CCDC33

gene
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Also known as FLJ32855CT61CC2D3

Summary

CCDC33 (coiled-coil domain containing 33, HGNC:26552) is a protein-coding gene on chromosome 15q24.1, encoding Coiled-coil domain-containing protein 33 (Q8N5R6).

Predicted to be active in peroxisome.

Source: NCBI Gene 80125 — RefSeq curated summary.

At a glance

  • GWAS associations: 9
  • Clinical variants (ClinVar): 173 total — 1 pathogenic, 1 likely-pathogenic
  • MANE Select transcript: NM_025055

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26552
Approved symbolCCDC33
Namecoiled-coil domain containing 33
Location15q24.1
Locus typegene with protein product
StatusApproved
AliasesFLJ32855, CT61, CC2D3
Ensembl geneENSG00000140481
Ensembl biotypeprotein_coding
OMIM618525
Entrez80125

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 5 protein_coding, 5 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000268082, ENST00000321374, ENST00000398814, ENST00000558645, ENST00000558659, ENST00000558821, ENST00000559243, ENST00000560148, ENST00000560565, ENST00000561332, ENST00000563951, ENST00000635913

RefSeq mRNA: 3 — MANE Select: NM_025055 NM_001287181, NM_025055, NM_182791

CCDS: CCDS42058, CCDS42059, CCDS73753

Canonical transcript exons

ENST00000398814 — 19 exons

ExonStartEnd
ENSE000017291637424398574244148
ENSE000017872717423632674236740
ENSE000039937867433018974330354
ENSE000039937877433066374330751
ENSE000039937887426244074262573
ENSE000039937897433388174333967
ENSE000039937907433098174331112
ENSE000039937917428066874280801
ENSE000039937927427277174272891
ENSE000039937937428177874281849
ENSE000039937947427170374271794
ENSE000039937957433267974332845
ENSE000039937967433120374331296
ENSE000039937977433497574335088
ENSE000039937987427996374280092
ENSE000039937997429575474295948
ENSE000039938007426834274268458
ENSE000039938017426667874266787
ENSE000039938027433592574336141

Expression profiles

Bgee: expression breadth broad, 100 present calls, max score 98.28.

FANTOM5 (CAGE): breadth broad, TPM avg 1.6921 / max 102.8402, expressed in 377 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter IDTPM avgSamples expressed
1476730.7892244
1476720.7073247
1476820.043324
1476760.04069
1476740.028414
1476780.02735
1476810.01939
1476770.01603
1476800.01507
1476790.00572

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right uterine tubeUBERON:000130298.28gold quality
olfactory segment of nasal mucosaUBERON:000538691.90gold quality
left testisUBERON:000453385.22gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099184.88gold quality
testisUBERON:000047384.75gold quality
right testisUBERON:000453484.73gold quality
fallopian tubeUBERON:000388983.68gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047381.98gold quality
adrenal tissueUBERON:001830372.62gold quality
left uterine tubeUBERON:000130368.15gold quality
right lungUBERON:000216765.74gold quality
sural nerveUBERON:001548864.40silver quality
endocervixUBERON:000045863.48gold quality
pituitary glandUBERON:000000761.58gold quality
placentaUBERON:000198759.38gold quality
adenohypophysisUBERON:000219658.52gold quality
endometriumUBERON:000129558.33gold quality
adrenal glandUBERON:000236957.34gold quality
uterine cervixUBERON:000000256.71gold quality
right adrenal glandUBERON:000123356.22gold quality
left adrenal glandUBERON:000123456.21gold quality
stromal cell of endometriumCL:000225555.74gold quality
left adrenal gland cortexUBERON:003582555.64gold quality
lungUBERON:000204855.13gold quality
right adrenal gland cortexUBERON:003582754.93gold quality
hypothalamusUBERON:000189854.81gold quality
Ammon’s hornUBERON:000195453.98gold quality
cortical plateUBERON:000534351.19silver quality
caudate nucleusUBERON:000187350.82gold quality
upper lobe of left lungUBERON:000895250.79gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes10.24

