CCDC92

Summary

CCDC92 (coiled-coil domain containing 92, HGNC:29563) is a protein-coding gene on chromosome 12q24.31, encoding Coiled-coil domain-containing protein 92 (Q53HC0). Interferon-stimulated protein that plays a role in innate immunity.

Enables identical protein binding activity. Predicted to be involved in innate immune response and regulation of defense response to virus. Predicted to act upstream of or within several processes, including NLRP3 inflammasome complex assembly; connective tissue replacement involved in inflammatory response wound healing; and macrophage migration. Located in centriole and centrosome.

Source: NCBI Gene 80212 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• GWAS associations: 78 (top 1% of genes corpus-wide)
• Clinical variants (ClinVar): 68 total
• GTEx eGene: eQTL in 37 tissues, sQTL in 47 (q < 0.05)
• Constraint (gnomAD): pLI 0.25 (intermediate), LOEUF 0.74 (unconstrained)
• MANE Select transcript: NM_025140
• Notable: 68 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29563
Approved symbol	CCDC92
Name	coiled-coil domain containing 92
Location	12q24.31
Locus type	gene with protein product
Status	Approved
Aliases	FLJ22471
Ensembl gene	ENSG00000119242
Ensembl biotype	protein_coding
Entrez	80212

Gene structure

Transcript identifiers

Ensembl transcripts: 60 — 58 protein_coding, 2 protein_coding_CDS_not_defined

MANE Select: ENST00000238156

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

ENST00000238156, ENST00000535556, ENST00000539551, ENST00000539761, ENST00000542348, ENST00000544798, ENST00000545037, ENST00000545135, ENST00000545891, ENST00000902169, ENST00000902170, ENST00000902171, ENST00000902172, ENST00000902173, ENST00000902174, ENST00000902175, ENST00000902176, ENST00000902177, ENST00000902178, ENST00000902179, ENST00000902180, ENST00000902181, ENST00000902182, ENST00000902183, ENST00000902184, ENST00000902185, ENST00000902186, ENST00000902187, ENST00000902188, ENST00000902189, ENST00000902190, ENST00000902191, ENST00000902192, ENST00000902193, ENST00000902194, ENST00000902195, ENST00000902196, ENST00000963301, ENST00000963302, ENST00000963303, ENST00000963304, ENST00000963305, ENST00000963306, ENST00000963307, ENST00000963308, ENST00000963309, ENST00000963310, ENST00000963311, ENST00000963312, ENST00000963313, ENST00000963314, ENST00000963315, ENST00000963316, ENST00000963317, ENST00000963318, ENST00000963319, ENST00000963320, ENST00000973583, ENST00000973584, ENST00001136134

RefSeq mRNA: 6 — MANE Select: NM_025140 NM_001304957, NM_001304958, NM_001304959, NM_001304960, NM_001304961, NM_025140

CCDS: CCDS76619, CCDS9256

Canonical transcript exons

ENST00000238156 — 5 exons

Exon	Start	End
ENSE00001151387	123944272	123944364
ENSE00002213553	123935626	123937830
ENSE00002279623	123972529	123972831
ENSE00003526279	123943347	123943493
ENSE00003640703	123942744	123942785

Expression profiles

Bgee: expression breadth ubiquitous, 139 present calls, max score 97.81.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 21.4361 / max 188.4355, expressed in 1785 samples.

Highest expression (Bgee): anterior cingulate cortex, amygdala, temporal lobe, dorsolateral prefrontal cortex, Ammon’s horn.

Genetic regulation across tissues (GTEx eQTL / sQTL)

