CYLC2

gene
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Summary

CYLC2 (cylicin 2, HGNC:2583) is a protein-coding gene on chromosome 9q31.1, encoding Cylicin-2 (Q14093). Plays a role in the establishment of normal sperm morphology during spermatogenesis.

Cylicin II (CYCL2) is specifically expressed in testis and is part of the cytoskeletal calyx of mammalian sperm heads. Cylicin II may play a role in the morphogenesis of the sperm head.

Source: NCBI Gene 1539 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): autism spectrum disorder (Limited, GenCC)
  • GWAS associations: 5
  • Clinical variants (ClinVar): 80 total
  • MANE Select transcript: NM_001340

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2583
Approved symbolCYLC2
Namecylicin 2
Location9q31.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000155833
Ensembl biotypeprotein_coding
OMIM604035
Entrez1539

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000374798, ENST00000487798, ENST00000590560, ENST00000612124

RefSeq mRNA: 1 — MANE Select: NM_001340 NM_001340

CCDS: CCDS35085

Canonical transcript exons

ENST00000374798 — 8 exons

ExonStartEnd
ENSE00001464688103018325103018488
ENSE00001464689103016888103016961
ENSE00001520319103011982103012097
ENSE00001657203103004969103006378
ENSE00001717857103001578103001618
ENSE00001751362103003142103003263
ENSE00001757460103004695103004851
ENSE00003844183102995333102995397

Expression profiles

Bgee: expression breadth ubiquitous, 114 present calls, max score 95.83.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0499 / max 47.3639, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
977750.04993

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
spermCL:000001995.83gold quality
male germ cellCL:000001594.55gold quality
left testisUBERON:000453393.08gold quality
right testisUBERON:000453492.26gold quality
testisUBERON:000047389.87gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047381.88gold quality
adult organismUBERON:000702364.61gold quality
buccal mucosa cellCL:000233659.31silver quality
deciduaUBERON:000245056.55gold quality
tibialis anteriorUBERON:000138555.88silver quality
cranial nerve IIUBERON:000094154.60gold quality
ileal mucosaUBERON:000033154.07gold quality
pancreatic ductal cellCL:000207953.84silver quality
hair follicleUBERON:000207352.80gold quality
deltoidUBERON:000147650.61silver quality
quadriceps femorisUBERON:000137750.47gold quality
frontal poleUBERON:000279550.41gold quality
middle frontal gyrusUBERON:000270250.30gold quality
paraflocculusUBERON:000535150.18gold quality
Brodmann (1909) area 10UBERON:001354150.18gold quality
thymusUBERON:000237050.17gold quality
epithelial cell of pancreasCL:000008350.13gold quality
vastus lateralisUBERON:000137949.45gold quality
Brodmann (1909) area 46UBERON:000648349.30gold quality
blood vessel layerUBERON:000479749.29gold quality
cerebellar vermisUBERON:000472049.25gold quality
cervix squamous epitheliumUBERON:000692249.20gold quality
olfactory bulbUBERON:000226448.92gold quality
choroid plexus epitheliumUBERON:000391148.89gold quality
myocardiumUBERON:000234948.87gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes3.43
E-ENAD-17no15.84

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

38 targeting CYLC2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-518D-5P100.0067.51979
HSA-MIR-518E-5P100.0067.66954
HSA-MIR-518F-5P100.0067.51979
HSA-MIR-519A-5P100.0067.66954
HSA-MIR-519B-5P100.0067.66954
HSA-MIR-519C-5P100.0067.66954
HSA-MIR-520C-5P100.0067.51979
HSA-MIR-522-5P100.0067.66954
HSA-MIR-523-5P100.0067.66954
HSA-MIR-526A-5P100.0067.51979
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-3912-5P99.9566.11925
HSA-MIR-627-3P99.9071.423316
HSA-MIR-3140-3P99.8868.472069
HSA-MIR-94499.8270.853042
HSA-MIR-205-5P99.8170.051557
HSA-MIR-432099.7565.80793
HSA-MIR-4699-3P99.7170.153142
HSA-MIR-5004-3P99.5468.271371
HSA-MIR-766-3P99.4765.241811
HSA-MIR-183-3P99.4169.411598
HSA-MIR-103A-1-5P99.3967.781545
HSA-MIR-103A-2-5P99.3967.721577
HSA-MIR-442799.3470.331854
HSA-MIR-485-5P99.1064.781889
HSA-MIR-6884-5P99.1064.501987
HSA-MIR-382-3P98.8367.101074
HSA-MIR-6728-3P98.6367.631534
HSA-MIR-676-5P98.4968.871492