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting CCDC33, 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-4283100.0066.422097
HSA-MIR-6798-5P100.0065.77699
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-4650-5P99.9864.69999
HSA-MIR-426799.9666.532368
HSA-MIR-153-5P99.8973.866317
HSA-MIR-221-5P99.8665.451052
HSA-MIR-807399.8665.211118
HSA-MIR-444799.8567.812900
HSA-MIR-6764-5P99.7567.892304
HSA-MIR-24-3P99.5969.971934
HSA-MIR-447299.5666.081478
HSA-MIR-1207-5P99.4969.112983
HSA-MIR-608199.4866.071446
HSA-MIR-127599.4767.902749
HSA-MIR-616599.4467.121389
HSA-MIR-425199.4069.193363
HSA-MIR-425499.1165.151315
HSA-MIR-625-5P99.0268.642031
HSA-MIR-423-5P98.6967.481522
HSA-MIR-64898.6466.13553
HSA-MIR-3184-5P98.5667.131491
HSA-MIR-6827-5P98.4664.881256
HSA-MIR-4665-5P97.9167.691536
HSA-MIR-63797.9164.051517
HSA-MIR-366197.8367.30705
HSA-MIR-4715-5P97.6267.47506
HSA-MIR-335-5P97.1068.121022
HSA-MIR-63197.0566.93602

Literature-anchored findings (GeneRIF, showing 1)

  • Data show that CCDC33-dsRED fusion protein co-localized with a known peroxisomal protein, namely PXT1, and showed punctuate intracellular distribution. (PMID:20068295)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioccdc33ENSDARG00000051858
mus_musculusCcdc33ENSMUSG00000037716
rattus_norvegicusCcdc33ENSRNOG00000008219

Protein

Protein identifiers

Coiled-coil domain-containing protein 33Q8N5R6 (reviewed: Q8N5R6)

Alternative names: Cancer/testis antigen 61

All UniProt accessions (3): A0A1B0GV97, Q8N5R6, H0YMB8

Isoforms (5)

UniProt IDNamesCanonical?
Q8N5R6-11yes
Q8N5R6-22
Q8N5R6-44
Q8N5R6-55
Q8N5R6-66

RefSeq proteins (3): NP_001274110, NP_079331, NP_877592 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000008C2_domDomain
IPR035892C2_domain_sfHomologous_superfamily
IPR039889CCD33Family

Pfam: PF00168

UniProt features (22 total): splice variant 7, sequence variant 3, sequence conflict 3, compositionally biased region 3, region of interest 2, coiled-coil region 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N5R6-F172.340.24

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 56 (showing top): PIT1_Q6, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOCC_MICROBODY, RFX1_01, MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP, DODD_NASOPHARYNGEAL_CARCINOMA_DN, OKUMURA_INFLAMMATORY_RESPONSE_LPS, PR_Q2, DUAN_PRDM5_TARGETS, KRAS.600_UP.V1_DN, ZBTB18_TARGET_GENES, ZNF30_TARGET_GENES, ZNF391_TARGET_GENES, ZNF407_TARGET_GENES, ZNF423_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (1): peroxisome (GO:0005777)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding1
microbody1

Protein interactions and networks

STRING

1663 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CCDC33UBL7Q96S82629
CCDC33DRC7Q8IY82561
CCDC33CFAP157Q5JU67470
CCDC33ISLR2Q6UXK2451
CCDC33RIBC2Q9H4K1449
CCDC33SMARCB1Q12824434
CCDC33CFAP184Q2M329421
CCDC33LMAN1LQ9HAT1420
CCDC33GOLGA6AQ9NYA3418
CCDC33CCDC81Q6ZN84395
CCDC33MITD1Q8WV92393
CCDC33SMAD3P84022389
CCDC33CT62P0C5K7370
CCDC33BBS4Q96RK4367
CCDC33CLK3P49761366

IntAct

125 interactions, top by confidence:

ABTypeScore
MLH1CCDC33psi-mi:“MI:0915”(physical association)0.670
SMAD3CCDC33psi-mi:“MI:0915”(physical association)0.670
CCDC33SMAD3psi-mi:“MI:0915”(physical association)0.670
CCDC33MLH1psi-mi:“MI:0915”(physical association)0.670
CCDC33psi-mi:“MI:0915”(physical association)0.610
CCDC33GPN3psi-mi:“MI:0915”(physical association)0.610
GPN3CCDC33psi-mi:“MI:0915”(physical association)0.610
CCDC33SNF1psi-mi:“MI:0915”(physical association)0.560
CCDC33YPK2psi-mi:“MI:0915”(physical association)0.560
PRP4CCDC33psi-mi:“MI:0915”(physical association)0.560
CCDC33RAM2psi-mi:“MI:0915”(physical association)0.560
CCDC33GCD7psi-mi:“MI:0915”(physical association)0.560
CCDC33SEC6psi-mi:“MI:0915”(physical association)0.560
CCDC33MUD2psi-mi:“MI:0915”(physical association)0.560
RFS1CCDC33psi-mi:“MI:0915”(physical association)0.560
TAE1CCDC33psi-mi:“MI:0915”(physical association)0.560
AIR1CCDC33psi-mi:“MI:0915”(physical association)0.560
CCDC33YCH1psi-mi:“MI:0915”(physical association)0.560
CCDC33BIT61psi-mi:“MI:0915”(physical association)0.560
BTN2CCDC33psi-mi:“MI:0915”(physical association)0.560
CCDC33ITT1psi-mi:“MI:0915”(physical association)0.560

