CCDC63

Summary

CCDC63 (coiled-coil domain containing 63, HGNC:26669) is a protein-coding gene on chromosome 12q24.11, encoding Coiled-coil domain-containing protein 63 (Q8NA47). Plays a role in spermiogenesis.

Predicted to be involved in cilium movement; outer dynein arm assembly; and spermatid development. Predicted to be active in axoneme.

Source: NCBI Gene 160762 — RefSeq curated summary.

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 93 total
• MANE Select transcript: NM_152591

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26669
Approved symbol	CCDC63
Name	coiled-coil domain containing 63
Location	12q24.11
Locus type	gene with protein product
Status	Approved
Aliases	ODA5, FLJ35843
Ensembl gene	ENSG00000173093
Ensembl biotype	protein_coding
OMIM	617969
Entrez	160762

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000308208, ENST00000545036, ENST00000550317, ENST00000552694

RefSeq mRNA: 3 — MANE Select: NM_152591 NM_001286243, NM_001286244, NM_152591

CCDS: CCDS66470, CCDS73528, CCDS9151

Canonical transcript exons

ENST00000308208 — 12 exons

Exon	Start	End
ENSE00001230861	110879906	110880087
ENSE00001231240	110881115	110881296
ENSE00001290911	110898933	110899125
ENSE00001307685	110893076	110893150
ENSE00001315182	110904588	110904791
ENSE00001325598	110884030	110884250
ENSE00001327381	110852859	110852963
ENSE00002326068	110907331	110907535
ENSE00003478266	110873842	110873961
ENSE00003532905	110853405	110853574
ENSE00003556091	110858586	110858775
ENSE00003893478	110846987	110847105

Expression profiles

Bgee: expression breadth broad, 34 present calls, max score 82.57.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0319 / max 27.5162, expressed in 3 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
128011	0.0221	3
128010	0.0098	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	82.57	gold quality
right testis	UBERON:0004534	82.03	gold quality
testis	UBERON:0000473	79.80	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.52	gold quality
pancreatic ductal cell	CL:0002079	66.04	silver quality
heart right ventricle	UBERON:0002080	62.45	gold quality
myocardium	UBERON:0002349	60.59	gold quality
skeletal muscle tissue	UBERON:0001134	60.10	gold quality
nasal cavity epithelium	UBERON:0005384	59.96	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	59.68	gold quality
left ventricle myocardium	UBERON:0006566	59.67	gold quality
sperm	CL:0000019	59.64	silver quality
biceps brachii	UBERON:0001507	59.38	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	59.11	gold quality
muscle of leg	UBERON:0001383	58.88	gold quality
apex of heart	UBERON:0002098	58.44	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	58.28	gold quality
gastrocnemius	UBERON:0001388	58.22	gold quality
muscle tissue	UBERON:0002385	57.22	gold quality
quadriceps femoris	UBERON:0001377	55.83	gold quality
kidney epithelium	UBERON:0004819	55.55	gold quality
vastus lateralis	UBERON:0001379	55.46	gold quality
epithelial cell of pancreas	CL:0000083	55.38	gold quality
tibialis anterior	UBERON:0001385	55.22	silver quality
deltoid	UBERON:0001476	55.10	gold quality
cartilage tissue	UBERON:0002418	55.05	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
adult organism	UBERON:0007023	52.92	gold quality
cardiac ventricle	UBERON:0002082	51.32	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.27

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
rattus_norvegicus	Ccdc63	ENSRNOG00000034266
drosophila_melanogaster	Ccdc114	FBGN0038452

Paralogs (3): ODAD1 (ENSG00000105479), ODAD3 (ENSG00000198003), TMEM141 (ENSG00000244187)

Protein

Protein identifiers

Coiled-coil domain-containing protein 63 — Q8NA47 (reviewed: Q8NA47)

All UniProt accessions (2): Q8NA47, G3V217

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in spermiogenesis. Involved in the elongation of flagella and the formation of sperm heads.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8NA47-1	1	yes
Q8NA47-2	2

RefSeq proteins (3): NP_001273172, NP_001273173, NP_689804* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR049258	ODAD1_CC	Domain
IPR051876	ODA-DC/CCD	Family

Pfam: PF21773

UniProt features (9 total): coiled-coil region 3, chain 1, region of interest 1, compositionally biased region 1, splice variant 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NA47-F1	78.75	0.42