CCDC92 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 37 tissues and its splicing (sQTL) in 47 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 84 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Artery Tibial	sqtl	5.2e-142	+1.30	12:123948159:C:T
Adipose Subcutaneous	sqtl	2.7e-103	+1.15	12:123940602:C:T
Muscle Skeletal	sqtl	1.1e-99	+0.99	12:123940602:C:T
Esophagus Muscularis	sqtl	2.0e-86	+1.25	12:123944732:G:A
Adipose Visceral Omentum	sqtl	1.1e-82	+1.17	12:123940602:C:T
Nerve Tibial	sqtl	1.6e-82	+1.10	12:123944732:G:A
Cells Cultured fibroblasts	sqtl	5.8e-73	+1.00	12:123944732:G:A
Testis	sqtl	2.5e-72	+1.24	12:123944732:G:A
Artery Aorta	sqtl	4.0e-71	+1.19	12:123944732:G:A
Lung	sqtl	1.7e-61	+0.99	12:123944732:G:A
Breast Mammary Tissue	sqtl	6.8e-57	+1.09	12:123940602:C:T
Esophagus Gastroesophageal Junction	sqtl	1.6e-53	+1.21	12:124002996:C:T
Colon Sigmoid	sqtl	7.1e-50	+1.19	12:123940602:C:T
Brain Frontal Cortex BA9	sqtl	6.3e-42	+1.48	12:123940602:C:T
Heart Atrial Appendage	sqtl	2.9e-40	+1.08	12:123940602:C:T
Brain Cortex	sqtl	3.2e-38	+1.32	12:123940602:C:T
Thyroid	sqtl	1.4e-37	+0.83	12:123994090:G:T
Heart Left Ventricle	sqtl	2.1e-36	+1.08	12:123946972:C:T
Artery Coronary	sqtl	1.6e-34	+1.25	12:124002996:C:T
Colon Transverse	sqtl	1.4e-31	+0.90	12:124009993:C:T

FANTOM5 promoters

showing 10 of 13 alternative TSS:

Promoter ID	TPM avg	Samples expressed
133971	10.0510	1724
133970	5.2508	1612
133969	1.6722	982
133966	1.1942	702
133972	1.1873	809
133975	0.4525	145
133977	0.4088	147
133976	0.3892	135
133968	0.3091	136
133967	0.2963	130

