CABCOCO1

Summary

CABCOCO1 (ciliary associated calcium binding coiled-coil 1, HGNC:28678) is a protein-coding gene on chromosome 10q21.2, encoding Ciliary-associated calcium-binding coiled-coil protein 1 (Q8IVU9). Calcium-binding protein.

Predicted to enable calcium ion binding activity. Predicted to act upstream of or within sperm flagellum assembly. Predicted to be located in centrosome; cytoplasm; and sperm flagellum.

Source: NCBI Gene 219621 — RefSeq curated summary.

At a glance

• GWAS associations: 31
• Clinical variants (ClinVar): 6 total
• MANE Select transcript: NM_001366906

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28678
Approved symbol	CABCOCO1
Name	ciliary associated calcium binding coiled-coil 1
Location	10q21.2
Locus type	gene with protein product
Status	Approved
Aliases	bA63A2.1, Em:AC022398.2, MGC44593, ARIEL
Ensembl gene	ENSG00000183346
Ensembl biotype	protein_coding
Entrez	219621

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000330194, ENST00000389639, ENST00000648843, ENST00000860936, ENST00000941429, ENST00000941430

RefSeq mRNA: 5 — MANE Select: NM_001366906 NM_001366905, NM_001366906, NM_001366907, NM_001366908, NM_173554

CCDS: CCDS7262, CCDS91247

Canonical transcript exons

ENST00000648843 — 8 exons

Exon	Start	End
ENSE00001735220	61760863	61761003
ENSE00001741328	61760059	61760181
ENSE00001785695	61765939	61766766
ENSE00002259466	61690549	61690621
ENSE00003707075	61686041	61686185
ENSE00003831413	61672632	61672735
ENSE00003838488	61662929	61663032
ENSE00003900289	61681143	61681312

Expression profiles

Bgee: expression breadth ubiquitous, 151 present calls, max score 92.47.

FANTOM5 (CAGE): breadth broad, TPM avg 1.2191 / max 108.5483, expressed in 416 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
105052	0.9431	346
105051	0.2760	146

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
olfactory segment of nasal mucosa	UBERON:0005386	92.47	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.37	gold quality
right uterine tube	UBERON:0001302	89.36	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	84.34	gold quality
bronchial epithelial cell	CL:0002328	83.48	gold quality
stromal cell of endometrium	CL:0002255	81.87	gold quality
bronchus	UBERON:0002185	81.72	gold quality
spinal cord	UBERON:0002240	80.67	gold quality
left testis	UBERON:0004533	77.31	gold quality
mucosa of paranasal sinus	UBERON:0005030	76.56	silver quality
right testis	UBERON:0004534	76.20	gold quality
ventricular zone	UBERON:0003053	75.76	gold quality
prefrontal cortex	UBERON:0000451	75.74	gold quality
testis	UBERON:0000473	74.73	gold quality
mucosa of stomach	UBERON:0001199	74.50	gold quality
calcaneal tendon	UBERON:0003701	74.47	gold quality
right lung	UBERON:0002167	72.73	gold quality
fallopian tube	UBERON:0003889	72.23	gold quality
hypothalamus	UBERON:0001898	72.11	gold quality
right coronary artery	UBERON:0001625	72.06	gold quality
oviduct epithelium	UBERON:0004804	71.68	silver quality
adenohypophysis	UBERON:0002196	71.03	gold quality
anterior cingulate cortex	UBERON:0009835	69.70	gold quality
amygdala	UBERON:0001876	69.68	gold quality
Brodmann (1909) area 9	UBERON:0013540	69.26	gold quality
pituitary gland	UBERON:0000007	69.25	gold quality
epithelium of nasopharynx	UBERON:0001951	69.24	silver quality
substantia nigra	UBERON:0002038	69.04	gold quality
nucleus accumbens	UBERON:0001882	68.89	gold quality
caudate nucleus	UBERON:0001873	68.53	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

54 targeting CABCOCO1, 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-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-6845-3P	99.94	66.88	1439
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
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488
HSA-MIR-548I	99.94	71.25	3481
HSA-MIR-548J-5P	99.94	71.14	3489
HSA-MIR-548O-5P	99.94	71.24	3488
HSA-MIR-548W	99.94	71.24	3488

