ZFTRAF1

gene
On this page

Also known as CHRPKIAA0496MGC13010

Summary

ZFTRAF1 (zinc finger TRAF-type and ring finger containing 1, HGNC:17806) is a protein-coding gene on chromosome 8q24.3, encoding Zinc finger TRAF-type-containing protein 1 (P0DTL6).

Predicted to enable zinc ion binding activity. Predicted to be located in nuclear envelope and perinuclear region of cytoplasm. Predicted to be active in nucleus.

Source: NCBI Gene 50626 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): complex neurodevelopmental disorder (Limited, GenCC) — +1 more curated relationship
  • GWAS associations: 10
  • Clinical variants (ClinVar): 1 total
  • MANE Select transcript: NM_001330618

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:17806
Approved symbolZFTRAF1
Namezinc finger TRAF-type and ring finger containing 1
Location8q24.3
Locus typegene with protein product
StatusApproved
AliasesCHRP, KIAA0496, MGC13010
Ensembl geneENSG00000187954
Ensembl biotypeprotein_coding
OMIM616635
Entrez50626

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 retained_intron, 2 protein_coding

ENST00000528558, ENST00000528663, ENST00000530374, ENST00000533173, ENST00000959494

RefSeq mRNA: 3 — MANE Select: NM_001330618 NM_001330618, NM_001408047, NM_001408048

CCDS: CCDS83335

Canonical transcript exons

ENST00000530374 — 4 exons

ExonStartEnd
ENSE00002163517144462283144462871
ENSE00004474034144449582144450770
ENSE00004474158144453222144453460
ENSE00004474165144452359144452570

Expression profiles

Bgee: expression breadth ubiquitous, 260 present calls, max score 97.33.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.7729 / max 180.2029, expressed in 1815 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
9568410.72041796
9568510.60341733
956864.44911585

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right hemisphere of cerebellumUBERON:001489097.33gold quality
apex of heartUBERON:000209897.25gold quality
cerebellar hemisphereUBERON:000224597.06gold quality
cerebellar cortexUBERON:000212996.91gold quality
left testisUBERON:000453396.74gold quality
right testisUBERON:000453496.69gold quality
adenohypophysisUBERON:000219696.66gold quality
right frontal lobeUBERON:000281096.15gold quality
right adrenal glandUBERON:000123396.05gold quality
right adrenal gland cortexUBERON:003582795.87gold quality
left adrenal gland cortexUBERON:003582595.85gold quality
lower esophagus mucosaUBERON:003583495.78gold quality
pituitary glandUBERON:000000795.69gold quality
body of pancreasUBERON:000115095.65gold quality
right coronary arteryUBERON:000162595.56gold quality
left adrenal glandUBERON:000123495.51gold quality
endocervixUBERON:000045895.30gold quality
cerebellumUBERON:000203795.16gold quality
muscle layer of sigmoid colonUBERON:003580595.08gold quality
adrenal cortexUBERON:000123594.98gold quality
cingulate cortexUBERON:000302794.98gold quality
right ovaryUBERON:000211894.95gold quality
anterior cingulate cortexUBERON:000983594.93gold quality
esophagogastric junction muscularis propriaUBERON:003584194.91gold quality
body of uterusUBERON:000985394.90gold quality
right lobe of thyroid glandUBERON:000111994.88gold quality
nucleus accumbensUBERON:000188294.87gold quality
mucosa of transverse colonUBERON:000499194.85gold quality
lower esophagus muscularis layerUBERON:003583394.84gold quality
body of stomachUBERON:000116194.83gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes7.19

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting ZFTRAF1, 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-1468-3P99.9672.743797
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-149-3P99.7268.223963
HSA-MIR-6883-5P99.6968.053785
HSA-MIR-1249-5P99.6166.552049
HSA-MIR-6797-5P99.6166.552084
HSA-MIR-3191-5P99.2466.521722
HSA-MIR-3074-5P98.8266.561414
HSA-MIR-222-5P98.7569.171242
HSA-MIR-3944-5P98.5067.55997
HSA-MIR-1910-3P98.4467.511695
HSA-MIR-6511A-5P98.1367.471770
HSA-MIR-3663-5P97.0164.84713
HSA-MIR-60195.9867.59421
HSA-MIR-120489.5065.56109