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusCylc2ENSMUSG00000039555
rattus_norvegicusCylc2ENSRNOG00000022406

Paralogs (1): CYLC1 (ENSG00000183035)

Protein

Protein identifiers

Cylicin-2Q14093 (reviewed: Q14093)

Alternative names: Cylicin II, Multiple-band polypeptide II

All UniProt accessions (1): Q14093

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in the establishment of normal sperm morphology during spermatogenesis. It is required for acrosome attachment to the nuclear envelope, and proper manchette elongation and disassembly.

Subcellular location. Cytoplasm. Cytoskeleton. Perinuclear theca. Calyx.

Tissue specificity. Testis.

RefSeq proteins (1): NP_001331* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR026189CYLCFamily
IPR029354Cylicin_NDomain

Pfam: PF15241

UniProt features (17 total): sequence variant 5, compositionally biased region 4, region of interest 4, repeat 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q14093-F150.390.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 58 (showing top): XU_HGF_TARGETS_REPRESSED_BY_AKT1_DN, GOBP_MALE_GAMETE_GENERATION, MODULE_120, WEBER_METHYLATED_LCP_IN_FIBROBLAST_DN, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, MODULE_175, GOMF_STRUCTURAL_CONSTITUENT_OF_CYTOSKELETON, GOMF_STRUCTURAL_MOLECULE_ACTIVITY, IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP, NFE2L2.V2, GSE13522_CTRL_VS_T_CRUZI_BRAZIL_STRAIN_INF_SKIN_DN, GOCC_EXTERNAL_ENCAPSULATING_STRUCTURE, MIR6867_5P, GSE10856_CTRL_VS_TNFRSF6B_IN_MACROPHAGE_DN, MIR103A_2_5P

GO Biological Process (3): spermatogenesis (GO:0007283), cell differentiation (GO:0030154), cytoskeleton organization (GO:0007010)

GO Molecular Function (1): structural constituent of cytoskeleton (GO:0005200)

GO Cellular Component (5): nucleus (GO:0005634), cytoskeletal calyx (GO:0033150), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), perinuclear theca (GO:0033011)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoskeleton2
cellular anatomical structure2
developmental process involved in reproduction1
male gamete generation1
cellular developmental process1
organelle organization1
structural molecule activity1
cytoskeleton organization1
intracellular membrane-bounded organelle1
perinuclear theca1
intracellular anatomical structure1
intracellular membraneless organelle1
perinuclear region of cytoplasm1

Protein interactions and networks

STRING

646 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CYLC2CCINQ13939962
CYLC2CATSPERGQ6ZRH7565
CYLC2CSNK2A2IPA0A1B0GTH6547
CYLC2SPATA6Q9NWH7514
CYLC2CBY2Q8NA61512
CYLC2SPATA31E1Q6ZUB1507
CYLC2OR2T10Q8NGZ9505
CYLC2CLXNQ9HAE3484
CYLC2ZCCHC2Q9C0B9461
CYLC2OR52M1Q8NGK5434
CYLC2DHX35Q9H5Z1425
CYLC2ZNF555Q8NEP9418
CYLC2SPMIP9Q96LM6396
CYLC2ARMC3Q5W041391
CYLC2SPATA24Q86W54378

IntAct

16 interactions, top by confidence:

ABTypeScore
CYLC2RSL1D1psi-mi:“MI:0915”(physical association)0.400
CYLC2HNRNPMpsi-mi:“MI:0915”(physical association)0.400
AURKACYLC2psi-mi:“MI:0915”(physical association)0.370
BUB1CYLC2psi-mi:“MI:0915”(physical association)0.370
CYLC2CDKN2Apsi-mi:“MI:0915”(physical association)0.370
EGFRCYLC2psi-mi:“MI:0915”(physical association)0.370
CYLC2ERBB2psi-mi:“MI:0915”(physical association)0.370
MAP2K4CYLC2psi-mi:“MI:0915”(physical association)0.370
MCCCYLC2psi-mi:“MI:0915”(physical association)0.370
MLH1CYLC2psi-mi:“MI:0915”(physical association)0.370
MLH3CYLC2psi-mi:“MI:0915”(physical association)0.370
MUTYHCYLC2psi-mi:“MI:0915”(physical association)0.370
NRASCYLC2psi-mi:“MI:0915”(physical association)0.370
CYLC2SMAD2psi-mi:“MI:0915”(physical association)0.370
CYLC2STK11psi-mi:“MI:0915”(physical association)0.370

