ZC2HC1C

gene
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Summary

ZC2HC1C (zinc finger C2HC-type containing 1C, HGNC:20354) is a protein-coding gene on chromosome 14q24.3, encoding Zinc finger C2HC domain-containing protein 1C (Q53FD0).

Predicted to enable zinc ion binding activity.

Source: NCBI Gene 79696 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): neurodevelopmental disorder (Limited, GenCC)
  • GWAS associations: 2
  • Clinical variants (ClinVar): 74 total
  • MANE Select transcript: NM_024643

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:20354
Approved symbolZC2HC1C
Namezinc finger C2HC-type containing 1C
Location14q24.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000119703
Ensembl biotypeprotein_coding
Entrez79696

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 15 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000238686, ENST00000439583, ENST00000524913, ENST00000525046, ENST00000526130, ENST00000526748, ENST00000532198, ENST00000534151, ENST00000554763, ENST00000673663, ENST00000673981, ENST00000674017, ENST00000674086, ENST00000674094, ENST00000674097, ENST00000875427, ENST00000875428, ENST00000946640

RefSeq mRNA: 3 — MANE Select: NM_024643 NM_001042430, NM_001330191, NM_024643

CCDS: CCDS41972, CCDS45138, CCDS81829

Canonical transcript exons

ENST00000524913 — 3 exons

ExonStartEnd
ENSE000012863397507055575071911
ENSE000021423617507753275079988
ENSE000021432267506964175069749

Expression profiles

Bgee: expression breadth ubiquitous, 181 present calls, max score 95.34.

FANTOM5 (CAGE): breadth broad, TPM avg 1.4127 / max 246.2924, expressed in 542 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1406011.1352441
1405990.2358104
1406000.041711

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
left testisUBERON:000453395.34gold quality
right testisUBERON:000453494.96gold quality
testisUBERON:000047392.96gold quality
adult organismUBERON:000702388.68gold quality
right uterine tubeUBERON:000130288.22gold quality
bronchial epithelial cellCL:000232887.16gold quality
epithelium of bronchusUBERON:000203185.08gold quality
corpus epididymisUBERON:000435983.97gold quality
bronchusUBERON:000218583.51gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047382.25gold quality
olfactory segment of nasal mucosaUBERON:000538680.42gold quality
apex of heartUBERON:000209879.88gold quality
right lobe of thyroid glandUBERON:000111979.66gold quality
cauda epididymisUBERON:000436078.60gold quality
right lobe of liverUBERON:000111478.17gold quality
left lobe of thyroid glandUBERON:000112078.14gold quality
adenohypophysisUBERON:000219678.05gold quality
spermCL:000001978.04gold quality
male germ cellCL:000001577.54gold quality
thyroid glandUBERON:000204677.35gold quality
pituitary glandUBERON:000000777.03gold quality
mucosa of paranasal sinusUBERON:000503076.67silver quality
caput epididymisUBERON:000435875.98gold quality
body of pancreasUBERON:000115075.97gold quality
heart left ventricleUBERON:000208475.97gold quality
mucosa of transverse colonUBERON:000499175.95gold quality
islet of LangerhansUBERON:000000675.57gold quality
cardiac ventricleUBERON:000208275.36gold quality
gastrocnemiusUBERON:000138875.20gold quality
pancreasUBERON:000126474.60gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes3.57

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

101 targeting ZC2HC1C, 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-4692100.0067.322066
HSA-MIR-3925-3P100.0069.951237
HSA-MIR-451499.9967.101870
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-118499.9968.191458
HSA-MIR-548P99.9872.253784
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-5195-3P99.9270.921877
HSA-MIR-145-5P99.9271.131836
HSA-MIR-6499-3P99.9066.381212
HSA-MIR-391999.8769.452489
HSA-MIR-1211999.8768.351653
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-6817-3P99.7968.352126
HSA-MIR-548AG99.7769.251492
HSA-MIR-3156-3P99.7666.72939
HSA-MIR-149-3P99.7268.223963
HSA-MIR-518A-5P99.7069.012209
HSA-MIR-52799.7069.012209
HSA-MIR-548AI99.6969.241494
HSA-MIR-548BA99.6969.141514
HSA-MIR-570-5P99.6969.241494
HSA-MIR-6883-5P99.6968.053785
HSA-MIR-5004-5P99.6866.631294
HSA-MIR-7-5P99.6770.531809
HSA-MIR-10394-5P99.6566.831852
HSA-MIR-120599.6566.761826
HSA-MIR-7156-5P99.6468.811369