Top tissues by expression

showing 100 of 139 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
anterior cingulate cortex	UBERON:0009835	97.81	gold quality
amygdala	UBERON:0001876	97.66	gold quality
temporal lobe	UBERON:0001871	97.65	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	97.64	gold quality
Ammon’s horn	UBERON:0001954	97.62	gold quality
primary visual cortex	UBERON:0002436	97.62	gold quality
superior frontal gyrus	UBERON:0002661	97.59	gold quality
right frontal lobe	UBERON:0002810	97.47	gold quality
cerebral cortex	UBERON:0000956	97.40	gold quality
frontal cortex	UBERON:0001870	97.40	gold quality
Brodmann (1909) area 9	UBERON:0013540	97.40	gold quality
prefrontal cortex	UBERON:0000451	97.34	gold quality
hypothalamus	UBERON:0001898	97.25	gold quality
telencephalon	UBERON:0001893	97.03	gold quality
substantia nigra	UBERON:0002038	96.88	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	96.77	gold quality
putamen	UBERON:0001874	96.69	gold quality
apex of heart	UBERON:0002098	96.69	gold quality
nucleus accumbens	UBERON:0001882	96.64	gold quality
brain	UBERON:0000955	96.43	gold quality
caudate nucleus	UBERON:0001873	96.42	gold quality
left testis	UBERON:0004533	95.73	gold quality
heart left ventricle	UBERON:0002084	95.56	gold quality
right testis	UBERON:0004534	95.56	gold quality
popliteal artery	UBERON:0002250	95.03	gold quality
tibial artery	UBERON:0007610	95.02	gold quality
right hemisphere of cerebellum	UBERON:0014890	94.97	gold quality
thoracic aorta	UBERON:0001515	94.94	gold quality
descending thoracic aorta	UBERON:0002345	94.94	gold quality
right coronary artery	UBERON:0001625	94.92	gold quality
ascending aorta	UBERON:0001496	94.89	gold quality
gastrocnemius	UBERON:0001388	94.82	gold quality
testis	UBERON:0000473	94.79	gold quality
lower esophagus muscularis layer	UBERON:0035833	94.71	gold quality
lower esophagus	UBERON:0013473	94.67	gold quality
right atrium auricular region	UBERON:0006631	94.65	gold quality
heart	UBERON:0000948	94.64	gold quality
pituitary gland	UBERON:0000007	94.61	gold quality
left coronary artery	UBERON:0001626	94.57	gold quality
cerebellum	UBERON:0002037	94.53	gold quality
cerebellar hemisphere	UBERON:0002245	94.53	gold quality
cerebellar cortex	UBERON:0002129	94.52	gold quality
muscle of leg	UBERON:0001383	94.39	gold quality
adenohypophysis	UBERON:0002196	94.32	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	94.05	gold quality
mucosa of stomach	UBERON:0001199	93.91	gold quality
subcutaneous adipose tissue	UBERON:0002190	93.84	gold quality
cortical plate	UBERON:0005343	93.82	gold quality
hindlimb stylopod muscle	UBERON:0004252	93.80	gold quality
adipose tissue	UBERON:0001013	93.74	gold quality
omental fat pad	UBERON:0010414	93.62	gold quality
muscle layer of sigmoid colon	UBERON:0035805	93.56	gold quality
stromal cell of endometrium	CL:0002255	93.09	gold quality
right lung	UBERON:0002167	93.06	gold quality
left uterine tube	UBERON:0001303	92.74	gold quality
myometrium	UBERON:0001296	92.42	gold quality
endocervix	UBERON:0000458	92.38	gold quality
body of uterus	UBERON:0009853	92.10	gold quality
right lobe of thyroid gland	UBERON:0001119	91.90	gold quality
left lobe of thyroid gland	UBERON:0001120	91.87	gold quality
thyroid gland	UBERON:0002046	91.53	gold quality
thoracic mammary gland	UBERON:0005200	91.52	gold quality
material anatomical entity	UBERON:0000465	91.35	gold quality
multicellular organism	UBERON:0000468	91.35	gold quality
skeletal muscle tissue	UBERON:0001134	91.35	gold quality
upper lobe of left lung	UBERON:0008952	91.35	gold quality
anatomical system	UBERON:0000467	91.34	gold quality
adult mammalian kidney	UBERON:0000082	91.26	gold quality
tibial nerve	UBERON:0001323	91.24	gold quality
placenta	UBERON:0001987	91.23	gold quality
metanephros cortex	UBERON:0010533	91.23	gold quality
fundus of stomach	UBERON:0001160	91.20	gold quality
sural nerve	UBERON:0015488	91.12	gold quality
cortex of kidney	UBERON:0001225	90.95	gold quality
muscle tissue	UBERON:0002385	90.81	gold quality
right ovary	UBERON:0002118	90.79	gold quality
ectocervix	UBERON:0012249	90.45	gold quality
granulocyte	CL:0000094	90.42	gold quality
prostate gland	UBERON:0002367	90.39	gold quality
right uterine tube	UBERON:0001302	90.37	gold quality
small intestine Peyer’s patch	UBERON:0003454	90.15	gold quality
kidney	UBERON:0002113	90.06	gold quality
embryo	UBERON:0000922	90.03	gold quality
ganglionic eminence	UBERON:0004023	90.03	gold quality
left ovary	UBERON:0002119	90.01	gold quality
colon	UBERON:0001155	89.99	gold quality
lung	UBERON:0002048	89.96	gold quality
small intestine	UBERON:0002108	89.89	gold quality
ovary	UBERON:0000992	89.87	gold quality
monocyte	CL:0000576	89.86	gold quality
leukocyte	CL:0000738	89.72	gold quality
right lobe of liver	UBERON:0001114	89.72	gold quality
fallopian tube	UBERON:0003889	89.66	gold quality
intestine	UBERON:0000160	89.62	gold quality
esophagus	UBERON:0001043	89.62	gold quality
uterine cervix	UBERON:0000002	89.44	gold quality
smooth muscle tissue	UBERON:0001135	89.33	gold quality
urinary bladder	UBERON:0001255	89.27	gold quality
body of stomach	UBERON:0001161	89.04	gold quality
left adrenal gland	UBERON:0001234	88.88	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.14