BioGRID (28): CYLC2 (Negative Genetic), CYLC2 (Proximity Label-MS), CYLC2 (Proximity Label-MS), CYLC2 (Two-hybrid), CYLC2 (Two-hybrid), CYLC2 (Two-hybrid), CYLC2 (Two-hybrid), CYLC2 (Two-hybrid), CYLC2 (Two-hybrid), CYLC2 (Two-hybrid), CYLC2 (Two-hybrid), CYLC2 (Two-hybrid), CYLC2 (Two-hybrid), CYLC2 (Two-hybrid), CYLC2 (Two-hybrid)

ESM2 similar proteins: A0A060XQP6, A0A1S4FQ37, A2VD23, A3KQQ9, A7E371, B3A0Q3, B3EWZ0, B3EWZ1, B3EWZ4, B7W112, D1FQ14, E9Q9K5, G5EC21, O01949, O16883, O43493, O46203, O55188, O84462, P08721, P10451, P10923, P13665, P14287, P19814, P23498, P31096, P31097, P31098, P31936, P35662, P35663, P98193, Q13316, Q14093, Q28139, Q5MIT9, Q5SRN2, Q5UQ32, Q62313

Diamond homologs: A0A1B0GR13, A0A571BEE2, P35662, P35663, Q14093, Q28092

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 15 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Cell Cycle513.9×7e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance64
Likely benign12
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

726 predictions. Top by Δscore:

VariantEffectΔscore
9:103001573:A:AGacceptor_gain1.0000
9:103001576:A:AGacceptor_gain1.0000
9:103001577:G:GGacceptor_gain1.0000
9:103003140:A:AGacceptor_gain1.0000
9:103003141:G:GAacceptor_gain1.0000
9:103003141:GTCA:Gacceptor_gain1.0000
9:103003264:G:GGdonor_gain1.0000
9:102995393:AGATT:Adonor_gain0.9900
9:102995394:GATT:Gdonor_gain0.9900
9:102995394:GATTG:Gdonor_gain0.9900
9:102995395:ATT:Adonor_gain0.9900
9:102995398:G:GGdonor_gain0.9900
9:103001577:GC:Gacceptor_gain0.9900
9:103001577:GCC:Gacceptor_gain0.9900
9:103003141:GT:Gacceptor_gain0.9900
9:103003141:GTC:Gacceptor_gain0.9900
9:103003260:TTCTG:Tdonor_loss0.9900
9:103003262:CTG:Cdonor_loss0.9900
9:103003263:TGTAA:Tdonor_loss0.9900
9:103003264:G:GCdonor_loss0.9900
9:103003265:T:TCdonor_loss0.9900
9:103003275:A:Tdonor_gain0.9900
9:102995362:C:Tdonor_gain0.9800
9:102995396:TT:Tdonor_gain0.9800
9:102995396:TTG:Tdonor_loss0.9800
9:102995397:TGT:Tdonor_loss0.9800
9:102995398:G:Tdonor_loss0.9800
9:102995399:TAAGT:Tdonor_loss0.9800
9:103001574:A:Gacceptor_gain0.9800
9:103001615:CCAG:Cdonor_loss0.9800

