CCNYL1

Summary

CCNYL1 (cyclin Y like 1, HGNC:26868) is a protein-coding gene on chromosome 2q33.3, encoding Cyclin-Y-like protein 1 (Q8N7R7). Key regulator of Wnt signaling implicated in various biological processes including male fertility, embryonic neurogenesis and cortex development.

Predicted to enable protein kinase binding activity. Predicted to be involved in regulation of canonical Wnt signaling pathway. Predicted to act upstream of or within flagellated sperm motility; regulation of protein kinase activity; and spermatogenesis. Located in plasma membrane.

Source: NCBI Gene 151195 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 44 total
• MANE Select transcript: NM_001330218

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26868
Approved symbol	CCNYL1
Name	cyclin Y like 1
Location	2q33.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ40432
Ensembl gene	ENSG00000163249
Ensembl biotype	protein_coding
OMIM	620559
Entrez	151195

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 10 protein_coding, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000295414, ENST00000339882, ENST00000392209, ENST00000420321, ENST00000420822, ENST00000452312, ENST00000468768, ENST00000650811, ENST00000930497, ENST00000930498, ENST00000930499, ENST00000930500, ENST00000930501

RefSeq mRNA: 3 — MANE Select: NM_001330218 NM_001142300, NM_001330218, NM_152523

CCDS: CCDS2377, CCDS46503, CCDS82564

Canonical transcript exons

ENST00000295414 — 10 exons

Exon	Start	End
ENSE00001072745	207733947	207734047
ENSE00001286242	207740655	207740706
ENSE00001286266	207726842	207726876
ENSE00001286291	207753588	207756174
ENSE00001755884	207711640	207712116
ENSE00002433124	207724800	207724874
ENSE00003525108	207742223	207742342
ENSE00003578398	207747047	207747213
ENSE00003602165	207750957	207751119
ENSE00003691050	207737411	207737446

Expression profiles

Bgee: expression breadth ubiquitous, 218 present calls, max score 98.84.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.2811 / max 248.5179, expressed in 1802 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
24896	15.4118	1796
24894	1.2890	686
24895	0.5803	353

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	98.84	gold quality
oocyte	CL:0000023	98.52	gold quality
sperm	CL:0000019	95.92	gold quality
rectum	UBERON:0001052	89.66	gold quality
right coronary artery	UBERON:0001625	88.36	gold quality
mucosa of stomach	UBERON:0001199	88.10	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.98	gold quality
calcaneal tendon	UBERON:0003701	87.60	gold quality
body of pancreas	UBERON:0001150	87.28	gold quality
esophagus squamous epithelium	UBERON:0006920	87.03	gold quality
bone marrow cell	CL:0002092	87.02	gold quality
mucosa of transverse colon	UBERON:0004991	87.00	gold quality
esophagus mucosa	UBERON:0002469	86.63	gold quality
transverse colon	UBERON:0001157	86.53	gold quality
colonic epithelium	UBERON:0000397	85.69	gold quality
mucosa of sigmoid colon	UBERON:0004993	85.41	gold quality
lower esophagus mucosa	UBERON:0035834	85.37	gold quality
pancreas	UBERON:0001264	85.24	gold quality
right lobe of liver	UBERON:0001114	85.03	gold quality
monocyte	CL:0000576	85.02	gold quality
smooth muscle tissue	UBERON:0001135	84.95	gold quality
islet of Langerhans	UBERON:0000006	84.80	gold quality
leukocyte	CL:0000738	84.76	gold quality
colonic mucosa	UBERON:0000317	84.51	gold quality
esophagus	UBERON:0001043	84.39	gold quality
left coronary artery	UBERON:0001626	84.36	gold quality
colon	UBERON:0001155	84.32	gold quality
omental fat pad	UBERON:0010414	84.24	gold quality
peritoneum	UBERON:0002358	84.13	gold quality
large intestine	UBERON:0000059	84.12	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	11.48
E-ENAD-17	no	46.16

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

131 targeting CCNYL1, 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-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-767-5P	99.95	70.85	993
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccnyl1	ENSDARG00000099692
mus_musculus	Ccnyl1	ENSMUSG00000070871
rattus_norvegicus	Ccnyl1	ENSRNOG00000023807
drosophila_melanogaster	CycY	FBGN0032378
caenorhabditis_elegans		WBGENE00022697

Paralogs (2): CCNY (ENSG00000108100), CCNYL1B (ENSG00000284209)

Protein

Protein identifiers

Cyclin-Y-like protein 1 — Q8N7R7 (reviewed: Q8N7R7)

All UniProt accessions (5): A0A494C0K2, C9IYB8, Q8N7R7, H7BZD2, H7C0P7

UniProt curated annotations — full annotation on UniProt →

Function. Key regulator of Wnt signaling implicated in various biological processes including male fertility, embryonic neurogenesis and cortex development. Activates the cyclin-dependent kinase CDK16, and promotes sperm maturation.