HPA expression

RNA tissue specificity: Tissue enhanced

showing 60 of 77 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Hippocampus	tissue	103.1	medium
Postcentral gyrus	tissue	100.3
Locus coeruleus	tissue	80.1
Nucleus accumbens	tissue	65.2
Spinal cord	tissue	57.9
Cerebral cortex	tissue	56.0	high
Somatosensory cortex	tissue	56.0
Pituitary gland	tissue	55.5
Pons	tissue	52.7
Frontal cortex	tissue	52.7
Occipital cortex	tissue	50.8
Caudate putamen	tissue	49.4
Superior colliculi	tissue	47.8
Thalamus	tissue	47.7
Medulla oblongata	tissue	46.6
Motor cortex	tissue	46.0
Prefrontal cortex	tissue	44.4
Cerebellum	tissue	44.2	high
Temporal cortex	tissue	41.0
Choroid plexus	tissue	40.7
Retrosplenial and cingulate cortex	tissue	40.3
Midbrain	tissue	39.7
Hippocampal formation	tissue	39.6
Entorhinal cortex	tissue	39.6
Basal ganglia	tissue	38.4	medium
Retrosplenial cortex	tissue	38.0
Insular cortex	tissue	37.7
Putamen	tissue	37.6
Ventral forebrain	tissue	36.1
Substantia nigra	tissue	36.0
Hypothalamus	tissue	34.6
Septum	tissue	33.1
Periaqueductal gray	tissue	32.9
Amygdala	tissue	30.2
Vagina	tissue	26.9	not detected
Olfactory bulb	tissue	19.6
Corpus callosum	tissue	15.5
Skeletal muscle	tissue	9.7	not detected
Heart muscle	tissue	9.4	not detected
Testis	tissue	9.0	low
Lung	tissue	7.8	low
Adipose tissue	tissue	7.6	not detected
Tongue	tissue	7.1
Retina	tissue	6.7
Epididymis	tissue	6.7	low
Placenta	tissue	6.6	medium
Thyroid gland	tissue	5.5	not detected
Duodenum	tissue	5.5	medium
Small intestine	tissue	5.4	medium
Parathyroid gland	tissue	5.2	not detected
Smooth muscle	tissue	5.1	not detected
Seminal vesicle	tissue	4.4	low
Fallopian tube	tissue	4.4	medium
Pancreas	tissue	4.3	medium
Stomach 1	tissue	4.2	medium
Endometrium 1	tissue	4.1	medium
Ovary	tissue	3.9	not detected
Kidney	tissue	3.9	medium
Cervix	tissue	3.8	not detected
Liver	tissue	3.8	low

Brain sub-regions (HPA Brain Atlas): detected in 191; highest nTPM — Precentral gyrus (154.1), Hippocampus, CA3 (114.5), Supplementary motor cortex (113.4), Hippocampus, CA1 (112.1), Subcentral gyrus, S2 (111.9).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting CCDC92 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 38 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-4425	100.00	67.59	1049
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-4517	99.76	69.19	1867
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-12124	99.68	69.17	2700
HSA-MIR-561-3P	99.64	70.90	3647
HSA-MIR-298	99.63	67.56	1916
HSA-MIR-142-5P	99.48	70.92	2416
HSA-MIR-5590-3P	99.48	70.91	2429
HSA-MIR-302A-5P	99.39	68.21	1913
HSA-MIR-1261	98.62	68.10	896
HSA-MIR-5089-5P	98.45	66.06	1388
HSA-MIR-3650	97.88	64.89	693
HSA-MIR-1279	97.83	67.50	1898
HSA-MIR-450B-3P	97.56	66.12	512
HSA-MIR-4642	97.52	67.60	916
HSA-MIR-769-3P	97.06	64.83	464
HSA-MIR-3616-3P	96.96	65.45	983

Functional genomics

gnomAD constraint: pLI 0.246, LOEUF 0.738, missense Z 0.798 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000238156 — one region, missense o/e 0.91.

Literature-anchored findings (GeneRIF, showing 4)

• Mutation in CCDC92 gene is associated with insulin-resistant cardiometabolic disease. (PMID:27841877)
• Phenome-wide association scanning showed that CCDC92 likely affects coronary artery disease through insulin resistance pathways, whereas experimental analysis suggests that ARHGEF26 influences the transendothelial migration of leukocytes. (PMID:28714974)
• The genotypic and allelic frequencies of the rs11057401 SNP of CCDC92 gene were significantly different between the patients with coronary heart disease and controls. (PMID:29439709)
• Novel genetic variants of CCDC92 were associated with both Diabetes and Coronary Artery Disease . (PMID:29731020)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccdc92	ENSDARG00000041750
mus_musculus	Ccdc92	ENSMUSG00000037979
rattus_norvegicus	Ccdc92	ENSRNOG00000021691

Paralogs (1): CCDC92B (ENSG00000277200)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:106485) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 36 distinct phenotype terms.