Literature-anchored findings (GeneRIF, showing 1)

  • Screening of candidate genes at GLC3B and GLC3C loci in Chinese primary congenital glaucoma patients with targeted next generation sequencing. (PMID:36193031)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriozc2hc1cENSDARG00000070526
mus_musculusZc2hc1cENSMUSG00000045064
rattus_norvegicusZc2hc1cENSRNOG00000027115

Protein

Protein identifiers

Zinc finger C2HC domain-containing protein 1CQ53FD0 (reviewed: Q53FD0)

All UniProt accessions (5): Q53FD0, A0A669KB15, E9PMG6, H0YE08, J3KMY6

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the ZC2HC1 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q53FD0-11yes
Q53FD0-22

RefSeq proteins (3): NP_001035895, NP_001317120, NP_078919* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR026104ZNF_C2HC_dom_1CFamily
IPR049899Znf_C2HC_C3HDomain

UniProt features (15 total): binding site 4, region of interest 3, compositionally biased region 3, chain 1, zinc finger region 1, splice variant 1, sequence conflict 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q53FD0-F161.230.16

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (4): 394; 406; 410; 391

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 112 (showing top): CMYB_01, CAGCAGG_MIR370, chr14q24, TGANTCA_AP1_C, GNF2_CCNA1, NRF2_Q4, AACTTT_UNKNOWN, LEE_LIVER_CANCER_E2F1_DN, CART1_01, AACTGGA_MIR145, NFE2_01, ACACTCC_MIR122A, LEE_LIVER_CANCER_MYC_TGFA_DN, LEE_LIVER_CANCER_MYC_DN, DODD_NASOPHARYNGEAL_CARCINOMA_DN

GO Biological Process (0):

GO Molecular Function (3): zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
transition metal ion binding1
binding1
cation binding1

Protein interactions and networks

STRING

626 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZC2HC1COR5T1Q8NG75571
ZC2HC1CRPS6KL1Q9Y6S9544
ZC2HC1CMLH3P49751449
ZC2HC1COR2W1Q9Y3N9447
ZC2HC1CVWA3AA6NCI4446
ZC2HC1CNEK9Q8TD19442
ZC2HC1CC5orf34Q96MH7433
ZC2HC1CMEDAGQ5VYS4433
ZC2HC1CZNF557Q8N988432
ZC2HC1CSERPINB11Q96P15432
ZC2HC1CMIER2Q8N344431
ZC2HC1CZNF721Q8TF20417
ZC2HC1CCCDC32Q9BV29397
ZC2HC1CZNF358Q9NW07392
ZC2HC1CPAMR1Q6UXH9386

IntAct

70 interactions, top by confidence:

ABTypeScore
KRT15ZC2HC1Cpsi-mi:“MI:0915”(physical association)0.670
ZC2HC1CMTUS2psi-mi:“MI:0915”(physical association)0.670
TFIP11ZC2HC1Cpsi-mi:“MI:0915”(physical association)0.670
ZC2HC1CKRT15psi-mi:“MI:0915”(physical association)0.670
ZC2HC1CTFIP11psi-mi:“MI:0915”(physical association)0.670
MTUS2ZC2HC1Cpsi-mi:“MI:0915”(physical association)0.670
PNMA1ZC2HC1Cpsi-mi:“MI:0915”(physical association)0.600
ZC2HC1CPNMA1psi-mi:“MI:0915”(physical association)0.600
ZC2HC1CFSD2psi-mi:“MI:0915”(physical association)0.560
GFAPZC2HC1Cpsi-mi:“MI:0915”(physical association)0.560
TRIM27ZC2HC1Cpsi-mi:“MI:0915”(physical association)0.560
ZC2HC1CSFNpsi-mi:“MI:0915”(physical association)0.560
TRIM23ZC2HC1Cpsi-mi:“MI:0915”(physical association)0.560
TRAF2ZC2HC1Cpsi-mi:“MI:0915”(physical association)0.560
TRAF1ZC2HC1Cpsi-mi:“MI:0915”(physical association)0.560
KRT40ZC2HC1Cpsi-mi:“MI:0915”(physical association)0.560
BANPZC2HC1Cpsi-mi:“MI:0915”(physical association)0.560
ZC2HC1CCBY2psi-mi:“MI:0915”(physical association)0.560
HOOK2ZC2HC1Cpsi-mi:“MI:0915”(physical association)0.560
CCDC136ZC2HC1Cpsi-mi:“MI:0915”(physical association)0.560
ZC2HC1CSPAG5psi-mi:“MI:0915”(physical association)0.560
RABGEF1ZC2HC1Cpsi-mi:“MI:0915”(physical association)0.560

BioGRID (110): ZC2HC1C (Two-hybrid), ZC2HC1C (Two-hybrid), ZC2HC1C (Two-hybrid), ZC2HC1C (Two-hybrid), ZC2HC1C (Two-hybrid), ZC2HC1C (Two-hybrid), ZC2HC1C (Two-hybrid), ZC2HC1C (Two-hybrid), ZC2HC1C (Two-hybrid), ZC2HC1C (Two-hybrid), ZC2HC1C (Two-hybrid), ZC2HC1C (Two-hybrid), ZC2HC1C (Two-hybrid), ZC2HC1C (Two-hybrid), ZC2HC1C (Two-hybrid)

ESM2 similar proteins: A0A1I8MUL8, A0A1L8H8C0, A0A1L8HFX9, A2AG58, A2AJT9, B9UYK6, C5IY45, E9Q309, E9Q4F7, O94687, P0DW16, P31629, P61129, P78332, P97868, Q01613, Q08D57, Q09JY9, Q17QQ9, Q27IV2, Q2T9M9, Q498L0, Q4R731, Q53FD0, Q5F3P8, Q5JSZ5, Q5LJZ2, Q5PPL1, Q5R6I3, Q5SW79, Q5T481, Q5VT06, Q62504, Q66J90, Q6IMN6, Q6P9P0, Q6UB99, Q7Z6E9, Q865B7, Q8BYK8

Diamond homologs: A4FUE7, Q22122, Q32KN7, Q53FD0, Q5PPV5, Q5REC0, Q5TFG8, Q618K0, Q6AYP4, Q7SXT7, Q8BJH1, Q8CCG1, Q96GY0, Q9BGW4, Q9D534, Q5R498

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance61
Likely benign9
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3634 predictions. Top by Δscore:

VariantEffectΔscore
14:75087231:C:CCacceptor_gain1.0000
14:75097267:TTAT:Tacceptor_gain1.0000
14:75100988:TCA:Tdonor_loss1.0000
14:75100989:CA:Cdonor_loss1.0000
14:75100990:A:ACdonor_gain1.0000
14:75100991:C:CCdonor_gain1.0000
14:75100991:C:CTdonor_loss1.0000
14:75100991:CCAT:Cdonor_gain1.0000
14:75101149:TCGCT:Tacceptor_gain1.0000
14:75101150:CGCT:Cacceptor_gain1.0000
14:75101150:CGCTC:Cacceptor_gain1.0000
14:75101152:CT:Cacceptor_gain1.0000
14:75101152:CTCTG:Cacceptor_loss1.0000
14:75101153:TCTG:Tacceptor_gain1.0000
14:75101154:C:Aacceptor_loss1.0000
14:75101154:C:CCacceptor_gain1.0000
14:75101154:C:Gacceptor_gain1.0000
14:75101155:T:Aacceptor_loss1.0000
14:75101166:C:CTacceptor_gain1.0000
14:75101167:A:Tacceptor_gain1.0000
14:75101650:AACTT:Adonor_loss1.0000
14:75101651:ACTTA:Adonor_loss1.0000
14:75101652:CTTA:Cdonor_loss1.0000
14:75101653:TTAC:Tdonor_loss1.0000
14:75101654:TACC:Tdonor_loss1.0000
14:75101655:A:ACdonor_gain1.0000
14:75101655:AC:Adonor_gain1.0000
14:75101655:ACCA:Adonor_loss1.0000
14:75101655:ACCAT:Adonor_gain1.0000
14:75101656:C:CGdonor_gain1.0000