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 47 (showing top): GOBP_MALE_GAMETE_GENERATION, GOBP_AXONEMAL_DYNEIN_COMPLEX_ASSEMBLY, GOBP_CILIUM_ORGANIZATION, GOBP_CILIUM_MOVEMENT, GOBP_OUTER_DYNEIN_ARM_ASSEMBLY, GOBP_ORGANELLE_ASSEMBLY, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, GOBP_MICROTUBULE_BUNDLE_FORMATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOBP_CELL_PROJECTION_ORGANIZATION, GOBP_AXONEME_ASSEMBLY, GOCC_CYTOPLASMIC_REGION, GOCC_CILIUM, chr12q24, GOBP_MICROTUBULE_CYTOSKELETON_ORGANIZATION

GO Biological Process (5): cilium movement (GO:0003341), spermatid development (GO:0007286), outer dynein arm assembly (GO:0036158), spermatogenesis (GO:0007283), cell differentiation (GO:0030154)

GO Molecular Function (0):

GO Cellular Component (1): axoneme (GO:0005930)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
microtubule-based movement	1
germ cell development	1
spermatid differentiation	1
axonemal dynein complex assembly	1
developmental process involved in reproduction	1
male gamete generation	1
cellular developmental process	1
cytoskeleton	1
microtubule	1
ciliary plasm	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1141 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC63	ODAD2	Q5T2S8	793
CCDC63	ODAD3	A5D8V7	765
CCDC63	HECTD4	Q9Y4D8	700
CCDC63	ODAD4	Q96NG3	592
CCDC63	LRRC56	Q8IYG6	575
CCDC63	MNS1	Q8NEH6	565
CCDC63	OR4F6	Q8NGB9	544
CCDC63	DNAAF3	Q8N9W5	521
CCDC63	DNAAF2	Q9NVR5	511
CCDC63	CFAP36	Q96G28	510
CCDC63	DAW1	Q8N136	494
CCDC63	OR52E4	Q8NGH9	482
CCDC63	TTC29	Q8NA56	467
CCDC63	DNAAF19	Q8IW40	462
CCDC63	KCNH3	Q9ULD8	449

IntAct

4 interactions, top by confidence:

A	B	Type	Score
CCDC63	H2BC5	psi-mi:“MI:0915”(physical association)	0.400
CCDC63	H2BC9	psi-mi:“MI:0915”(physical association)	0.400
PROM1	CCDC63	psi-mi:“MI:0403”(colocalization)	0.270

BioGRID (4): CCDC63 (Proximity Label-MS), HIST1H2BH (Proximity Label-MS), CCDC63 (Proximity Label-MS), TRPM2 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0AUP1, A0JMY4, A3KQH2, D6REC4, E1C760, F1QRC1, F1RKB1, F7AEX0, Q15051, Q17QH9, Q2IA00, Q32KY1, Q3USS3, Q3V079, Q3ZC62, Q45GW3, Q4R6T7, Q4R7Y8, Q4R8R3, Q4R8Y5, Q4V8E4, Q5PQQ6, Q5XI65, Q5XIR6, Q6P0R8, Q6P5U8, Q7T0Y4, Q7Z4T9, Q80VN0, Q8BP00, Q8BRC6, Q8C6E0, Q8C9J3, Q8CDK3, Q8CDV6, Q8HZY8, Q8NA47, Q8NA54, Q8NCU4, Q8ND07

Diamond homologs: Q2T9W3, Q4V8F7, Q8CDV6, Q8NA47

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	77
Likely benign	8
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1886 predictions. Top by Δscore:

Variant	Effect	Δscore
12:110847101:CACTG:C	donor_gain	1.0000
12:110847102:ACTG:A	donor_gain	1.0000
12:110847103:CTG:C	donor_gain	1.0000
12:110847104:TG:T	donor_gain	1.0000
12:110847105:GG:G	donor_gain	1.0000
12:110847105:GGT:G	donor_loss	1.0000
12:110847106:G:GA	donor_loss	1.0000
12:110847106:G:GG	donor_gain	1.0000
12:110847107:T:A	donor_loss	1.0000
12:110852074:G:GT	donor_gain	1.0000
12:110853512:G:GT	donor_gain	1.0000
12:110853568:G:GG	donor_gain	1.0000
12:110853570:CAGTA:C	donor_gain	1.0000
12:110853572:GTA:G	donor_gain	1.0000
12:110853573:TA:T	donor_gain	1.0000
12:110853575:G:GG	donor_gain	1.0000
12:110858716:G:GT	donor_gain	1.0000
12:110858719:GACTA:G	donor_gain	1.0000
12:110873962:G:GG	donor_gain	1.0000
12:110880053:GCCAT:G	donor_gain	1.0000
12:110880057:T:TG	donor_gain	1.0000
12:110880074:GCCTA:G	donor_gain	1.0000
12:110881114:GGGT:G	acceptor_gain	1.0000
12:110881289:G:GT	donor_gain	1.0000
12:110881290:G:T	donor_gain	1.0000
12:110881293:G:GT	donor_gain	1.0000
12:110881293:GAAGG:G	donor_loss	1.0000
12:110881294:A:T	donor_gain	1.0000
12:110881294:AAGG:A	donor_loss	1.0000
12:110881310:G:GT	donor_gain	1.0000