Mouse phenotype (MP)	Records
decreased circulating cholesterol level	2
increased bone mineral density	1
decreased circulating LDL cholesterol level	1
decreased inflammatory response	1
decreased brain weight	1
decreased circulating triglyceride level	1
increased insulin sensitivity	1
increased circulating serum albumin level	1
abnormal white adipose tissue morphology	1
decreased liver weight	1
decreased macrophage cell number	1
abnormal auditory brainstem response	1
increased energy expenditure	1
increased oxygen consumption	1
improved glucose tolerance	1
increased blood urea nitrogen level	1
decreased susceptibility to diet-induced obesity	1
decreased circulating leptin level	1
abnormal white adipose tissue physiology	1
decreased circulating interleukin-18 level	1
decreased circulating interleukin-1 beta level	1
decreased subcutaneous adipose tissue amount	1
increased brown fat cell number	1
decreased white fat cell size	1
decreased brown fat cell size	1

+11 more (showing top 25).

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
MIR6880	ncRNA	102466204
RFLNA	protein-coding	144347
ZNF664	protein-coding	144348
DNAH10	protein-coding	196385
DNAH10OS	ncRNA	642797
NCOR2	protein-coding	9612
ZNF664-RFLNA	protein-coding	100533183
ATP6V0A2	protein-coding	23545
TCTN2	protein-coding	79867

Protein

Protein identifiers

Coiled-coil domain-containing protein 92 — Q53HC0 (reviewed: Q53HC0)

Alternative names: Limkain beta-2

All UniProt accessions (5): F5GXK2, F5H285, F5H2Z7, Q53HC0, F5H7P8

UniProt curated annotations — full annotation on UniProt →

Function. Interferon-stimulated protein that plays a role in innate immunity. Strongly inhibits ebolavirus transcription and replication. Forms a complex with viral RNA-bound nucleocapsid NP and thereby prevents the transport of NP to the cell surface.

Subunit / interactions. Interacts with CEP164. (Microbial infection) Interacts with ebolavirus protein NP; this interaction sequesters NP in the cytoplasm.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Centriole.

Post-translational modifications. Phosphorylated at Ser-209 by TTBK2.

Induction. Up to threefold after interferon treatment.

Isoforms (2)

UniProt ID	Names	Canonical?
Q53HC0-1	1	yes
Q53HC0-2	2

RefSeq proteins (6): NP_001291886, NP_001291887, NP_001291888, NP_001291889, NP_001291890, NP_079416* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR039496	CCDC92/74_N	Domain
IPR040370	CCDC74A/CCDC74B/CCDC92	Family

Pfam: PF14916

UniProt features (11 total): sequence variant 3, coiled-coil region 2, compositionally biased region 2, chain 1, region of interest 1, modified residue 1, splice variant 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q53HC0-F1	73.80	0.41

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): centrosome; nucleoplasm; vesicles

Antibody reliability (HPA): IH approved · 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 (1)

Type	Positions
Phosphoserine	209

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: 189 (showing top): GCM_MAP4K4, GOBP_RESPONSE_TO_NITROGEN_COMPOUND, GOBP_HEPATICOBILIARY_SYSTEM_DEVELOPMENT, GOBP_MYELOID_LEUKOCYTE_MIGRATION, GOBP_INFLAMMATORY_RESPONSE, GOBP_REGULATION_OF_DEFENSE_RESPONSE_TO_VIRUS, RORA1_01, TGACCTY_ERR1_Q2, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_WOUND_HEALING, GOBP_POSITIVE_REGULATION_OF_RESPONSE_TO_EXTERNAL_STIMULUS, GOBP_LEUKOCYTE_MIGRATION, GOBP_REGULATION_OF_IMMUNE_RESPONSE, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM

GO Biological Process (3): innate immune response (GO:0045087), regulation of defense response to virus (GO:0050688), immune system process (GO:0002376)

GO Molecular Function (2): identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (3): cytoplasm (GO:0005737), centrosome (GO:0005813), centriole (GO:0005814)

GO top-level categories

14 GO namespaces:

Category	Terms
microtubule organizing center	2
immune response	1
defense response to symbiont	1
regulation of response to biotic stimulus	1
regulation of defense response	1
regulation of response to external stimulus	1
defense response to virus	1
biological_process	1
protein binding	1
binding	1
intracellular anatomical structure	1
cellular anatomical structure	1
centriole	1
intracellular membraneless organelle	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 3 of 8 annotations. The rest are phylogenetic / computational / electronic (IEA).