BioGRID (236): CCDC33 (Two-hybrid), CCDC33 (Two-hybrid), CCDC33 (Two-hybrid), CCDC33 (Two-hybrid), CCDC33 (Two-hybrid), CCDC33 (Two-hybrid), CCDC33 (Two-hybrid), CCDC33 (Two-hybrid), CCDC33 (Two-hybrid), CCDC33 (Two-hybrid), CCDC33 (Two-hybrid), CCDC33 (Two-hybrid), CCDC33 (Two-hybrid), CCDC33 (Two-hybrid), CCDC33 (Two-hybrid)

ESM2 similar proteins: A0JM13, A1A4L4, A2RRS8, B0DOB4, D4A039, O00750, O70167, O70173, Q08EC4, Q1LXR6, Q3ULW6, Q3UQI9, Q3V0L5, Q3ZAV8, Q4AC94, Q4G0A6, Q52KB6, Q5DTU0, Q5F479, Q5JV73, Q5SUS0, Q5T0N1, Q5XIR4, Q5XIZ9, Q6IFT4, Q6IRN0, Q6IRU7, Q6P1H6, Q6P4K6, Q6PF55, Q6REY9, Q6ZPF3, Q7TP65, Q7Z2Z1, Q80TQ5, Q80VH0, Q8C008, Q8IWE5, Q8N4X5, Q8N5R6

Diamond homologs: Q3ULW6, Q5XIR4, Q8N5R6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic1
Uncertain significance132
Likely benign22
Benign7

Top pathogenic / likely-pathogenic (2)

Variant IDHGVSClassification
1703679GRCh37/hg19 15q24.1-24.2(chr15:74398068-76054094)Pathogenic
3892576NM_001199040.2(STRA6):c.45G>A (p.Trp15Ter)Likely pathogenic

SpliceAI

3062 predictions. Top by Δscore:

VariantEffectΔscore
15:74244144:GTGGT:Gdonor_gain1.0000
15:74244145:TGGT:Tdonor_gain1.0000
15:74244146:GGTG:Gdonor_gain1.0000
15:74244146:GGTGT:Gdonor_loss1.0000
15:74244147:GT:Gdonor_gain1.0000
15:74244147:GTGT:Gdonor_loss1.0000
15:74244149:G:GGdonor_gain1.0000
15:74266676:A:AGacceptor_gain1.0000
15:74266676:A:Cacceptor_loss1.0000
15:74266676:AGAT:Aacceptor_gain1.0000
15:74266677:G:GAacceptor_gain1.0000
15:74266677:GA:Gacceptor_gain1.0000
15:74266677:GAT:Gacceptor_gain1.0000
15:74266677:GATG:Gacceptor_gain1.0000
15:74266677:GATGT:Gacceptor_gain1.0000
15:74266785:AAG:Adonor_gain1.0000
15:74266785:AAGGT:Adonor_loss1.0000
15:74266787:GG:Gdonor_loss1.0000
15:74266789:T:Adonor_loss1.0000
15:74268457:AGG:Adonor_loss1.0000
15:74271697:CTCCA:Cacceptor_loss1.0000
15:74271698:TCCA:Tacceptor_loss1.0000
15:74271699:CCA:Cacceptor_loss1.0000
15:74271701:A:AGacceptor_gain1.0000
15:74271701:A:Gacceptor_loss1.0000
15:74271702:G:GTacceptor_gain1.0000
15:74271702:GAT:Gacceptor_gain1.0000
15:74271702:GATC:Gacceptor_gain1.0000
15:74271702:GATCT:Gacceptor_gain1.0000
15:74271787:GAATT:Gdonor_gain1.0000