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cabcoco1	ENSDARG00000086310
mus_musculus	Cabcoco1	ENSMUSG00000019945
rattus_norvegicus	Cabcoco1	ENSRNOG00000000634

Protein

Protein identifiers

Ciliary-associated calcium-binding coiled-coil protein 1 — Q8IVU9 (reviewed: Q8IVU9)

All UniProt accessions (3): A0A7I2UT39, Q8IVU9, H0Y3I3

UniProt curated annotations — full annotation on UniProt →

Function. Calcium-binding protein. May be involved in the control of sperm flagellar movement.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Cell projection. Cilium. Flagellum.

RefSeq proteins (5): NP_001353834, NP_001353835, NP_001353836, NP_001353837, NP_775825 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR032727	CLAMP	Family

Pfam: PF14769

UniProt features (3 total): chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IVU9-F1	77.74	0.38

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 61 (showing top): chr10q21, GOCC_MICROTUBULE_ORGANIZING_CENTER, NKX61_01, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, GOCC_CENTROSOME, OCT1_07, YY1_01, RAAGNYNNCTTY_UNKNOWN, GOCC_MOTILE_CILIUM, SANSOM_APC_TARGETS, SANSOM_APC_TARGETS_REQUIRE_MYC, GOCC_CILIUM, BOCHKIS_FOXA2_TARGETS, RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_UP, DODD_NASOPHARYNGEAL_CARCINOMA_DN

GO Biological Process (0):

GO Molecular Function (3): calcium ion binding (GO:0005509), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (7): cytoplasm (GO:0005737), centrosome (GO:0005813), sperm flagellum (GO:0036126), cytoskeleton (GO:0005856), cilium (GO:0005929), motile cilium (GO:0031514), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
metal ion binding	1
binding	1
cation binding	1
intracellular anatomical structure	1
centriole	1
microtubule organizing center	1
9+2 motile cilium	1
intracellular membraneless organelle	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cilium	1

Protein interactions and networks

STRING

472 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CABCOCO1	PLCD3	Q8N3E9	669
CABCOCO1	ZNF652	Q9Y2D9	668
CABCOCO1	CFAP90	A4QMS7	595
CABCOCO1	PLEKHA7	Q6IQ23	529
CABCOCO1	ATP2B1	P20020	507
CABCOCO1	CACNB2	Q08289	479
CABCOCO1	SH2B3	Q9UQQ2	479
CABCOCO1	ULK4	Q96C45	477
CABCOCO1	CFAP96	A7E2U8	475
CABCOCO1	FAM221B	A6H8Z2	474
CABCOCO1	CYP17A1	P05093	451
CABCOCO1	MTHFR	P42898	445
CABCOCO1	CFAP184	Q2M329	424
CABCOCO1	CFAP299	Q6V702	399
CABCOCO1	ULK3	Q6PHR2	398

IntAct

13 interactions, top by confidence:

A	B	Type	Score
CABCOCO1	KLF11	psi-mi:“MI:0915”(physical association)	0.560
HTT	CABCOCO1	psi-mi:“MI:0915”(physical association)	0.560
CABCOCO1	NME2P1	psi-mi:“MI:0914”(association)	0.530
FAP	CABCOCO1	psi-mi:“MI:0915”(physical association)	0.400
CFTR	CABCOCO1	psi-mi:“MI:0915”(physical association)	0.370
CABCOCO1	NARS1	psi-mi:“MI:0914”(association)	0.350

BioGRID (33): IFNA17 (Affinity Capture-MS), MOB3C (Affinity Capture-MS), NME2P1 (Affinity Capture-MS), VSIG8 (Affinity Capture-MS), IFNA17 (Affinity Capture-MS), VSIG8 (Affinity Capture-MS), NME2P1 (Affinity Capture-MS), MOB3C (Affinity Capture-MS), FAM207A (Affinity Capture-MS), HMOX2 (Affinity Capture-MS), SNX2 (Affinity Capture-MS), RMDN1 (Affinity Capture-MS), SNX1 (Affinity Capture-MS), GNPDA2 (Affinity Capture-MS), TOMM34 (Affinity Capture-MS)

