Gene Gene information from NCBI Gene database.
Entrez ID 463
Gene name Zinc finger homeobox 3
Gene symbol ZFHX3
Synonyms (NCBI Gene)
ATBF1ATBTATFB8C16orf47SCA4ZFH-3ZNF927
Chromosome 16
Chromosome location 16q22.2-q22.3
Summary This gene encodes a transcription factor with multiple homeodomains and zinc finger motifs, and regulates myogenic and neuronal differentiation. The encoded protein suppresses expression of the alpha-fetoprotein gene by binding to an AT-rich enhancer moti
SNPs SNP information provided by dbSNP.
1
SNP ID Visualize variation Clinical significance Consequence
rs140602496 C>A,T Conflicting-interpretations-of-pathogenicity Intron variant, coding sequence variant, genic downstream transcript variant, missense variant
miRNA miRNA information provided by mirtarbase database.
943
miRTarBase ID miRNA Experiments Reference
MIRT019620 hsa-miR-340-5p Sequencing 20371350
MIRT027177 hsa-miR-103a-3p Sequencing 20371350
MIRT027754 hsa-miR-98-5p Microarray 19088304
MIRT031857 hsa-miR-16-5p Sequencing 20371350
MIRT047244 hsa-miR-181b-5p CLASH 23622248
Transcription factors Transcription factors information provided by TRRUST V2 database.
1
Transcription factor Regulation Reference
ESR1 Activation 21367855
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
46
GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IDA 11312261, 11314020
GO:0000785 Component Chromatin ISA
GO:0000976 Function Transcription cis-regulatory region binding IDA 11312261
GO:0000978 Function RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
GO:0000978 Function RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA 7507206
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
104155 777 ENSG00000140836
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q15911
Protein name Zinc finger homeobox protein 3 (AT motif-binding factor 1) (AT-binding transcription factor 1) (Alpha-fetoprotein enhancer-binding protein) (Zinc finger homeodomain protein 3) (ZFH-3)
Protein function Transcriptional regulator which can act as an activator or a repressor. Inhibits the enhancer element of the AFP gene by binding to its AT-rich core sequence. In concert with SMAD-dependent TGF-beta signaling can repress the transcription of AFP