AlphaMissense

4931 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000019677 (15:74228591 G>T), RS1000058120 (15:74254448 C>A), RS1000066575 (15:74221968 G>A,C), RS1000068947 (15:74260518 T>C), RS1000106241 (15:74329492 A>G), RS1000114292 (15:74252363 A>G), RS1000124938 (15:74267187 A>G), RS1000136287 (15:74209706 A>G,T), RS1000155433 (15:74255486 G>A), RS1000182990 (15:74299765 A>G), RS1000185742 (15:74238809 A>C), RS1000228135 (15:74302551 C>T), RS1000245502 (15:74222154 C>A,T), RS1000248532 (15:74305633 C>T), RS1000288058 (15:74232976 C>T)

Disease associations

OMIM: gene MIM:618525 | disease phenotypes: MIM:601186

GenCC curated gene-disease

Mondo (2): hearing loss disorder (MONDO:0005365), Matthew-Wood syndrome (MONDO:0011010)

Orphanet (1): Matthew-Wood syndrome (Orphanet:2470)

HPO phenotypes

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

GWAS associations

9 associations (top):

StudyTraitp-value
GCST001762_349Obesity-related traits3.000000e-06
GCST001762_659Obesity-related traits1.000000e-06
GCST002875_114Diisocyanate-induced asthma1.000000e-06
GCST004412_7Craniofacial microsomia1.000000e-23
GCST006627_9Diastolic blood pressure1.000000e-10
GCST007267_110Systolic blood pressure3.000000e-11
GCST009085_1Bacterial meningitis4.000000e-08
GCST010108_19Coffee consumption (cups per day)7.000000e-13
GCST012227_514Hip circumference adjusted for BMI6.000000e-09

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0005116urinary metabolite measurement
EFO:0006995response to diisocyanate
EFO:0006336diastolic blood pressure
EFO:0006335systolic blood pressure
EFO:0006782cups of coffee per day measurement
EFO:0008039BMI-adjusted hip circumference

MeSH disease descriptors (2)

