CCDC87

Summary

CCDC87 (coiled-coil domain containing 87, HGNC:25579) is a protein-coding gene on chromosome 11q13.2, encoding Coiled-coil domain-containing protein 87 (Q9NVE4). Plays a role in spermatogenesis, where it is important for normal sperm head morphology.

Predicted to be involved in positive regulation of acrosome reaction and positive regulation of fertilization.

Source: NCBI Gene 55231 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 141 total
• MANE Select transcript: NM_018219

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25579
Approved symbol	CCDC87
Name	coiled-coil domain containing 87
Location	11q13.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ10786
Ensembl gene	ENSG00000182791
Ensembl biotype	protein_coding
Entrez	55231

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000333861

RefSeq mRNA: 1 — MANE Select: NM_018219 NM_018219

CCDS: CCDS8145

Canonical transcript exons

ENST00000333861 — 1 exons

Exon	Start	End
ENSE00001315117	66590176	66593063

Expression profiles

Bgee: expression breadth ubiquitous, 107 present calls, max score 84.14.

FANTOM5 (CAGE): breadth broad, TPM avg 0.8894 / max 61.3476, expressed in 449 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
120817	0.7778	395
120818	0.1116	47

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.14	gold quality
left testis	UBERON:0004533	78.29	gold quality
right testis	UBERON:0004534	77.80	gold quality
testis	UBERON:0000473	76.23	gold quality
triceps brachii	UBERON:0001509	65.06	gold quality
adult organism	UBERON:0007023	64.93	gold quality
gluteal muscle	UBERON:0002000	64.88	gold quality
male germ cell	CL:0000015	62.49	gold quality
sperm	CL:0000019	62.02	gold quality
tongue squamous epithelium	UBERON:0006919	61.67	gold quality
secondary oocyte	CL:0000655	61.60	gold quality
olfactory bulb	UBERON:0002264	61.46	gold quality
type B pancreatic cell	CL:0000169	61.33	gold quality
islet of Langerhans	UBERON:0000006	60.91	gold quality
quadriceps femoris	UBERON:0001377	60.41	gold quality
vastus lateralis	UBERON:0001379	59.88	gold quality
nasal cavity epithelium	UBERON:0005384	57.40	gold quality
pancreatic ductal cell	CL:0002079	56.16	silver quality
prefrontal cortex	UBERON:0000451	56.02	gold quality
cortical plate	UBERON:0005343	54.74	silver quality
myocardium	UBERON:0002349	54.55	gold quality
muscle tissue	UBERON:0002385	54.11	silver quality
oocyte	CL:0000023	53.29	gold quality
smooth muscle tissue	UBERON:0001135	53.18	gold quality
deltoid	UBERON:0001476	52.69	gold quality
epithelial cell of pancreas	CL:0000083	52.31	gold quality
Brodmann (1909) area 46	UBERON:0006483	51.90	gold quality
left ventricle myocardium	UBERON:0006566	51.86	gold quality
hindlimb stylopod muscle	UBERON:0004252	50.09	silver quality
thymus	UBERON:0002370	49.94	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.13

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

17 targeting CCDC87, 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-570-3P	99.96	72.41	4910
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-6857-5P	99.87	65.32	985
HSA-MIR-6079	99.84	68.54	1170
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-4708-3P	99.51	67.99	870
HSA-MIR-3612	99.45	66.02	1333
HSA-MIR-650	99.45	65.77	1309
HSA-MIR-6828-5P	99.31	69.21	1433
HSA-MIR-3190-5P	98.87	64.89	1345
HSA-MIR-4450	98.26	68.35	725
HSA-MIR-1226-5P	96.50	65.28	643
HSA-MIR-6782-5P	96.45	64.42	612
HSA-MIR-601	95.98	67.59	421
HSA-MIR-6888-5P	95.89	63.78	831
HSA-MIR-4474-5P	94.23	67.95	568

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccdc87	ENSDARG00000045683
mus_musculus	Ccdc87	ENSMUSG00000067872
rattus_norvegicus	Ccdc87	ENSRNOG00000071751

Protein

Protein identifiers

Coiled-coil domain-containing protein 87 — Q9NVE4 (reviewed: Q9NVE4)

All UniProt accessions (1): Q9NVE4

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in spermatogenesis, where it is important for normal sperm head morphology. Also required for the acrosome reaction and thus normal male fertility.

Similarity. Belongs to the CCDC87 family.