PDB 2DA1 , 2DA2 , 2DA3
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00096 zf-C2H2 726 750 Zinc finger, C2H2 type Domain
PF00096 zf-C2H2 1596 1620 Zinc finger, C2H2 type Domain
PF00046 Homeodomain 2146 2202 Homeodomain Domain
PF00046 Homeodomain 2243 2299 Homeodomain Domain
PF00046 Homeodomain 2642 2698 Homeodomain Domain
PF00046 Homeodomain 2947 3003 Homeodomain Domain
Tissue specificity TISSUE SPECIFICITY: Not found in normal gastric mucosa but found in gastric carcinoma cells (at protein level). Expression is higher in ER-positive breast tumors than ER-negative breast tumors (at protein level). {ECO:0000269|PubMed:17330845, ECO:0000269|
Sequence
MEGCDSPVVSGKDNGCGIPQHQQWTELNSTHLPDKPSSMEQSTGESHGPLDSLRAPFNER
LAESTASAGPPSEPASKEVTCNECSASFASLQTYMEHHCPSARPPPPLREESASDTGEEG
DEESDVENLAGEIVYQPDGSAYIVESLSQLTQGGGACGSGSGSGPLPSLFLNSLPGAGGK
QGDPSCAAPVYPQIINTFHIASSFGKWFEGPDQAFPNTSALAGLSPVLHSFRVFDVRHKS
NKDYLNSDGSAKSSCVSKDVPNNVDLSKFDGFVLYGKRKPILMCFLCKLSFGYVRSFVTH
AVHDHRMTLSEDERKILSNKNISAIIQGIGKDKEPLVSFLEPKNKNFQHPLVSTANLIGP
GHSFYGKFSGIRMEGEEALPAGSAAGPEQPQAGLLTPSTLLNLGGLTSSVLKTPITSVPL
GPLASSPTKSSEGKDSGAAEGEKQEVGDGDCFSEKVEPAEEEAEEEEEEEEAEEEEEEEE
EEEEEEEDEGCKGLFPSELDEELEDRPHEEPGAAAGSSSKKDLALSNQSISNSPLMPNVL
QTLSRGTASTSSNSASSFVVFDGANRRNRLSFNSEGVRANVAEGGRRLDFADESANKDNA
TAPEPNESTEGDDGGFVPHHQHAGSLCELGVGECPSGSGVECPKCDTVLGSSRSLGGHMT
MMHSRNSCKTLKCPKCNWHYKYQQTLEAHMKEKHPEPGGSCVYCKSGQPHPRLARGESYT
CGYKPFRCEVCNYSTTTKGNLSIHMQSDKHLNNMQNLQNGGGEQVFSHTAGAAAAAVAAA
AAAANISSSCGAPSPTKPKTKPTWRCEVCDYETNVARNLRIHMTSEKHMHNMMLLQQNMT
QIQHNRHLGLGSLPSPAEAELYQYYLAQNMNLPNLKMDSAASDAQFMMSGFQLDPAGPMA
AMTPALVGGEIPLDMRLGGGQLVSEELMNLGESFIQTNDPSLKLFQCAVCNKFTTDNLDM
LGLHMNVERSLSEDEWKAVMGDSYQCKLCRYNTQLKANFQLHCKTDKHVQKYQLVAHIKE
GGKANEWRLKCVAIGNPVHLKCNACDYYTNSLEKLRLHTVNSRHEASLKLYKHLQQHESG
VEGESCYYHCVLCNYSTKAKLNLIQHVRSMKHQRSESLRKLQRLQKGLPEEDEDLGQIFT
IRRCPSTDPEEAIEDVEGPSETAADPEELAKDQEGGASSSQAEKELTDSPATSKRISFPG
SSESPLSSKRPKTAEEIKPEQMYQCPYCKYSNADVNRLRVHAMTQHSVQPMLRCPLCQDM
LNNKIHLQLHLTHLHSVAPDCVEKLIMTVTTPEMVMPSSMFLPAAVPDRDGNSNLEEAGK
QPETSEDLGKNILPSASTEQSGDLKPSPADPGSVREDSGFICWKKGCNQVFKTSAALQTH
FNEVHAKRPQLPVSDRHVYKYRCNQCSLAFKTIEKLQLHSQYHVIRAATMCCLCQRSFRT
FQALKKHLETSHLELSEADIQQLYGGLLANGDLLAMGDPTLAEDHTIIVEEDKEEESDLE