DescriptorNameTree numbers
D034381Hearing LossC09.218.458.341; C10.597.751.418.341; C23.888.592.763.393.341
C537768Anophthalmia with pulmonary hypoplasia (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases methylation, affects cotreatment, increases methylation, decreases expression2
Benzo(a)pyreneaffects methylation, increases methylation2
2,4,6-tribromophenoldecreases expression1
decabromobiphenyl etherdecreases expression1
sodium arsenitedecreases expression1
tetrabromobisphenol Adecreases expression1
benzo(e)pyreneincreases methylation1
aflatoxin B2increases methylation1
cupric chloridedecreases expression1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
pentabrominated diphenyl ether 100decreases expression1
hexabrominated diphenyl ether 153decreases expression1
Resveratrolaffects cotreatment, decreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Air Pollutantsincreases expression, increases abundance1
Atrazineincreases expression1
Cadmiumincreases abundance, decreases expression1
Copperdecreases expression, affects cotreatment1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Methapyrileneincreases methylation1
Silicon Dioxidedecreases expression1
Smokeincreases abundance, increases expression1
Thiramdecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Valproic Acidincreases methylation1
Cadmium Chloridedecreases expression, increases abundance1
Magnetite Nanoparticlesincreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00205881PHASE4COMPLETEDBilateral Benefit in Adult Users of the HiRes 90K Bionic Ear System
NCT00331539PHASE4UNKNOWNRelationship Between Auto NRT and Behavioural T & C Levels With the Nucleus Freedom Cochlear Implant
NCT00424307PHASE4UNKNOWNBilateral Cochlear Implant Benefit in Young Children
NCT00765635PHASE4COMPLETEDChlorobutanol, Potassium Carbonate, and Irrigation in Cerumen Removal
NCT03321006PHASE4COMPLETEDTreating Hearing Loss to Improve Mood and Cognition in Older Adults
NCT01499901PHASE3WITHDRAWNComparison of the Bilateral Sequential and Simultaneous Cochlear Implantation in the Deaf Children
NCT02561091PHASE3COMPLETEDAM-111 in the Treatment of Acute Inner Ear Hearing Loss
NCT03331627PHASE3COMPLETEDSafety and Efficacy of STR001-IT and STR001-ER in Patients With SSHL
NCT05532657PHASE3ACTIVE_NOT_RECRUITINGACHIEVE Brain Health Follow-Up Study
NCT00013455PHASE2COMPLETEDQuantifying Auditory Perceptual Learning Following Hearing Aid Fitting
NCT00323427PHASE2COMPLETEDClinical Trial of the Living Well With Hearing Loss Workshop
NCT00552786PHASE2COMPLETEDAntioxidation Medication for Noise-induced Hearing Loss
NCT00802425PHASE2COMPLETEDEfficacy of AM-111 in Patients With Acute Sensorineural Hearing Loss
NCT01139281PHASE2COMPLETEDThe Protective Effect of Ginkgo Biloba Extract on Cisplatin-induced Ototoxicity in Humans
NCT01451853PHASE2UNKNOWNSPI-1005 for Prevention and Treatment of Chemotherapy Induced Hearing Loss
NCT01588925PHASE2COMPLETEDHearing Preservation Using Dexamethasone and Hyaluronic Acid for Cochlear Implantation
NCT01773278PHASE2RECRUITINGCholesterol and Antioxidant Treatment in Patients With Smith-Lemli-Opitz Syndrome (SLOS)
NCT02832128PHASE2COMPLETEDEvaluating Possible Improvement in Speech and Hearing Tests After 28 Days of Dosing of the Study Drug AUT00063 Compared to Placebo (QuicKfire)
NCT04915183PHASE2RECRUITINGAtorvastatin to Reduce Cisplatin-Induced Hearing Loss Among Individuals With Head and Neck Cancer
NCT05258773PHASE2COMPLETEDEvaluation of the Presence of SENS-401 in the Perilymph
NCT06340633PHASE2RECRUITINGSPI-1005 in Adults Receiving Cochlear Implant
NCT00582946PHASE1COMPLETEDWide-Bandwidth Open Canal Hearing Aid For Better Multitalker Speech Understanding
NCT00584155PHASE1WITHDRAWNProtection From Cisplatin Ototoxicity by Lactated Ringers
NCT01206829PHASE1UNKNOWNHearing Impairment, Cognitive Therapy and Coping
NCT01256229PHASE1COMPLETEDOutcomes In Children With Developmental Delay And Deafness
NCT01343394PHASE1WITHDRAWNSafety of Autologous Human Umbilical Cord Blood Mononuclear Fraction to Treat Acquired Hearing Loss in Children
NCT01452607PHASE1COMPLETEDStudy to Evaluate the Safety and Pharmacokinetics of SPI-1005
NCT02259595PHASE1COMPLETEDStudy to Determine the Safety, Tolerability, and Pharmacokinetic Profile of HPN-07 and HPN-07 Plus NAC
NCT04041440PHASE1COMPLETEDSpeech Recognition Training in Children With Hearing Loss
NCT07218913PHASE1RECRUITINGTesting the Addition of Pedmark to Cisplatin Chemotherapy for Reducing Drug-Induced Ear Damage in Men With Stage II-III Metastatic Testicular Germ Cell Tumors
NCT00486577PHASE2/PHASE3COMPLETEDChronic Electrical Stimulation of the Auditory Cortex for Intractable Tinnitus
NCT00789061PHASE2/PHASE3UNKNOWNApplying Proton Pump Inhibitor to Prevent and Treat Acute Fluctuating Hearing Loss in Patients With SLC26A4 Mutation
NCT01423409PHASE2/PHASE3COMPLETEDMulticenter Trial Assessing an Innovative VAS of Pain Among Deaf People
NCT05786378PHASE2/PHASE3UNKNOWNAssessment of The Efficacy of Intratympanic Platelet Rich Plasma for Treatment of Sensorineural Hearing Loss.
NCT01108601PHASE1/PHASE2UNKNOWNTranstympanic Ringer’s Lactate for the Prevention of Cisplatin Ototoxicity
NCT01621256PHASE1/PHASE2COMPLETEDEfficacy, Safety, and Tolerability of Ancrod in Patients With Sudden Hearing Loss
NCT06370351PHASE1/PHASE2RECRUITINGA Phase I/II Clinical Trial with SENS-501 in Children Suffering from Severe to Profound Hearing Loss Due to Otoferlin (OTOF) Mutations
NCT06545175PHASE1/PHASE2RECRUITINGIntracochlear Application of VSF1.01 for the Reduction of Cochlear Implant Surgery Related Trauma
NCT07304024PHASE1/PHASE2RECRUITINGA Treatment for a Form of Age-Related Central Auditory Processing Disorder Consisting of Clemastine Fumarate Plus Engineered Sound
NCT01109576EARLY_PHASE1COMPLETEDWorkshops for Veterans With Vision and Hearing Loss