AlphaMissense

2320 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:103004742:G:CW76C0.991
9:103004742:G:TW76C0.991
9:103003192:T:CF37L0.989
9:103003194:T:AF37L0.989
9:103003194:T:GF37L0.989
9:103004740:T:AW76R0.989
9:103004740:T:CW76R0.989
9:103003180:T:CF33L0.984
9:103003182:T:AF33L0.984
9:103003182:T:GF33L0.984
9:103003165:T:AW28R0.983
9:103003165:T:CW28R0.983
9:103003227:A:CR48S0.983
9:103003227:A:TR48S0.983
9:103004744:T:CM77T0.974
9:103003193:T:CF37S0.973
9:103004789:T:CL92S0.973
9:103003200:A:CK39N0.972
9:103003200:A:TK39N0.972
9:103003170:T:AN29K0.971
9:103003170:T:GN29K0.971
9:103003167:G:CW28C0.970
9:103003167:G:TW28C0.970
9:103004765:T:CI84T0.969
9:103004799:G:CR95S0.967
9:103004799:G:TR95S0.967
9:103004756:T:CL81S0.964
9:103003193:T:GF37C0.961
9:103003187:T:CL35P0.959
9:103004792:C:AA93D0.959

dbSNP variants (sampled 300 via entrez): RS1000073503 (9:103015861 T>A), RS1000152321 (9:102999096 G>A), RS1000182484 (9:103018575 A>G), RS1000206693 (9:102998733 A>G), RS1000286313 (9:103012153 G>A), RS1000555773 (9:103018356 C>T), RS1000617442 (9:103014382 T>A,C), RS1000673998 (9:103014227 TAA>T), RS1000832304 (9:103008597 C>A), RS1000942363 (9:103008668 T>C), RS1001087279 (9:103003761 A>C), RS1001123304 (9:102997185 G>T), RS1001158895 (9:102997884 A>T), RS1001182259 (9:102996407 T>G), RS1001204216 (9:103008287 T>A)

Disease associations

OMIM: gene MIM:604035 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
autism spectrum disorderLimitedAutosomal dominant

Mondo (2): primary ovarian failure (MONDO:0005387), autism spectrum disorder (MONDO:0005258)

Orphanet (1): NON RARE IN EUROPE: Primary ovarian failure (Orphanet:619)

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST001762_829Obesity-related traits7.000000e-06
GCST002682_9Tourette’s syndrome or obsessive-compulsive disorder5.000000e-06
GCST009391_1177Metabolite levels4.000000e-06
GCST010396_101Gut microbiota (bacterial taxa, hurdle binary method)4.000000e-07
GCST012015_4Chronic rhinosinusitis5.000000e-06

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004338body weight
EFO:0010454adenosine monophosphate measurement
EFO:0007874gut microbiome measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
D016649Primary Ovarian InsufficiencyC12.050.351.500.056.630.750; C12.100.250.056.630.750; C19.391.630.750