Literature-anchored findings (GeneRIF, showing 2)

  • High CYHR1 expression is associated with Esophageal Squamous Cell Carcinoma. (PMID:26676980)
  • Biallelic loss-of-function variants of ZFTRAF1 cause neurodevelopmental disorder with microcephaly and hypotonia. (PMID:38641995)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriozftraf1ENSDARG00000061057
mus_musculusGm57852ENSMUSG00000121583
rattus_norvegicusTmem276-zftraf1ENSRNOG00000014811
drosophila_melanogasterCG32486FBGN0266918

Protein

Protein identifiers

Zinc finger TRAF-type-containing protein 1P0DTL6 (reviewed: P0DTL6)

Alternative names: Cysteine and histidine-rich protein 1

All UniProt accessions (1): P0DTL6

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Interacts with LGALS3.

Subcellular location. Cytoplasm. Perinuclear region.

Similarity. Belongs to the ZFTRAF1 family.

Isoforms (4)

UniProt IDNamesCanonical?
P0DTL6-55yes
P0DTL6-11
P0DTL6-22
P0DTL6-44

RefSeq proteins (3): NP_001317547, NP_001394976, NP_001394977 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001293Znf_TRAFDomain
IPR001841Znf_RINGDomain
IPR013083Znf_RING/FYVE/PHDHomologous_superfamily
IPR039338ZFTRAF1Family
IPR049548Sina-like_RINGDomain

Pfam: PF21362

UniProt features (9 total): splice variant 4, zinc finger region 2, chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P0DTL6-F182.710.68

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 86 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_DN, TSENG_IRS1_TARGETS_UP, TGCGCANK_UNKNOWN, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, CASTELLANO_NRAS_TARGETS_DN, BLALOCK_ALZHEIMERS_DISEASE_UP, MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN, SCHLOSSER_SERUM_RESPONSE_AUGMENTED_BY_MYC, BERENJENO_TRANSFORMED_BY_RHOA_UP, PARENT_MTOR_SIGNALING_UP, GOCC_NUCLEAR_ENVELOPE, NUYTTEN_EZH2_TARGETS_DN, NIKOLSKY_BREAST_CANCER_8Q23_Q24_AMPLICON, SWEET_LUNG_CANCER_KRAS_UP

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 (4): nucleus (GO:0005634), nuclear envelope (GO:0005635), perinuclear region of cytoplasm (GO:0048471), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
transition metal ion binding1
binding1
cation binding1
intracellular membrane-bounded organelle1
nucleus1
endomembrane system1
organelle envelope1
cytoplasm1
intracellular anatomical structure1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

34 interactions, top by confidence:

ABTypeScore
UBE2KZFTRAF1psi-mi:“MI:0914”(association)0.620
UBE2KZFTRAF1psi-mi:“MI:0915”(physical association)0.620
HAO2EIF4G3psi-mi:“MI:0914”(association)0.530
TNFAIP3UBBpsi-mi:“MI:0914”(association)0.530
VPS36UBBpsi-mi:“MI:0914”(association)0.530
DEGS1ZFTRAF1psi-mi:“MI:0915”(physical association)0.400
Ube2kpsi-mi:“MI:0914”(association)0.350
Ube2kZFTRAF1psi-mi:“MI:0914”(association)0.350
FAM189BKLRG2psi-mi:“MI:0914”(association)0.350
SLC45A2TMEM63Apsi-mi:“MI:0914”(association)0.350
SDC1ARVCFpsi-mi:“MI:0914”(association)0.350
DNAJB2UBBpsi-mi:“MI:0914”(association)0.350
LITAFSDCBPpsi-mi:“MI:0914”(association)0.350
EPN3MID1psi-mi:“MI:0914”(association)0.350
RABGEF1GAKpsi-mi:“MI:0914”(association)0.350
PLXNB2C2CD4Bpsi-mi:“MI:0914”(association)0.350
LRRC73THAP12psi-mi:“MI:0914”(association)0.350
TLCD5TOM1L1psi-mi:“MI:0914”(association)0.350
RNF5ZFTRAF1psi-mi:“MI:0914”(association)0.350
PNMA6AZFTRAF1psi-mi:“MI:0914”(association)0.350
LRRC73SLC27A2psi-mi:“MI:0914”(association)0.350
STX5ZFTRAF1psi-mi:“MI:0914”(association)0.350
IL23RZFTRAF1psi-mi:“MI:0914”(association)0.350