AlphaMissense

3001 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
14:75071834:T:CF421L0.996
14:75071836:T:AF421L0.996
14:75071836:T:GF421L0.996
14:75071760:G:CR396P0.991
14:75071759:C:AR396S0.990
14:75071766:T:CF398S0.988
14:75071789:C:GH406D0.983
14:75071835:T:GF421C0.983
14:75071791:C:AH406Q0.982
14:75071791:C:GH406Q0.982
14:75071766:T:GF398C0.981
14:75071744:T:CC391R0.980
14:75071765:T:CF398L0.978
14:75071767:C:AF398L0.978
14:75071767:C:GF398L0.978
14:75071801:T:AC410S0.978
14:75071802:G:CC410S0.978
14:75071827:G:CR418S0.978
14:75071827:G:TR418S0.978
14:75071861:G:CG430R0.977
14:75071744:T:AC391S0.976
14:75071745:G:CC391S0.976
14:75071754:G:AC394Y0.976
14:75077558:G:CW455C0.976
14:75077558:G:TW455C0.976
14:75071753:T:AC394S0.975
14:75071754:G:CC394S0.975
14:75071801:T:CC410R0.975
14:75071803:C:GC410W0.975
14:75071802:G:AC410Y0.974

dbSNP variants (sampled 300 via entrez): RS1000008765 (14:75076708 T>C), RS1000060993 (14:75077105 T>C), RS1000300669 (14:75074258 T>C), RS1000336708 (14:75070589 C>A,T), RS1000686640 (14:75078954 G>C), RS1000738359 (14:75079319 G>GA), RS1001273923 (14:75068177 G>A), RS1001737679 (14:75074896 T>C), RS1002023672 (14:75073020 TCCC>T), RS1002275324 (14:75072022 C>T), RS1002351165 (14:75078423 A>G), RS1002405040 (14:75078754 T>G), RS1002740591 (14:75076273 T>G), RS1002775717 (14:75068894 G>C), RS1002958151 (14:75075086 C>T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
neurodevelopmental disorderLimitedAutosomal recessive

Mondo (1): neurodevelopmental disorder (MONDO:0700092)

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST006940_131Neurociticism1.000000e-13
GCST010002_156Refractive error7.000000e-25

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0007660neuroticism measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
D065886Neurodevelopmental DisordersF03.625

