77105846	donor_loss	0.9900	5
14:77098363	donor_loss	0.9800
14:77105654	acceptor_gain	0.9800
14:77105655–77105656	acceptor_loss	0.9800	6
14:77105844–77105846	donor_loss	0.9800	3
14:77098372	donor_gain	0.9600
14:77109810–77109811	acceptor_loss	0.9600	6
14:77109982–77109983	donor_loss	0.9600	5

AlphaMissense

440 missense substitutions predicted likely pathogenic (of 2,595 scored), across 119 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
F317	8	0.956	0.998
N319	8	0.950	0.994
D41	8	0.949	0.986
D46	8	0.907	0.977
N343	8	0.879	0.979
F44	7	0.975	0.997
W112	7	0.898	0.983
I332	7	0.890	0.995
I163	7	0.847	0.984
T320	6	0.980	0.990
G328	6	0.974	0.997
P155	6	0.949	0.969
L329	6	0.944	0.999
K162	6	0.917	0.979
G43	6	0.915	0.986
M95	6	0.907	0.943
W372	6	0.905	0.960
K40	6	0.901	0.976
R316	6	0.895	0.990
K335	6	0.891	0.983

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

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

1 prognostic cancer types:

Cancer	Prognostic	p-value
Kidney Renal Clear Cell Carcinoma (TCGA)	favorable	2.03e-07

Disease associations

OMIM: gene MIM:616995 | disease phenotypes:

GWAS associations

3 associations:

Study	Trait	p-value
GCST90011899_148	Aspartate aminotransferase levels	3e-9
GCST90011898_72	Alanine aminotransferase levels	3e-8
GCST008759_16	Intake of total sugars	4e-6

EFO canonical traits (from GWAS)

2 canonical traits:

EFO ID	Trait name
EFO:0010158	sugar consumption measurement
EFO:0004736	aspartate aminotransferase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Smoke	decreases expression, increases abundance, increases expression	2
sodium arsenite	decreases expression	1
abrine	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases expression	1
Carbamazepine	affects expression	1
Cisplatin	increases expression	1
Doxorubicin	decreases expression	1
Hydrogen Peroxide	increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Quercetin	decreases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	affects expression	1
Cyclosporine	increases expression	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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