ESM2 similar proteins: A5WW08, A7XUJ6, B5DF45, B6CJY4, B6CJY5, O00463, O15344, O70583, P0DTL6, P0DW87, P0DW89, P39429, P70191, P70196, P82457, P82458, Q08CH8, Q12933, Q13114, Q28DL4, Q29RQ5, Q2TAD9, Q3KPU8, Q3MV19, Q3U9F6, Q3ZCC3, Q5FWP4, Q5R4L1, Q60803, Q61382, Q6DJN2, Q6GNX1, Q6IWL4, Q6J1I7, Q6P256, Q80WG7, Q8N2W9, Q91ZY8, Q95KF1, Q96A37

Diamond homologs: P0DTL6, P0DW87, P0DW89, P0DW91, P93748, Q08CH8, Q2TAD9, Q6GNX1, Q9M2P4, Q9VZV5, A8X679, O43255, P21461, P29304, P61092, P61093, Q06985, Q06986, Q10L91, Q7SYL3, Q7XA77, Q7ZVG6, Q84JL3, Q84K34, Q86MW9, Q8I147, Q8IUQ4, Q8R4T2, Q8S3N1, Q8T3Y0, Q920M9, Q93WE4, Q965X6, Q9C6H2, Q9C6H3, Q9C6H4, Q9C9M0, Q9FKD5, Q9FKD6, Q9FKD7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance1
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

947 predictions. Top by Δscore:

VariantEffectΔscore
8:144450766:GACCT:Gacceptor_gain1.0000
8:144450767:ACCT:Aacceptor_gain1.0000
8:144450768:CCTC:Cacceptor_gain1.0000
8:144450769:CT:Cacceptor_gain1.0000
8:144450770:TC:Tacceptor_loss1.0000
8:144450771:C:CCacceptor_gain1.0000
8:144450771:CT:Cacceptor_loss1.0000
8:144450773:G:Cacceptor_gain1.0000
8:144450773:G:GCacceptor_gain1.0000
8:144450780:C:CTacceptor_gain1.0000
8:144450781:A:Tacceptor_gain1.0000
8:144450784:C:CTacceptor_gain1.0000
8:144450785:A:Tacceptor_gain1.0000
8:144450970:C:CTacceptor_gain1.0000
8:144452357:A:ACdonor_gain1.0000
8:144452357:A:Cdonor_loss1.0000
8:144452358:C:CCdonor_gain1.0000
8:144452566:TTACC:Tacceptor_gain1.0000
8:144452568:ACCC:Aacceptor_loss1.0000
8:144452569:CC:Cacceptor_gain1.0000
8:144452570:CC:Cacceptor_gain1.0000
8:144452570:CCTGG:Cacceptor_loss1.0000
8:144452571:C:CCacceptor_gain1.0000
8:144453217:GTTA:Gdonor_loss1.0000
8:144453218:TTAC:Tdonor_loss1.0000
8:144453219:TACCT:Tdonor_loss1.0000
8:144453220:AC:Adonor_loss1.0000
8:144453221:C:Gdonor_loss1.0000
8:144453234:T:TAdonor_gain1.0000
8:144450790:C:CTacceptor_gain0.9900

