CCDC159

Summary

CCDC159 (coiled-coil domain containing 159, HGNC:26996) is a protein-coding gene on chromosome 19p13.2, encoding Coiled-coil domain-containing protein 159 (P0C7I6). Functions during spermatid development; may participate in the centrosome reduction procedure of spermatids and is required for the formation of the connecting piece/sperm head-tail coupling apparatus (HTCA) and the correct and tight attachment of the flagellum to the nuclear en….

Predicted to be involved in spermatid development. Predicted to act upstream of or within several processes, including regulation of phosphatase activity; single fertilization; and sperm flagellum assembly. Predicted to be located in sperm head-tail coupling apparatus.

Source: NCBI Gene 126075 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 68 total
• MANE Select transcript: NM_001080503

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26996
Approved symbol	CCDC159
Name	coiled-coil domain containing 159
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000183401
Ensembl biotype	protein_coding
Entrez	126075

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 13 protein_coding, 7 retained_intron, 3 protein_coding_CDS_not_defined, 3 nonsense_mediated_decay

ENST00000458408, ENST00000586451, ENST00000586479, ENST00000587100, ENST00000587531, ENST00000587868, ENST00000588464, ENST00000588592, ENST00000588790, ENST00000588821, ENST00000589016, ENST00000589022, ENST00000589186, ENST00000589477, ENST00000590054, ENST00000590636, ENST00000590919, ENST00000591260, ENST00000591691, ENST00000592723, ENST00000853369, ENST00000853370, ENST00000853371, ENST00000853372, ENST00000853373, ENST00000937509

RefSeq mRNA: 1 — MANE Select: NM_001080503 NM_001080503

CCDS: CCDS45976

Canonical transcript exons

ENST00000458408 — 11 exons

Exon	Start	End
ENSE00001674872	11346519	11346627
ENSE00003518810	11354873	11354944
ENSE00003524243	11350118	11350199
ENSE00003537579	11354580	11354696
ENSE00003575455	11353451	11353572
ENSE00003578997	11349938	11350026
ENSE00003582524	11350808	11351003
ENSE00003654679	11352057	11352133
ENSE00003657413	11349654	11349687
ENSE00003788521	11351906	11351973
ENSE00003892265	11353792	11353874

Expression profiles

Bgee: expression breadth ubiquitous, 221 present calls, max score 97.88.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.5702 / max 171.3050, expressed in 1787 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
173910	7.7076	1742
173911	3.5034	1291
173908	0.1655	116
173912	0.1006	24
173909	0.0931	67

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	97.88	gold quality
right adrenal gland cortex	UBERON:0035827	97.27	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	97.14	gold quality
right adrenal gland	UBERON:0001233	97.09	gold quality
left adrenal gland cortex	UBERON:0035825	96.60	gold quality
right testis	UBERON:0004534	96.54	gold quality
left testis	UBERON:0004533	96.47	gold quality
left adrenal gland	UBERON:0001234	96.41	gold quality
right uterine tube	UBERON:0001302	96.35	gold quality
sural nerve	UBERON:0015488	96.24	gold quality
adenohypophysis	UBERON:0002196	96.20	gold quality
right lobe of thyroid gland	UBERON:0001119	96.12	gold quality
monocyte	CL:0000576	95.89	gold quality
left ovary	UBERON:0002119	95.79	gold quality
right ovary	UBERON:0002118	95.77	gold quality
leukocyte	CL:0000738	95.61	gold quality
adrenal cortex	UBERON:0001235	95.60	gold quality
left uterine tube	UBERON:0001303	95.37	gold quality
left lobe of thyroid gland	UBERON:0001120	95.36	gold quality
right lobe of liver	UBERON:0001114	95.31	gold quality
spleen	UBERON:0002106	95.27	gold quality
spinal cord	UBERON:0002240	95.20	gold quality
endocervix	UBERON:0000458	95.17	gold quality
pituitary gland	UBERON:0000007	95.11	gold quality
body of stomach	UBERON:0001161	95.03	gold quality
body of uterus	UBERON:0009853	95.02	gold quality
apex of heart	UBERON:0002098	94.91	gold quality
adrenal gland	UBERON:0002369	94.90	gold quality
muscle layer of sigmoid colon	UBERON:0035805	94.74	gold quality
thyroid gland	UBERON:0002046	94.59	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-CURD-112	yes	5.70
E-ANND-3	yes	3.44
E-GEOD-99795	no	62.60

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccdc159	ENSMUSG00000006241
rattus_norvegicus	Ccdc159	ENSRNOG00000011799

Protein

Protein identifiers

Coiled-coil domain-containing protein 159 — P0C7I6 (reviewed: P0C7I6)

All UniProt accessions (8): K7EJK8, K7EKC7, K7EKR4, K7EKU9, K7EN56, K7ENC2, K7EPH8, P0C7I6

UniProt curated annotations — full annotation on UniProt →

Function. Functions during spermatid development; may participate in the centrosome reduction procedure of spermatids and is required for the formation of the connecting piece/sperm head-tail coupling apparatus (HTCA) and the correct and tight attachment of the flagellum to the nuclear envelope.