AlphaMissense

3768 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:110904615:T:C	L457P	0.988
12:110899111:T:C	L443P	0.985
12:110898960:G:C	A393P	0.980
12:110884204:T:C	L343P	0.979
12:110904618:T:C	L458P	0.979
12:110873951:G:C	R160P	0.977
12:110879970:T:C	L185P	0.974
12:110879952:G:C	R179P	0.973
12:110881236:T:C	F265L	0.973
12:110881238:C:A	F265L	0.973
12:110881238:C:G	F265L	0.973
12:110884185:T:C	F337L	0.973
12:110884187:C:A	F337L	0.973
12:110884187:C:G	F337L	0.973
12:110853496:T:C	L34P	0.971
12:110858765:T:C	L120P	0.971
12:110873954:T:C	L161S	0.962
12:110853487:T:C	L31P	0.959
12:110904598:A:C	E451D	0.958
12:110904598:A:T	E451D	0.958
12:110879918:T:C	F168L	0.957
12:110879920:T:A	F168L	0.957
12:110879920:T:G	F168L	0.957
12:110881204:G:C	R254P	0.956
12:110899033:T:C	L417P	0.953
12:110881122:G:C	A227P	0.951
12:110858603:T:C	L66P	0.950
12:110858744:T:C	L113P	0.948
12:110904605:A:C	T454P	0.948
12:110879949:T:C	L178P	0.947

dbSNP variants (sampled 300 via entrez): RS1000078999 (12:110883252 G>C), RS1000155181 (12:110842656 G>A,T), RS1000159845 (12:110853720 G>A), RS1000193401 (12:110897456 G>C), RS1000331861 (12:110876486 G>A), RS1000334206 (12:110907260 G>A), RS1000353125 (12:110879607 G>A), RS1000388029 (12:110869764 A>G,T), RS1000396978 (12:110903594 C>A,T), RS1000441844 (12:110869508 C>T), RS1000588298 (12:110845481 G>A), RS1000679550 (12:110858530 C>A,G), RS1000737024 (12:110861380 C>G), RS1000844373 (12:110901577 T>C), RS1000872283 (12:110903964 A>G)

Disease associations

OMIM: gene MIM:617969 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

10 associations (top):

Study	Trait	p-value
GCST000954_3	Alcohol consumption	1.000000e-23
GCST000994_2	Drinking behavior	9.000000e-120
GCST001842_1	Drinking behavior	3.000000e-215
GCST004267_5	Blood osmolality (transformed sodium)	2.000000e-06
GCST004404_2	Alcohol consumption (drinkers vs non-drinkers)	4.000000e-28
GCST005878_1	Metabolic syndrome (multivariate analysis)	2.000000e-09
GCST005878_2	Metabolic syndrome (multivariate analysis)	8.000000e-09
GCST008103_58	Bipolar disorder	4.000000e-07
GCST010083_173	Hemoglobin levels	1.000000e-10
GCST010476_21	Myocardial infarction	5.000000e-07

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004329	alcohol drinking
EFO:0004315	drinking behavior
EFO:0000195	metabolic syndrome
EFO:0004509	hemoglobin measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression, increases methylation	3
pirinixic acid	increases activity, increases expression, affects binding	1
bisphenol A	decreases expression	1
ethyl-p-hydroxybenzoate	decreases expression	1
benzo(e)pyrene	affects methylation	1
CGP 52608	affects binding, increases reaction	1
nutlin 3	affects cotreatment, increases expression	1
jinfukang	increases expression, affects cotreatment	1
Ethanol	affects response to substance	1
Atrazine	increases expression	1
Camptothecin	increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Dactinomycin	affects cotreatment, increases expression	1
Methapyrilene	affects methylation	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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