ESM2 similar proteins: A0A571BF63, A1A535, A1L1K1, A2AVJ5, A7YY97, B5X5N3, F1QJX5, F1QN74, O60268, P04143, P47805, P58238, P97371, P97372, Q06323, Q1LUV9, Q2NL11, Q3SYZ9, Q561Q8, Q561X3, Q5E9G3, Q5E9R0, Q5FWU8, Q5M8Y7, Q5PQS3, Q5SPP5, Q5XG48, Q61BU1, Q62264, Q63797, Q63798, Q64L94, Q6FN16, Q6MZQ0, Q6P7D5, Q6PFJ7, Q6TNU3, Q6ZQ18, Q863Z0, Q8AWD1

Diamond homologs: Q8CDT7, Q8IVU9

SIGNOR signaling

0 interactions.

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	2
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1458 predictions. Top by Δscore:

Variant	Effect	Δscore
10:61686036:TTCA:T	acceptor_loss	1.0000
10:61686037:TCA:T	acceptor_loss	1.0000
10:61686038:CA:C	acceptor_loss	1.0000
10:61686039:A:AG	acceptor_gain	1.0000
10:61686039:A:AT	acceptor_loss	1.0000
10:61686040:G:GG	acceptor_gain	1.0000
10:61686040:G:GT	acceptor_loss	1.0000
10:61686040:GC:G	acceptor_gain	1.0000
10:61686040:GCA:G	acceptor_gain	1.0000
10:61686040:GCACT:G	acceptor_gain	1.0000
10:61686182:TCAGG:T	donor_loss	1.0000
10:61686183:CAG:C	donor_loss	1.0000
10:61686184:AG:A	donor_loss	1.0000
10:61686185:GGTA:G	donor_loss	1.0000
10:61686186:G:A	donor_loss	1.0000
10:61686187:T:A	donor_loss	1.0000
10:61690548:GCTT:G	acceptor_gain	1.0000
10:61760058:GCAA:G	acceptor_gain	1.0000
10:61672736:G:GG	donor_gain	0.9900
10:61681313:G:GG	donor_gain	0.9900
10:61686040:GCAC:G	acceptor_gain	0.9900
10:61690547:A:AG	acceptor_gain	0.9900
10:61690548:G:GG	acceptor_gain	0.9900
10:61756928:A:T	donor_gain	0.9900
10:61760057:A:AG	acceptor_gain	0.9900
10:61760058:G:GG	acceptor_gain	0.9900
10:61760853:A:AG	acceptor_gain	0.9900
10:61663030:G:GT	donor_gain	0.9800
10:61663162:GCTG:G	donor_gain	0.9800
10:61672734:GA:G	donor_gain	0.9800

AlphaMissense

1958 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:61686184:A:C	S72R	0.960
10:61690549:C:A	S72R	0.960
10:61690549:C:G	S72R	0.960
10:61686154:G:C	A62P	0.948
10:61681249:T:C	F3L	0.940
10:61681251:C:A	F3L	0.940
10:61681251:C:G	F3L	0.940
10:61765988:G:C	R201P	0.935
10:61765958:T:C	L191P	0.930
10:61681273:T:C	F11L	0.910
10:61681275:T:A	F11L	0.910
10:61681275:T:G	F11L	0.910
10:61686160:G:C	A64P	0.904
10:61690569:T:C	L79P	0.902
10:61690583:T:C	F84L	0.899
10:61690585:C:A	F84L	0.899
10:61690585:C:G	F84L	0.899
10:61686077:T:C	L36P	0.897
10:61686064:A:C	S32R	0.890
10:61686066:C:A	S32R	0.890
10:61686066:C:G	S32R	0.890
10:61681298:T:C	L19P	0.884
10:61760116:G:A	G116R	0.878
10:61760116:G:C	G116R	0.878
10:61690571:T:G	Y80D	0.874
10:61686139:T:C	F57L	0.871
10:61686141:T:A	F57L	0.871
10:61686141:T:G	F57L	0.871
10:61766000:T:C	L205S	0.862
10:61765984:G:C	A200P	0.859

dbSNP variants (sampled 300 via entrez): RS1000039755 (10:61737358 T>A,C), RS1000039827 (10:61683659 C>A), RS1000067522 (10:61687162 G>A), RS1000071909 (10:61758845 G>A), RS1000115368 (10:61729374 A>C,T), RS1000147383 (10:61711289 T>C), RS1000151789 (10:61707010 G>A), RS1000169507 (10:61763880 G>A), RS1000208947 (10:61682477 A>G), RS1000219430 (10:61665747 C>A), RS1000229816 (10:61717052 G>C), RS1000262644 (10:61668597 C>T), RS1000315926 (10:61755154 T>C), RS1000346638 (10:61680989 T>A), RS1000368204 (10:61754766 CTTG>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