Subunit / interactions. Interacts with DYNLT2. Interacts with GGNBP1. Interacts with OSBP2.

Isoforms (4)

UniProt ID	Names	Canonical?
P0C7I6-2	2	yes
P0C7I6-6	3
P0C7I6-7	4
P0C7I6-8	5

RefSeq proteins (1): NP_001073972* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR039284	CCDC159/163	Family

UniProt features (7 total): splice variant 3, chain 1, region of interest 1, coiled-coil region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0C7I6-F1	77.97	0.54

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 108 (showing top): GOBP_SINGLE_FERTILIZATION, GOBP_MALE_GAMETE_GENERATION, GOBP_CILIUM_ORGANIZATION, GOBP_CILIUM_MOVEMENT, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, GOBP_ORGANELLE_ASSEMBLY, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOBP_MOTILE_CILIUM_ASSEMBLY, GOBP_CELL_PROJECTION_ORGANIZATION, GOBP_FERTILIZATION, chr19p13, KOYAMA_SEMA3B_TARGETS_DN, ASH1L_TARGET_GENES, CBX5_TARGET_GENES

GO Biological Process (6): spermatid development (GO:0007286), single fertilization (GO:0007338), gene expression (GO:0010467), sperm flagellum assembly (GO:0120316), spermatogenesis (GO:0007283), cell differentiation (GO:0030154)

GO Molecular Function (0):

GO Cellular Component (1): sperm head-tail coupling apparatus (GO:0120212)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
developmental process involved in reproduction	2
germ cell development	1
spermatid differentiation	1
fertilization	1
macromolecule biosynthetic process	1
spermatid development	1
flagellated sperm motility	1
motile cilium assembly	1
male gamete generation	1
cellular developmental process	1
cellular anatomical structure	1

Protein interactions and networks

STRING

66 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC159	CCDC146	Q8IYE0	517
CCDC159	PLPPR2	Q96GM1	506
CCDC159	SWSAP1	Q6NVH7	479
CCDC159	SINHCAF	Q9NP50	474
CCDC159	CIAO3	Q9H6Q4	470
CCDC159	UROS	P10746	468
CCDC159	TMEM205	Q6UW68	451
CCDC159	RELT	Q969Z4	429
CCDC159	SASH1	O94885	391
CCDC159	ANXA8L1	Q5VT79	352
CCDC159	RNF7	Q9UBF6	345
CCDC159	DOCK6	Q96HP0	324
CCDC159	FLCN	Q8NFG4	321
CCDC159	GREB1	Q4ZG55	310
CCDC159	RAB3D	O95716	290

IntAct

2 interactions, top by confidence:

A	B	Type	Score
CCDC159	MBD1	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (2): SLTM (Cross-Linking-MS (XL-MS)), CCDC159 (Two-hybrid)

ESM2 similar proteins: A2IDD5, A4IFI1, A8MT33, D3Z5T1, E9PGG2, E9PVD1, P0C7I6, P97432, P97817, Q01850, Q2M243, Q2T9R2, Q32LC2, Q3SYW5, Q3TVI4, Q3TYX8, Q3USH1, Q499E4, Q4KMA0, Q4R3X1, Q501R9, Q569K6, Q5R8C5, Q5RD40, Q5SWA1, Q5T7N3, Q6P9J5, Q6ZNE9, Q6ZSG2, Q80VJ8, Q86Z20, Q8BFW3, Q8BVF4, Q8C0G2, Q8C963, Q8IYY4, Q8K3I4, Q8N0S2, Q8N6L0, Q8NFW9

Diamond homologs: P0C7I6, Q8C963

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	46
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2400 predictions. Top by Δscore:

Variant	Effect	Δscore
19:11345248:GTAC:G	donor_loss	1.0000
19:11345249:TAC:T	donor_loss	1.0000
19:11349933:CACA:C	acceptor_loss	1.0000
19:11349934:ACAGC:A	acceptor_loss	1.0000
19:11349935:CAGC:C	acceptor_loss	1.0000
19:11349936:A:AG	acceptor_gain	1.0000
19:11349937:G:GC	acceptor_gain	1.0000
19:11349937:GC:G	acceptor_gain	1.0000
19:11349937:GCC:G	acceptor_gain	1.0000
19:11349937:GCCA:G	acceptor_gain	1.0000
19:11349937:GCCAA:G	acceptor_gain	1.0000
19:11350022:CCAAG:C	donor_loss	1.0000
19:11350023:CAAG:C	donor_loss	1.0000
19:11350024:AAG:A	donor_loss	1.0000
19:11350025:AGGT:A	donor_loss	1.0000
19:11350026:GG:G	donor_loss	1.0000
19:11350027:G:GA	donor_loss	1.0000
19:11350028:T:A	donor_loss	1.0000
19:11350197:AAG:A	donor_loss	1.0000
19:11350198:AGG:A	donor_loss	1.0000
19:11350199:GG:G	donor_loss	1.0000
19:11350200:GT:G	donor_loss	1.0000
19:11350201:T:G	donor_loss	1.0000
19:11350990:G:GT	donor_gain	1.0000
19:11352055:A:AG	acceptor_gain	1.0000
19:11352056:G:GG	acceptor_gain	1.0000
19:11352056:GAAGC:G	acceptor_gain	1.0000
19:11352129:GCAAA:G	donor_gain	1.0000
19:11352134:G:GG	donor_gain	1.0000
19:11353537:G:GT	donor_gain	1.0000

AlphaMissense

1960 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:11350131:T:C	L53P	0.991
19:11350152:T:C	L60S	0.991
19:11350127:T:C	F52L	0.989
19:11350129:C:A	F52L	0.989
19:11350129:C:G	F52L	0.989
19:11350010:T:C	L43S	0.984
19:11351929:T:C	L149P	0.983
19:11351909:G:C	K142N	0.982
19:11351909:G:T	K142N	0.982
19:11351971:T:C	L163P	0.982
19:11350121:T:C	F50L	0.981
19:11350123:C:A	F50L	0.981
19:11350123:C:G	F50L	0.981
19:11350185:T:C	I71T	0.980
19:11350131:T:A	L53Q	0.979
19:11350122:T:C	F50S	0.976
19:11350139:T:C	S56P	0.974
19:11351917:T:C	L145P	0.973
19:11349998:T:C	L39P	0.972
19:11350194:T:C	L74P	0.972
19:11353455:T:C	L191P	0.968
19:11350131:T:G	L53R	0.967
19:11353560:T:C	L226P	0.967
19:11351913:T:C	F144L	0.964
19:11351915:C:A	F144L	0.964
19:11351915:C:G	F144L	0.964
19:11350015:G:C	A45P	0.963
19:11350185:T:G	I71S	0.961
19:11350994:T:C	I138T	0.961
19:11350183:G:C	K70N	0.960

dbSNP variants (sampled 300 via entrez): RS1000172972 (19:11354992 C>A,T), RS1000212178 (19:11351302 C>A,T), RS1000270331 (19:11344732 G>C), RS1000949909 (19:11349770 C>A,T), RS1001168866 (19:11352817 G>A), RS1001271723 (19:11346682 G>A,T), RS1001362699 (19:11351381 G>A), RS1001411563 (19:11351039 G>A), RS1001620277 (19:11353136 T>C), RS1002668936 (19:11345023 T>A,C,G), RS1003004280 (19:11349272 G>A), RS1003334766 (19:11348208 G>A), RS1003916260 (19:11354305 G>A), RS1003930313 (19:11349026 A>T), RS1004010686 (19:11350885 T>C,G)

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

0 associations (top):

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
rs7251786	CCDC159, PLPPR2, TMEM205		0.00	0

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
triphenyl phosphate	affects expression	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
bisphenol S	increases expression	1
jinfukang	affects cotreatment, increases expression	1
Sunitinib	decreases expression	1
Air Pollutants	increases abundance, affects expression	1
Benzo(a)pyrene	decreases methylation	1
Cisplatin	affects cotreatment, increases expression	1
Estradiol	decreases expression	1
Nicotine	increases expression	1
Ozone	affects expression, increases abundance	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	increases expression	1
Triclosan	increases expression	1
Valproic Acid	increases methylation	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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