AlphaMissense

2619 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
8:144450429:C:GA347P1.000
8:144450431:A:GL346P1.000
8:144450431:A:TL346Q1.000
8:144450434:A:GL345P1.000
8:144450563:A:GL302P1.000
8:144450627:G:TR281S1.000
8:144450665:A:TV268D1.000
8:144450671:G:TA266D1.000
8:144450672:C:GA266P1.000
8:144450677:A:GL264P1.000
8:144450684:A:GW262R1.000
8:144450684:A:TW262R1.000
8:144450720:A:CY250D1.000
8:144450736:G:CF244L1.000
8:144450736:G:TF244L1.000
8:144450737:A:GF244S1.000
8:144450738:A:GF244L1.000
8:144450749:C:GR240P1.000
8:144450750:G:TR240S1.000
8:144450753:A:CY239D1.000
8:144452491:A:GC189R1.000
8:144452531:C:AW175C1.000
8:144452531:C:GW175C1.000
8:144452533:A:GW175R1.000
8:144452533:A:TW175R1.000
8:144452538:C:GC173S1.000
8:144452539:A:GC173R1.000
8:144452539:A:TC173S1.000
8:144452559:C:GC166S1.000
8:144452560:A:GC166R1.000

dbSNP variants (sampled 300 via entrez): RS1000026052 (8:144459645 G>A), RS1000209806 (8:144462357 T>C), RS1000336116 (8:144462617 G>A), RS1000379339 (8:144455239 C>T), RS1000452034 (8:144462340 G>A,C), RS1000574372 (8:144461753 A>C), RS1000759903 (8:144455272 G>A), RS1000859411 (8:144449839 T>C), RS1000988999 (8:144461596 C>G), RS1001105885 (8:144454091 G>A), RS1001120547 (8:144450037 G>A,C), RS1001195114 (8:144459601 C>G), RS1001196453 (8:144463603 A>C,G), RS1001206207 (8:144463374 C>G,T), RS1001220384 (8:144451437 G>A)

Disease associations

OMIM: gene MIM:616635 | disease phenotypes: MIM:249500

GenCC curated gene-disease

DiseaseClassificationInheritance
complex neurodevelopmental disorderLimitedAutosomal recessive
neurodevelopmental disorderLimitedAutosomal recessive

Mondo (3): autosomal recessive non-syndromic intellectual disability (MONDO:0019502), complex neurodevelopmental disorder (MONDO:0100038), neurodevelopmental disorder (MONDO:0700092)

Orphanet (1): Autosomal recessive non-syndromic intellectual disability (Orphanet:88616)

HPO phenotypes

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

GWAS associations

10 associations (top):

StudyTraitp-value
GCST002598_30Educational attainment9.000000e-06
GCST003795_8Age at first birth6.000000e-07
GCST006045_10Age at first birth6.000000e-09
GCST006269_728General cognitive ability1.000000e-08
GCST006879_12Blood metabolite levels4.000000e-10
GCST006879_13Blood metabolite levels2.000000e-09
GCST006879_14Blood metabolite levels2.000000e-11
GCST006879_5Blood metabolite levels2.000000e-12
GCST008595_130Cognitive ability, years of educational attainment or schizophrenia (pleiotropy)1.000000e-09
GCST90000050_61Age at first birth6.000000e-09

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004784self reported educational attainment
EFO:0009101age at first birth measurement
EFO:0004337intelligence

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

26 total (human), top 26 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases expression, affects cotreatment, increases expression2
Nickeldecreases expression2
aristolochic acid Iincreases expression1
testosterone enanthateaffects expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
K 7174decreases expression1
Resveratrolaffects cotreatment, increases expression1
Fulvestrantincreases methylation1
Acetaminophenincreases expression1
Air Pollutantsdecreases expression1
Air Pollutants, Occupationaldecreases expression1
Arsenicaffects methylation1
Benzo(a)pyreneincreases methylation1
Cadmiumincreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Diethylhexyl Phthalatedecreases expression1
Ethyl Methanesulfonateincreases expression1
Indomethacinaffects cotreatment, increases expression1
Methyl Methanesulfonateincreases expression1
Plant Extractsincreases expression, affects cotreatment1
Selenomethionineaffects expression1
Tretinoinincreases expression1
Valproic Acidincreases methylation1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression1
Copper Sulfatedecreases expression1
Vitamin K 3affects expression1

Clinical trials (associated diseases)

204 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
NCT06310681Not specifiedCOMPLETEDPilot Testing of a Co-adapted Group Programme for Parents/Carers of Children With Complex Neurodisability
NCT07303049Not specifiedNOT_YET_RECRUITINGCognitive Benefit of Intensive Rehabilitation Using Rhythmic Music Training in Children With Complex Neurodevelopmental Disorder
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