Subunit / interactions. Interacts with CDK16; this interaction mutually increases the stability of CDK16 and CCNYL1 and increases the kinase activity of CDK16.

Subcellular location. Cell membrane.

Similarity. Belongs to the cyclin family. Cyclin Y subfamily.

Isoforms (3)

UniProt ID	Names	Canonical?
Q8N7R7-1	1	yes
Q8N7R7-2	2
Q8N7R7-3	3

RefSeq proteins (3): NP_001135772, NP_001317147, NP_689736 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006671	Cyclin_N	Domain
IPR012399	Cyclin_Y	Family
IPR013763	Cyclin-like_dom	Domain
IPR036915	Cyclin-like_sf	Homologous_superfamily

Pfam: PF00134

UniProt features (8 total): modified residue 4, splice variant 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N7R7-F1	75.10	0.47

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 (4): 67, 105, 112, 344

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 176 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, GOBP_REGULATION_OF_WNT_SIGNALING_PATHWAY, GOBP_MALE_GAMETE_GENERATION, GGGTGGRR_PAX4_03, GOMF_KINASE_ACTIVATOR_ACTIVITY, GOBP_CANONICAL_WNT_SIGNALING_PATHWAY, GOBP_CILIUM_MOVEMENT, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, ZIC1_01, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN, USF_02, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, MASSARWEH_TAMOXIFEN_RESISTANCE_UP, MAX_01

GO Biological Process (7): regulation of protein phosphorylation (GO:0001932), spermatogenesis (GO:0007283), nervous system development (GO:0007399), cell differentiation (GO:0030154), flagellated sperm motility (GO:0030317), regulation of canonical Wnt signaling pathway (GO:0060828), regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)

GO Molecular Function (2): protein kinase binding (GO:0019901), protein binding (GO:0005515)

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein phosphorylation	1
regulation of protein modification process	1
regulation of phosphorylation	1
developmental process involved in reproduction	1
male gamete generation	1
system development	1
cellular developmental process	1
cilium-dependent cell motility	1
cilium movement involved in cell motility	1
sperm motility	1
regulation of Wnt signaling pathway	1
canonical Wnt signaling pathway	1
cyclin-dependent protein serine/threonine kinase activity	1
regulation of protein serine/threonine kinase activity	1
kinase binding	1
binding	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

596 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCNYL1	CDK16	Q00536	857
CCNYL1	CDK14	O94921	573
CCNYL1	METTL21A	Q8WXB1	565
CCNYL1	ZNF614	Q8N883	544
CCNYL1	CLRN3	Q8NCR9	492
CCNYL1	TUBG2	Q9NRH3	465
CCNYL1	ZNF211	Q13398	464
CCNYL1	SPEM1	Q8N4L4	453
CCNYL1	CD300LB	A8K4G0	451
CCNYL1	CAMSAP1	Q5T5Y3	449
CCNYL1	PLEKHM3	Q6ZWE6	441
CCNYL1	CYB5R2	Q6BCY4	433
CCNYL1	LPXN	O60711	426
CCNYL1	SMC6	Q96SB8	426
CCNYL1	HSF2BP	O75031	422

IntAct

48 interactions, top by confidence:

A	B	Type	Score
CDK16	CCNYL1	psi-mi:“MI:0914”(association)	0.800
CDK16	CCNYL1	psi-mi:“MI:0915”(physical association)	0.800
BIRC2	HTRA2	psi-mi:“MI:0914”(association)	0.650
GYPA	TCAF2	psi-mi:“MI:0914”(association)	0.640
CDK16	CDK17	psi-mi:“MI:0914”(association)	0.620
FYTTD1	UBA6	psi-mi:“MI:0914”(association)	0.530
HOXB5	VPS37C	psi-mi:“MI:0914”(association)	0.530
GJB7	PALM3	psi-mi:“MI:0914”(association)	0.530
TMEM185A	TSPAN6	psi-mi:“MI:0914”(association)	0.530
PI4K2A	GABARAP	psi-mi:“MI:0914”(association)	0.530
TAS2R7	ATP2B4	psi-mi:“MI:0914”(association)	0.500
YWHAB	PLEKHG3	psi-mi:“MI:0914”(association)	0.480
GPC1	SNAP23	psi-mi:“MI:0915”(physical association)	0.400
GPC1	GANAB	psi-mi:“MI:0915”(physical association)	0.400
CDK16	PKM	psi-mi:“MI:0914”(association)	0.350
CKAP5	TACC3	psi-mi:“MI:0914”(association)	0.350
RTEL1-TNFRSF6B	FAM13A	psi-mi:“MI:0914”(association)	0.350
WEE1	CEP350	psi-mi:“MI:0914”(association)	0.350
CDK16	YWHAQ	psi-mi:“MI:0914”(association)	0.350
CDK17	ACACB	psi-mi:“MI:0914”(association)	0.350
YWHAE	DEPDC5	psi-mi:“MI:0914”(association)	0.350
HIDE1	TMEM120B	psi-mi:“MI:0914”(association)	0.350
GYPA	HYKK	psi-mi:“MI:0914”(association)	0.350
DUSP22	POTEF	psi-mi:“MI:0914”(association)	0.350
CERS2	VPS37C	psi-mi:“MI:0914”(association)	0.350
TACSTD2	RIMOC1	psi-mi:“MI:0914”(association)	0.350
HORMAD2	WASH3P	psi-mi:“MI:0914”(association)	0.350
FIS1	QSOX1	psi-mi:“MI:0914”(association)	0.350
CENPM	DNM1L	psi-mi:“MI:0914”(association)	0.350
CCNYL1	PPL	psi-mi:“MI:0914”(association)	0.350

BioGRID (97): CCNYL1 (Affinity Capture-RNA), CCNYL1 (Affinity Capture-RNA), CCNYL1 (Affinity Capture-MS), CCNYL1 (Affinity Capture-MS), CCNYL1 (Affinity Capture-MS), CCNYL1 (Affinity Capture-MS), CCNYL1 (Affinity Capture-MS), CCNYL1 (Affinity Capture-MS), CCNYL1 (Affinity Capture-MS), CCNYL1 (Affinity Capture-MS), CCNYL1 (Affinity Capture-MS), CCNYL1 (Affinity Capture-MS), CCNYL1 (Affinity Capture-MS), CCNY (Affinity Capture-MS), CCNYL1 (Affinity Capture-MS)

ESM2 similar proteins: A0A7H0DN99, A0A8V8TMC4, D3YUJ3, I2HAA0, O01501, O13818, O14260, O14332, O17657, O42575, O43008, P06776, P0C7X3, P17214, P25009, P30645, P34624, P36034, P38729, P52924, P53053, P53124, Q03080, Q05930, Q07788, Q08C99, Q08CI4, Q09792, Q10326, Q10PQ9, Q22695, Q28EL0, Q4R871, Q5IBH7, Q5ICL9, Q5MJ70, Q5T2Q4, Q5U5D0, Q6NRF4, Q75D04

Diamond homologs: A0A8V8TMC4, A6NIR3, D3YUJ3, P0C7X3, P34624, Q08CI4, Q28EL0, Q4R871, Q5T2Q4, Q5U5D0, Q5VUJ5, Q5VW22, Q6NRF4, Q8BGU5, Q8N7R7, Q8ND76, Q96P64, A1L520, A5PK26, O74345, O75689, O80925, O82171, O94601, O97902, P35197, P38682, P40529, Q04412, Q09531, Q0WQQ1, Q10165, Q10367, Q14161, Q15027, Q15057, Q17R07, Q1AAU6, Q1ZXH8, Q28CM8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	33
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1612 predictions. Top by Δscore:

Variant	Effect	Δscore
2:207712113:GAAG:G	donor_gain	1.0000
2:207712114:AAG:A	donor_gain	1.0000
2:207712115:AG:A	donor_gain	1.0000
2:207712115:AGG:A	donor_loss	1.0000
2:207712116:GG:G	donor_gain	1.0000
2:207712117:G:GA	donor_loss	1.0000
2:207712117:G:GG	donor_gain	1.0000
2:207712118:T:G	donor_loss	1.0000
2:207724795:TATA:T	acceptor_loss	1.0000
2:207724796:ATAG:A	acceptor_loss	1.0000
2:207724798:A:AG	acceptor_gain	1.0000
2:207724798:A:C	acceptor_loss	1.0000
2:207724799:G:GA	acceptor_gain	1.0000
2:207724799:GATTT:G	acceptor_gain	1.0000
2:207726840:A:AG	acceptor_gain	1.0000
2:207726841:G:GG	acceptor_gain	1.0000
2:207726841:GT:G	acceptor_gain	1.0000
2:207726875:AT:A	donor_gain	1.0000
2:207726877:G:GA	donor_loss	1.0000
2:207726877:G:GG	donor_gain	1.0000
2:207726878:T:G	donor_loss	1.0000
2:207740707:G:GG	donor_gain	1.0000
2:207742217:TTTCA:T	acceptor_loss	1.0000
2:207742218:TTCA:T	acceptor_loss	1.0000
2:207742219:TCA:T	acceptor_loss	1.0000
2:207742220:CA:C	acceptor_loss	1.0000
2:207742221:A:AG	acceptor_gain	1.0000
2:207742221:A:AT	acceptor_loss	1.0000
2:207742221:AGC:A	acceptor_gain	1.0000
2:207742222:G:GC	acceptor_gain	1.0000