31 associations (top):

Study	Trait	p-value
GCST000394_2	Diastolic blood pressure	1.000000e-09
GCST001236_3	Blood pressure	2.000000e-18
GCST001694_5	Response to taxane treatment (paclitaxel)	4.000000e-07
GCST001762_622	Obesity-related traits	7.000000e-06
GCST004776_53	Systolic blood pressure	1.000000e-12
GCST004777_19	Diastolic blood pressure	4.000000e-13
GCST005860_1	Cholangiocarcinoma in primary sclerosing cholangitis (time to event)	3.000000e-06
GCST006021_26	Systolic blood pressure	5.000000e-07
GCST006166_75	Diastolic blood pressure x alcohol consumption interaction (2df test)	9.000000e-35
GCST006167_24	Mean arterial pressure x alcohol consumption interaction (2df test)	1.000000e-13
GCST006167_84	Mean arterial pressure x alcohol consumption interaction (2df test)	1.000000e-15
GCST006169_30	Diastolic blood pressure x alcohol consumption (light vs heavy) interaction (2df test)	2.000000e-10
GCST006172_16	Mean arterial pressure x alcohol consumption (light vs heavy) interaction (2df test)	9.000000e-10
GCST006187_24	Diastolic blood pressure (cigarette smoking interaction)	5.000000e-25
GCST006187_25	Diastolic blood pressure (cigarette smoking interaction)	2.000000e-16
GCST006188_3	Systolic blood pressure (cigarette smoking interaction)	1.000000e-18
GCST006188_4	Systolic blood pressure (cigarette smoking interaction)	3.000000e-12
GCST006231_38	Mean arterial pressure	3.000000e-09
GCST006258_14	Diastolic blood pressure	3.000000e-18
GCST006259_60	Systolic blood pressure	2.000000e-13
GCST006434_108	Systolic blood pressure x alcohol consumption interaction (2df test)	4.000000e-16
GCST006434_95	Systolic blood pressure x alcohol consumption interaction (2df test)	9.000000e-24
GCST007094_97	Diastolic blood pressure	1.000000e-18
GCST007099_207	Systolic blood pressure	7.000000e-11
GCST007267_51	Systolic blood pressure	1.000000e-11
GCST007927_55	Medication use (beta blocking agents)	4.000000e-11
GCST007928_95	Medication use (diuretics)	4.000000e-16
GCST007929_17	Medication use (calcium channel blockers)	9.000000e-18
GCST007930_86	Medication use (agents acting on the renin-angiotensin system)	2.000000e-29
GCST008647_35	Urinary sodium excretion	4.000000e-10

EFO canonical traits (11, from GWAS)

EFO ID	Trait name
EFO:0006336	diastolic blood pressure
EFO:0006340	mean arterial pressure
EFO:0005106	body composition measurement
EFO:0006335	systolic blood pressure
EFO:0004329	alcohol drinking
EFO:0006527	smoking status measurement
EFO:0009929	Beta blocking agent use measurement
EFO:0009928	Diuretic use measurement
EFO:0009930	Calcium channel blocker use measurement
EFO:0009931	Agents acting on the renin-angiotensin system use measurement
EFO:0009282	sodium measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs1530440	CABCOCO1		0.00	0

CTD chemical–gene interactions

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression, decreases methylation	2
Tobacco Smoke Pollution	decreases methylation, decreases expression	2
jinfukang	decreases expression, affects cotreatment	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation, affects methylation	1
Cisplatin	decreases expression, affects cotreatment	1
Silicon Dioxide	decreases expression	1
Smoke	increases abundance, increases expression	1
Asbestos, Crocidolite	decreases expression	1

Clinical trials (associated diseases)

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