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases methylation, increases expression2
dicrotophosdecreases expression1
methylmercuric chloridedecreases expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
abrineincreases expression1
bisphenol Sdecreases methylation1
jinfukangincreases expression1
(+)-JQ1 compounddecreases expression1
Temozolomidedecreases expression1
Sunitinibdecreases expression1
Air Pollutantsincreases abundance, increases expression1
Benzo(a)pyrenedecreases methylation1
Cadmiumdecreases expression, increases abundance1
Doxorubicindecreases expression1
Lipopolysaccharidesaffects response to substance, increases expression1
Quercetindecreases expression1
Smokedecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Cyclosporinedecreases expression1
Cadmium Chloridedecreases expression, increases abundance1
Okadaic Acidincreases expression1
Copper Sulfatedecreases expression1
Particulate Matterincreases abundance, increases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT04586348PHASE4UNKNOWNPrenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115PHASE4UNKNOWNDouble-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT02559102PHASE3COMPLETEDDexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079PHASE3COMPLETEDStudy of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480PHASE3RECRUITINGReducing Missed Appointments
NCT07377032PHASE3RECRUITINGTAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT02909959PHASE2COMPLETEDSulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348PHASE2RECRUITINGSertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372PHASE2COMPLETEDSafety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT00503191PHASE1COMPLETEDNeuroModulation Technique Treatment of Autism
NCT04475848PHASE1COMPLETEDA Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398PHASE1COMPLETEDIAMA-6 Oral Dose Study in Healthy Adults
NCT01783041PHASE2/PHASE3COMPLETEDEffect of Early L-Carnitine Supplementation on Neurodevelopmental Outcomes in Very Preterm Infants
NCT05767385PHASE2/PHASE3RECRUITINGFetal Cerebrovascular Autoregulation in Congenital Heart Disease and Association With Neonatal Neurobehavior
NCT05675098EARLY_PHASE1NOT_YET_RECRUITINGCentral Nervous System Stimulants and Physical Function in Children With Cerebral Palsy
NCT00783783Not specifiedCOMPLETEDCYP2D6 Pharmacogenetics in Risperidone-Treated Children
NCT01778504Not specifiedRECRUITINGStudying Childhood-onset Behavioral, Psychiatric, and Developmental Disorders
NCT01850784Not specifiedUNKNOWNHigh Energy Formula Feeding in Infants With Congenital Heart Disease
NCT01922791Not specifiedCOMPLETEDNutrition and Pregnancy Intervention Study
NCT01942525Not specifiedUNKNOWNInfluence of Intrauterine Growth Restriction on Amplitude-integrated EEG in Preterm Infants
NCT02003170Not specifiedCOMPLETEDEtiology and Early Diagnosis of Neurodevelopmental Disorders
NCT02118649Not specifiedACTIVE_NOT_RECRUITINGEnhancing Behavior and Brain Response to Visual Targets Using a Computer Game
NCT02557191Not specifiedTERMINATEDBiomarkers, Neurodevelopment and Preterm Infants
NCT02690675Not specifiedCOMPLETEDIron Supplement Effect on Child Development
NCT02694003Not specifiedCOMPLETEDBetter Nights, Better Days for Children With Neurodevelopment Disorders
NCT02792894Not specifiedCOMPLETEDFamily Networks (FaNs) for Children With Developmental Disorders and Delays
NCT02871674Not specifiedUNKNOWNGood Night Project: Behavioural Sleep Interventions for Children With ADHD: A Randomised Controlled Trial
NCT02887157Not specifiedCOMPLETEDAnalyzing Retinal Microanatomy in ROP
NCT02898298Not specifiedCOMPLETEDPositive Emotion Regulation Training in Children, Adolescents and Young Adults With and Without Developmental Disorder
NCT02912780Not specifiedUNKNOWNIntroduction of Microsystems in a Level 3 Neonatal Intensive Care Unit
NCT03023293Not specifiedCOMPLETEDn-3 PUFAs, Irisin and Maternal Glucose Metabolism From Pregnancy to Postpartum
NCT03023644Not specifiedCOMPLETEDImproving Neurodevelopmental Outcomes in Children With Congenital Heart Disease: An Intervention Study
NCT03032991Not specifiedUNKNOWNEarly Biomarkers of Neurodevelopment in Offspring of Diabetic Mothers
NCT03088189Not specifiedTERMINATEDEffect of Parental Peri-conceptional Vitamin B12 Supplementation on Infant Neurocognitive Development in Offspring
NCT03096028Not specifiedCOMPLETEDDevelopmental Origins of Mental Health Disorders
NCT03148782Not specifiedCOMPLETEDBrain Plasticity Underlying Acquisition of New Organizational Skills in Children-R61 Phase
NCT03172104Not specifiedCOMPLETEDNeurobehavioural Development of Infants Born <30 Weeks Gestational Age Between Birth and Five Years of Age
NCT03222375Not specifiedRECRUITINGSQUED™ Series 28.1 Home-use and Treatment of Autowave Reverberator of Autism
NCT03229928Not specifiedCOMPLETEDClinical Testing of a Real-Time Behavior Measurement Tool: Measuring Outcomes for CHAnge
NCT03232489Not specifiedUNKNOWNStudy for the Evaluation of the Feasibility of Applying Advanced MRI Scanning in Pediatric Clinical Practice