RefSeq proteins (1): NP_060689* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR037383	CCDC87	Family

Pfam: PF03999

UniProt features (6 total): sequence variant 2, sequence conflict 2, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NVE4-F1	62.53	0.09

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 58 (showing top): GOBP_SINGLE_FERTILIZATION, GOBP_POSITIVE_REGULATION_OF_REPRODUCTIVE_PROCESS, GOBP_MALE_GAMETE_GENERATION, chr11q13, GOBP_REGULATION_OF_REPRODUCTIVE_PROCESS, GOBP_REGULATION_OF_ACROSOME_REACTION, GOBP_ACROSOME_REACTION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, NIKOLSKY_BREAST_CANCER_11Q12_Q14_AMPLICON, GOBP_FERTILIZATION, YGCGYRCGC_UNKNOWN, HATADA_METHYLATED_IN_LUNG_CANCER_UP, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_36HR, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D, GOBP_REGULATION_OF_FERTILIZATION

GO Biological Process (5): spermatogenesis (GO:0007283), single fertilization (GO:0007338), cell differentiation (GO:0030154), positive regulation of fertilization (GO:1905516), positive regulation of acrosome reaction (GO:2000344)

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
fertilization	2
positive regulation of reproductive process	2
developmental process involved in reproduction	1
male gamete generation	1
cellular developmental process	1
regulation of fertilization	1
acrosome reaction	1
regulation of acrosome reaction	1
binding	1

Protein interactions and networks

STRING

182 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC87	DCDC2B	A2VCK2	561
CCDC87	MIX23	Q4VC31	513
CCDC87	CCDC97	Q96F63	479
CCDC87	PRR14L	Q5THK1	477
CCDC87	FAM184B	Q9ULE4	451
CCDC87	ARHGAP6	O43182	365
CCDC87	UBR4	Q5T4S7	361
CCDC87	MIPEP	Q99797	344
CCDC87	ZNF451	Q9Y4E5	337
CCDC87	ANO5	Q75V66	324
CCDC87	ZNF329	Q86UD4	305
CCDC87	MTCL1	Q9Y4B5	301
CCDC87	PDE1C	Q14123	282
CCDC87	ZNF592	Q92610	262
CCDC87	SUN2	Q9UH99	251

IntAct

30 interactions, top by confidence:

A	B	Type	Score
GOLGA2	CCDC87	psi-mi:“MI:0915”(physical association)	0.720
SUN2	LMNA	psi-mi:“MI:0914”(association)	0.720
TRIM27	CCDC87	psi-mi:“MI:0915”(physical association)	0.560
CCDC87	KRT15	psi-mi:“MI:0915”(physical association)	0.560
USHBP1	CCDC87	psi-mi:“MI:0915”(physical association)	0.560
TRIM54	CCDC87	psi-mi:“MI:0915”(physical association)	0.560
CCDC87	USHBP1	psi-mi:“MI:0915”(physical association)	0.560
CCDC87	TRIM27	psi-mi:“MI:0915”(physical association)	0.560
CCDC87	TRIM54	psi-mi:“MI:0915”(physical association)	0.560
CDR2	CCDC87	psi-mi:“MI:0915”(physical association)	0.560
CCDC87	STAT3	psi-mi:“MI:0915”(physical association)	0.490
STAT3	CCDC87	psi-mi:“MI:0915”(physical association)	0.490
YAP1	CCDC87	psi-mi:“MI:0407”(direct interaction)	0.440
CCDC87	KASH5	psi-mi:“MI:0915”(physical association)	0.370
SUN2	MYO1C	psi-mi:“MI:0914”(association)	0.350
MKI67	ARHGAP10	psi-mi:“MI:0914”(association)	0.350
ESR2	PSMD11	psi-mi:“MI:0914”(association)	0.350
CCDC87	GOLGA2	psi-mi:“MI:0915”(physical association)	0.000
CCDC87	CDR2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (23): CCDC87 (Two-hybrid), CCDC87 (Two-hybrid), CCDC87 (Two-hybrid), TRIM54 (Two-hybrid), USHBP1 (Two-hybrid), CCDC155 (Two-hybrid), CCDC87 (Two-hybrid), CCDC87 (Affinity Capture-MS), CCDC87 (Affinity Capture-MS), CCDC87 (Affinity Capture-RNA), CCDC87 (Two-hybrid), CCDC87 (Two-hybrid), CCDC87 (Affinity Capture-MS), CCDC87 (Affinity Capture-MS), CCDC87 (Protein-peptide)

ESM2 similar proteins: A0JNF3, A1L253, A2AHC3, A3KP40, A5PLN7, A5WUN7, A6H5Y1, B1AXH1, B2GUZ2, D3Z8E6, E9PV87, E9Q309, H6D7E6, O14513, O60303, P0CAX8, P28290, Q14B48, Q1G7G9, Q2KHM9, Q32LN6, Q49A88, Q566N9, Q5HYW2, Q5PQL8, Q5REU9, Q5T5Y3, Q5VT06, Q60664, Q66H35, Q66MI6, Q6A000, Q6AYP4, Q6NSV7, Q6NXP0, Q6ZRS4, Q6ZVD7, Q80VP2, Q8BJS7, Q8CB14