AlphaMissense

2380 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:207724850:T:C	F91L	1.000
2:207724851:T:C	F91S	1.000
2:207724851:T:G	F91C	1.000
2:207724852:C:A	F91L	1.000
2:207724852:C:G	F91L	1.000
2:207733977:A:C	S121R	1.000
2:207733979:C:A	S121R	1.000
2:207733979:C:G	S121R	1.000
2:207733993:T:A	I126K	1.000
2:207733993:T:G	I126R	1.000
2:207734014:T:A	V133D	1.000
2:207734023:C:A	P136H	1.000
2:207737421:G:C	A148P	1.000
2:207737422:C:A	A148E	1.000
2:207737425:T:A	I149K	1.000
2:207737425:T:G	I149R	1.000
2:207737446:G:T	R156I	1.000
2:207742283:T:C	F194L	1.000
2:207742284:T:C	F194S	1.000
2:207742285:T:A	F194L	1.000
2:207742285:T:G	F194L	1.000
2:207742298:T:C	F199L	1.000
2:207742300:T:A	F199L	1.000
2:207742300:T:G	F199L	1.000
2:207742304:G:C	A201P	1.000
2:207742307:G:C	A202P	1.000
2:207742314:T:A	L204Q	1.000
2:207742314:T:C	L204P	1.000
2:207742317:C:T	T205I	1.000
2:207742322:G:A	E207K	1.000

dbSNP variants (sampled 300 via entrez): RS1000154338 (2:207724064 T>C,G), RS1000179612 (2:207740983 C>A,T), RS1000196925 (2:207710564 G>A,C), RS1000259394 (2:207753044 AAAAT>A), RS1000296213 (2:207751398 C>T), RS1000296587 (2:207736843 C>A), RS1000355485 (2:207722422 T>C), RS1000407081 (2:207735394 C>A,G), RS1000469069 (2:207717966 T>A), RS1000592763 (2:207754481 A>C,G), RS1000652874 (2:207711786 G>T), RS1000708786 (2:207717507 A>C), RS1000730875 (2:207724061 A>G), RS1000862179 (2:207744221 G>A), RS1000936248 (2:207741274 G>A,C,T)

Disease associations

OMIM: gene MIM:620559 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST004776_34	Systolic blood pressure	9.000000e-11
GCST004776_84	Systolic blood pressure	1.000000e-07
GCST006103_20	Interleukin-6 levels	4.000000e-06
GCST008157_64	Body fat mass	5.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0006335	systolic blood pressure
EFO:0004810	interleukin-6 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	7
trichostatin A	affects cotreatment, decreases expression, affects expression	4
(+)-JQ1 compound	increases expression	3
Acetaminophen	increases expression	2
Nickel	increases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tobacco Smoke Pollution	affects expression, increases expression	2
Cyclosporine	increases expression, decreases expression	2
FR900359	affects phosphorylation	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
methylparaben	decreases expression	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
di-n-butylphosphoric acid	affects expression	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
dorsomorphin	affects cotreatment, decreases expression	1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine	decreases expression, increases response to substance	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Air Pollutants	affects cotreatment, increases abundance, increases oxidation	1
Arbutin	increases expression	1
Cadmium	increases expression	1
Caffeine	affects phosphorylation	1
Drugs, Chinese Herbal	decreases expression	1
Estradiol	increases expression	1
Folic Acid	decreases expression	1
Hydrogen Peroxide	affects expression	1
Ozone	affects cotreatment, increases oxidation, increases abundance	1
Phenobarbital	affects expression	1
Rotenone	decreases expression	1
Smoke	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_SH54	HAP1 CCNYL1 (-)	Cancer cell line	Male

Clinical trials (associated diseases)

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