3 experimentally-supported GO terms:

GO term	NS	Evidence
centriole	CC	direct assay
centrosome	CC	direct assay
identical protein binding	MF	physical interaction

Protein interactions and networks

STRING

showing 15 of 696 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC92	ZNF664	Q8N3J9	715
CCDC92	DNAH10	Q8IVF4	655
CCDC92	CCDC70	Q6NSX1	495
CCDC92	CCDC125	Q86Z20	490
CCDC92	TTC39A	Q5SRH9	479
CCDC92	CFAP184	Q2M329	457
CCDC92	SART3	Q15020	453
CCDC92	SH2B3	Q9UQQ2	449
CCDC92	FAM168A	Q92567	447
CCDC92	TMEM132D	Q14C87	437
CCDC92	BICDL1	Q6ZP65	436
CCDC92	ZCCHC8	Q6NZY4	435
CCDC92	CCDC74B	Q96LY2	431
CCDC92	ANAPC7	Q9UJX3	430
CCDC92	CFAP263	Q9H0I3	420

IntAct

Human interaction partners of CCDC92 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

17 partners by confidence:

Partner	Interaction type	MIscore	Records
FHL2	physical association	0.780	10
TRIML2	physical association	0.740	5
CEP164	physical association	0.600	5
TP53BP2	physical association	0.560	4
CEP76	physical association	0.560	3
DISC1	physical association	0.560	3
TRIM27	physical association	0.560	3
YAF9	physical association	0.560	3
PSMD11	association	0.530	3
COG6	physical association	0.490	2
GOLGA2	physical association	0.490	2
FXR1	physical association	0.370	1
FXR2	physical association	0.370	1
PARL	association	0.350	1
VPS11	association	0.350	1
CHGB	physical association	0.000	1
PLEKHA5	physical association	0.000	1

BioGRID (106 interactions; top human partners by supporting records): PSMD10 (Affinity Capture-MS; 4 records), PSMD8 (Affinity Capture-MS; 4 records), UCHL5 (Affinity Capture-MS; 4 records), ADRM1 (Affinity Capture-MS; 3 records), CEP164 (Two-hybrid; 3 records), PSMC1 (Affinity Capture-MS; 3 records), PSMC3 (Affinity Capture-MS; 3 records), PSMC4 (Affinity Capture-MS; 3 records), PSMC5 (Affinity Capture-MS; 3 records), PSMC6 (Affinity Capture-MS; 3 records), PSMD11 (Affinity Capture-MS; 3 records), PSMD12 (Affinity Capture-MS; 3 records), PSMD13 (Affinity Capture-MS; 3 records), PSMD14 (Affinity Capture-MS; 3 records), PSMD2 (Affinity Capture-MS; 3 records)

Protein complexes (CORUM) (1)

Experimentally-characterized complexes this protein is a subunit of (★ = the complex contains a known drug target).

1 complexes by size:

Complex	Subunits	Members
CCDC92-CEP164 complex	2	CCDC92, CEP164

Disease & clinical

Genetic variants

Variant evidence for CCDC92: 68 ClinVar records (0 pathogenic / likely pathogenic); 78 GWAS associations.

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	62
Likely benign	1
Benign	0

AlphaMissense

632 missense substitutions predicted likely pathogenic (of 2,158 scored), across 188 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
F246	8	0.980	0.999
D242	8	0.972	0.993
H41	8	0.954	0.992
F36	8	0.953	0.998
M240	8	0.929	0.986
H163	8	0.884	0.987
D61	8	0.751	0.907
E51	7	0.929	0.972
C59	7	0.923	0.983
H49	7	0.922	0.986
M206	7	0.877	0.973
S209	7	0.866	0.987
E127	7	0.848	0.976
P243	6	0.966	0.993
P241	6	0.956	0.989
K208	6	0.953	0.984
K207	6	0.952	0.990
L45	6	0.904	0.998
R205	6	0.903	0.990
R203	6	0.889	0.986

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	0.000184

Disease associations

OMIM: gene `` | disease phenotypes:

GWAS associations

showing 30 of 78 associations:

Study	Trait	p-value
GCST007502_4	Waist-to-hip ratio adjusted for BMI (additive genetic model)	7e-51
GCST010926_4	Waist-to-hip ratio adjusted for BMI	2e-50
GCST007500_29	Waist-to-hip ratio adjusted for BMI (additive genetic model)	1e-41
GCST007487_12	Waist-to-hip ratio adjusted for BMI (additive genetic model)	6e-38
GCST007483_4	Waist-to-hip ratio adjusted for BMI (additive genetic model)	7e-37
GCST010244_61	Triglyceride levels	4e-35
GCST90020027_453	Waist-hip index	9e-31
GCST90020025_1826	Waist-to-hip ratio adjusted for BMI	6e-30
GCST90020027_444	Waist-hip index	8e-26
GCST90020025_1813	Waist-to-hip ratio adjusted for BMI	1e-24
GCST90020026_115	Hip index	3e-24
GCST90002385_435	High light scatter reticulocyte count	1e-23
GCST90020024_1059	A body shape index	4e-23
GCST90020029_161	Waist circumference adjusted for body mass index	2e-21
GCST004576_49	Waist-to-hip ratio adjusted for body mass index	8e-21
GCST90002386_345	High light scatter reticulocyte percentage of red cells	2e-20
GCST004576_48	Waist-to-hip ratio adjusted for body mass index	1e-19
GCST004578_59	Waist-to-hip ratio adjusted for BMI in active individuals	1e-19
GCST90002405_340	Reticulocyte count	2e-19
GCST004567_13	Waist-to-hip ratio adjusted for BMI (joint analysis for main effect and physical activity interaction)	3e-19
GCST004578_132	Waist-to-hip ratio adjusted for BMI in active individuals	6e-19
GCST004567_62	Waist-to-hip ratio adjusted for BMI (joint analysis for main effect and physical activity interaction)	3e-18
GCST004578_72	Waist-to-hip ratio adjusted for BMI in active individuals	3e-18
GCST004567_106	Waist-to-hip ratio adjusted for BMI (joint analysis for main effect and physical activity interaction)	4e-18
GCST004567_118	Waist-to-hip ratio adjusted for BMI (joint analysis for main effect and physical activity interaction)	4e-18
GCST004578_85	Waist-to-hip ratio adjusted for BMI in active individuals	4e-18
GCST004576_37	Waist-to-hip ratio adjusted for body mass index	5e-18
GCST90020024_1048	A body shape index	6e-18
GCST90020029_49	Waist circumference adjusted for body mass index	1e-17
GCST004505_21	Waist-to-hip ratio adjusted for BMI (adjusted for smoking behaviour)	4e-17

EFO canonical traits (from GWAS)

15 canonical traits:

EFO ID	Trait name
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004530	triglyceride measurement
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0004318	smoking behavior
EFO:0007789	BMI-adjusted waist circumference
EFO:0008002	physical activity measurement
EFO:0007986	reticulocyte count
EFO:0006941	grip strength measurement
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement
EFO:0010368	lysophosphatidylethanolamine 18:1 measurement
EFO:0008039	BMI-adjusted hip circumference
EFO:0004531	urate measurement
EFO:0004587	lymphocyte count
EFO:0004305	erythrocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, increases methylation, affects expression	4
Benzo(a)pyrene	increases expression, affects methylation	3
sodium arsenite	decreases expression, affects cotreatment, increases abundance	2
entinostat	decreases expression, increases expression, affects cotreatment	2
(+)-JQ1 compound	increases expression	2
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
pirinixic acid	affects binding, decreases expression, increases activity	1
bisphenol A	increases methylation	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
benzo(e)pyrene	decreases methylation	1
4-aminophenylarsenoxide	affects binding, decreases reaction	1
isobutyl alcohol	affects cotreatment, decreases expression, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
azoxystrobin	decreases expression	1
CGP 52608	affects binding, increases reaction	1
K 7174	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
ICG 001	increases expression	1
dorsomorphin	decreases expression, affects cotreatment	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Arsenic Trioxide	affects binding, decreases reaction	1
Acetaminophen	increases expression	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Atrazine	decreases expression	1
Cadmium	decreases expression, increases abundance	1
Copper	increases expression, affects binding	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B5JS	HAP1 CCDC92 (-) 2	Cancer cell line	Male
CVCL_B5JT	HAP1 CCDC92 (-) 3	Cancer cell line	Male
CVCL_XM51	HAP1 CCDC92 (-) 1	Cancer cell line	Male

Clinical trials (associated diseases)

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