Diamond homologs: Q8CDL9, Q9NVE4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	131
Likely benign	10
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

97 predictions. Top by Δscore:

Variant	Effect	Δscore
11:66592872:G:T	donor_gain	0.9900
11:66593041:G:GT	donor_gain	0.9900
11:66592872:G:GT	donor_gain	0.9700
11:66593042:A:T	donor_gain	0.9700
11:66593058:GTTAC:G	donor_gain	0.9700
11:66593059:TTACT:T	donor_gain	0.9700
11:66593056:GGGT:G	donor_gain	0.9300
11:66592941:G:GT	donor_gain	0.9100
11:66593047:A:T	donor_gain	0.8900
11:66592941:G:T	donor_gain	0.8800
11:66592924:G:T	donor_gain	0.8700
11:66592969:T:TA	donor_gain	0.8700
11:66592970:G:GA	donor_gain	0.8700
11:66592876:G:GT	donor_gain	0.8600
11:66592971:G:GG	donor_gain	0.8600
11:66593062:C:G	donor_gain	0.8500
11:66592968:G:GT	donor_gain	0.8100
11:66592924:G:GT	donor_gain	0.8000
11:66592992:C:T	donor_gain	0.8000
11:66592968:GTG:G	donor_gain	0.7900
11:66592986:C:G	donor_gain	0.7400
11:66592967:GGTG:G	donor_gain	0.7300
11:66592955:G:GT	donor_gain	0.7100
11:66592964:GCCG:G	donor_gain	0.7000
11:66592873:A:T	donor_gain	0.6600
11:66592966:C:A	donor_gain	0.6600
11:66592963:AGCC:A	donor_gain	0.5700
11:66593062:C:CG	donor_gain	0.5600
11:66592991:GC:G	donor_gain	0.5200
11:66592966:CGGTG:C	donor_loss	0.5100

AlphaMissense

5512 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:66592644:G:C	S124R	0.987
11:66592644:G:T	S124R	0.987
11:66592646:T:G	S124R	0.987
11:66592733:A:G	W95R	0.986
11:66592733:A:T	W95R	0.986
11:66592530:G:C	C162W	0.985
11:66592314:G:C	S234R	0.984
11:66592314:G:T	S234R	0.984
11:66592316:T:G	S234R	0.984
11:66592744:A:G	L91P	0.984
11:66592636:A:G	L127P	0.981
11:66592647:G:C	S123R	0.981
11:66592647:G:T	S123R	0.981
11:66592649:T:G	S123R	0.981
11:66592681:A:G	L112P	0.980
11:66592672:C:G	R115P	0.979
11:66592543:A:G	L158P	0.977
11:66592532:A:G	C162R	0.975
11:66592492:A:G	L175P	0.971
11:66592731:C:A	W95C	0.969
11:66592731:C:G	W95C	0.969
11:66592519:A:G	L166P	0.967
11:66592531:C:T	C162Y	0.967
11:66592678:C:G	R113P	0.966
11:66592669:A:G	L116P	0.964
11:66591177:A:C	F613L	0.963
11:66591177:A:T	F613L	0.963
11:66591179:A:G	F613L	0.963
11:66591192:G:C	F608L	0.962
11:66591192:G:T	F608L	0.962

dbSNP variants (sampled 300 via entrez): RS1000727023 (11:66594179 A>G), RS1001942552 (11:66594791 A>C,T), RS1002857887 (11:66592715 C>A,G,T), RS1003140973 (11:66592929 C>A), RS1003191553 (11:66593926 T>C), RS1003473448 (11:66594225 G>C), RS1003701432 (11:66589861 G>C), RS1003732738 (11:66589681 C>A,T), RS1005670519 (11:66589711 C>A), RS1005707688 (11:66594299 C>T), RS1006371587 (11:66594803 C>T), RS1007572179 (11:66594965 A>C), RS1007614575 (11:66590396 T>A), RS1008372278 (11:66591962 T>A,C), RS1010244995 (11:66594220 G>A)

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

2 associations (top):

Study	Trait	p-value
GCST001241_12	Bipolar disorder	2.000000e-07
GCST007576_250	Chronotype	5.000000e-13

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008328	chronotype measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
(+)-JQ1 compound	increases expression	2
Benzo(a)pyrene	increases methylation, affects methylation, increases expression	2
sotorasib	affects cotreatment, increases expression	1
sodium arsenite	increases expression	1
ferrous chloride	decreases expression	1
trametinib	increases expression, affects cotreatment	1
NVP-BKM120	increases expression, affects cotreatment	1
Sunitinib	decreases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Okadaic Acid	increases expression	1
S-Nitrosoglutathione	increases expression	1

Clinical trials (associated diseases)

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