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

ChemicalActions (top 5)PubMed papers
2-palmitoylglycerolincreases expression1
Silicon Dioxidedecreases expression1
Tamoxifenincreases expression1
Aflatoxin B1increases methylation1
Raloxifene Hydrochlorideincreases expression1
Magnetite Nanoparticlesdecreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00391261PHASE4COMPLETEDAn Open-label Trial of Metformin for Weight Control of Pediatric Patients on Antipsychotic Medications.
NCT01028820PHASE4COMPLETEDFMRI Brain Activation of Aripiprazole Treatment in Autism Spectrum Disorders
NCT01333865PHASE4COMPLETEDA Study of Memantine Hydrochloride (Namenda®) for Cognitive and Behavioral Impairment in Adults With Autism Spectrum Disorders
NCT01337700PHASE4COMPLETEDMilnacipran in Autism and the Functional Locus Coeruleus and Noradrenergic Model of Autism
NCT01695200PHASE4COMPLETEDOmega-3 Fatty Acids in Autism Spectrum Disorders
NCT02096952PHASE4COMPLETEDMethylphenidate ER Liquid Formulation in Adults With ASD and ADHD
NCT02235467PHASE4COMPLETEDMultisite Study: Parental Training Using Video Modelling to Develop Social Skills in Children With Autism
NCT02940574PHASE4COMPLETEDNeural and Behavioral Effects of Oxytocin in Autism Spectrum Disorders
NCT03333629PHASE4COMPLETEDPromoting Positive Outcomes for Individuals With ASD: Linking Early Detection, Treatment, and Long-term Outcomes
NCT03337646PHASE4COMPLETEDEvaluation of the Effect and Safety of Lisdexamfetamine in Children Aged 6-12 With ADHD and Autism
NCT03538431PHASE4COMPLETEDImproving Driving in Young People With Autism Spectrum Disorders
NCT03757585PHASE4COMPLETEDNatural Treatments for the Management of Emotional Dysregulation in Youth With Non-verbal Learning Disability (NVLD) and/or Autism Spectrum Disorders (ASD)
NCT04903353PHASE4COMPLETEDPragmatic Trial Comparing Weight Gain in Children With Autism Taking Risperidone Versus Aripiprazole
NCT05063656PHASE4COMPLETEDBiomarker-Driven Pharmacological Treatment of Adolescents With Autism Spectrum Disorder With Gabapentin
NCT05146245PHASE4UNKNOWNSafety and Pharmacokinetics of Antipsychotics in Children 2: Studying TDM in an RCT
NCT05916339PHASE4RECRUITINGAWARE: Management of ADHD in Autism Spectrum Disorder
NCT05954052PHASE4TERMINATEDA Study of Glutathione in Children With Autism Spectrum Disorder
NCT06853665PHASE4RECRUITINGThe TEAM Study - Treatment Efficacy for Autism/Attention Using Mixed Amphetamine
NCT07054697PHASE4COMPLETEDPilot-RCT With Individualized Homeopathic Treatment in the Children With Autism Spectrum Disorder
NCT07161804PHASE4COMPLETEDPilot RCT Using Homeopathic Medicines in ASD
NCT07439042PHASE4NOT_YET_RECRUITINGBuspirone for Anxiety in Autistic Youth
NCT00417066PHASE4COMPLETEDFlexible GnRH Antagonist vs Flare up GnRH Agonist Protocol in Poor Responders
NCT00732693PHASE4COMPLETEDEvaluation of Physiologic and Standard Sex Steroid Replacement Regimens in Women With Premature Ovarian Failure
NCT00837616PHASE4COMPLETEDEstrogen Dosing in Turner Syndrome: Pharmacology and Metabolism
NCT01853501PHASE4UNKNOWNEffects of ADSC Therapy in Women With POF
NCT02783937PHASE4COMPLETEDFilgrastim for Premature Ovarian Insufficiency
NCT03535480PHASE4UNKNOWNAutologous Bone Marrow Stem Cell Ovarian Transplantation to Restore Ovarian Function in Premature Ovarian Failure
NCT01302964PHASE3COMPLETEDMirtazapine Treatment of Anxiety in Children and Adolescents With Pervasive Developmental Disorders
NCT01706523PHASE3TERMINATEDOpen Label Extension Study of STX209 (Arbaclofen) in Autism Spectrum Disorders
NCT01825798PHASE3COMPLETEDTreatment of Overweight Induced by Antipsychotic Medication in Young People With Autism Spectrum Disorders (ASD)
NCT01972074PHASE3COMPLETEDBehavioral and Neural Response to Memantine in Adolescents With Autism Spectrum Disorder
NCT02985749PHASE3COMPLETEDA Study of Oxytocin for the Treatment of Social Impairment in Individuals With High Functioning Autism Spectrum Disorder
NCT03197922PHASE3COMPLETEDTreatment of Encopresis in Children With Autism Spectrum Disorders
NCT03504917PHASE3TERMINATEDA Study of Balovaptan in Adults With Autism Spectrum Disorder With a 2-Year Open-Label Extension
NCT03553875PHASE3TERMINATEDMemantine for the Treatment of Social Deficits in Youth With Disorders of Impaired Social Interactions
NCT03640156PHASE3COMPLETEDModulating Socially Adaptive Mirror System Functioning in Autism by Oxytocin
NCT03715153PHASE3TERMINATEDEfficacy and Safety of Bumetanide Oral Liquid Formulation in Children Aged From 2 to Less Than 7 Years Old With Autism Spectrum Disorder.
NCT03715166PHASE3TERMINATEDEfficacy and Safety of Bumetanide Oral Liquid Formulation in Children and Adolescents Aged From 7 to Less Than 18 Years Old With Autism Spectrum Disorder
NCT04233502PHASE3WITHDRAWNEfficacy and Safety of Slenyto for Insomnia in Children With ASD
NCT04578756PHASE3COMPLETEDOpen-Label, Flexible-dose Study to Evaluate the Long-Term Safety and Tolerability of Cariprazine in the Treatment of Pediatric Participants With Schizophrenia, Bipolar I Disorder, or Autism Spectrum Disorder