DKQSPTGSDSGSVQEDSGSEPKRALPFRKGPNFTMEKFLDPSRPYKCTVCKESFTQKNIL
LVHYNSVSHLHKLKRALQESATGQPEPTSSPDNKPFKCNTCNVAYSQSSTLEIHMRSVLH
QTKARAAKLEAASGSSNGTGNSSSISLSSSTPSPVSTSGSNTFTTSNPSSAGIAPSSNLL
SQVPTESVGMPPLGNPIGANIASPSEPKEANRKKLADMIASRQQQQQQQQQQQQQQQQQQ
QAQTLAQAQAQVQAHLQQELQQQAALIQSQLFNPTLLPHFPMTTETLLQLQQQQHLLFPF
YIPSAEFQLNPEVSLPVTSGALTLTGTGPGLLEDLKAQVQVPQQSHQQILPQQQQNQLSI
AQSHSALLQPSQHPEKKNKLVIKEKEKESQRERDSAEGGEGNTGPKETLPDALKAKEKKE
LAPGGGSEPSMLPPRIASDARGNATKALLENFGFELVIQYNENKQKVQKKNGKTDQGENL
EKLECDSCGKLFSNILILKSHQEHVHQNYFPFKQLERFAKQYRDHYDKLYPLRPQTPEPP
PPPPPPPPPPLPAAPPQPASTPAIPASAPPITSPTIAPAQPSVPLTQLSMPMELPIFSPL
MMQTMPLQTLPAQLPPQLGPVEPLPADLAQLYQHQLNPTLLQQQNKRPRTRITDDQLRVL
RQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQ
RNKDSPYNFSNPPITSLE
ELKIDSRPPSPEPPKQEYWGSKRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLN
LPTRVIVVWFQNARQKARK
NYENQGEGKDGERRELTNDRYIRTSNLNYQCKKCSLVFQRI
FDLIKHQKKLCYKDEDEEGQDDSQNEDSMDAMEILTPTSSSCSTPMPSQAYSAPAPSANN
TASSAFLQLTAEAEELATFNSKTEAGDEKPKLAEAPSAQPNQTQEKQGQPKPELQQQEQP
EQKTNTPQQKLPQLVSLPSLPQPPPQAPPPQCPLPQSSPSPSQLSHLPLKPLHTSTPQQL
ANLPPQLIPYQCDQCKLAFPSFEHWQEHQQLHFLSAQNQFIHPQFLDRSLDMPFMLFDPS
NPLLASQLLSGAIPQIPASSATSPSTPTSTMNTLKRKLEEKASASPGENDSGTGGEEPQR
DKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKGQ
FRAVGPAQAHRRCPFCRALFKAKTALEAHIRSRHWHEAKRAGYNLTLSAMLLDCDGGLQM
KGDIFDGTSFSHLPPSSSDGQGVPLSPVSKTMELSPRTLLSPSSIKVEGIEDFESPSMSS
VNLNFDQTKLDNDDCSSVNTAITDTTTGDEGNADNDSATGIATETKSSSAPNEGLTKAAM
MAMSEYEDRLSSGLVSPAPSFYSKEYDNEGTVDYSETSSLADPCSPSPGASGSAGKSGDS
GDRPGQKRFRTQMTNLQLKVLKSCFNDYRTPTMLECEVLGNDIGLPKRVVQVWFQNARAK
EKK
SKLSMAKHFGINQTSYEGPKTECTLCGIKYSARLSVRDHIFSQQHISKVKDTIGSQL
DKEKEYFDPATVRQLMAQQELDRIKKANEVLGLAAQQQGMFDNTPLQALNLPTAYPALQG
IPPVLLPGLNSPSLPGFTPSNTALTSPKPNLMGLPSTTVPSPGLPTSGLPNKPSSASLSS
PTPAQATMAMGPQQPPQQQQQQQQPQVQQPPPPPAAQPPPTPQLPLQQQQQRKDKDSEKV
KEKEKAHKGKGEPLPVPKKEKGEAPTATAATISAPLPTMEYAVDPAQLQALQAALTSDPT
ALLTSQFLPYFVPGFSPYYAPQIPGALQSGYLQPMYGMEGLFPYSPALSQALMGLSPGSL
LQQYQQYQQSLQEAIQQQQQRQLQQQQQQKVQQQQPKASQTPVPPGAPSPDKDPAKESPK
PEEQKNTPREVSPLLPKLPEEPEAESKSADSLYDPFIVPKVQYKLVCRKCQAGFSDEEAA
RSHLKSLCFFGQSVVNLQEMVLHVPTGGGGGGSGGGGGGGGGGGGGGSYHCLACESALCG
EEALSQHLESALHKHRTITRAARNAKEHPSLLPHSACFPDPSTASTSQSAAHSNDSPPPP
SAAAPSSASPHASRKSWPQVVSRASAAKPPSFPPLSSSSTVTSSSCSTSGVQPSMPTDDY
SEESDTDLSQKSDGPASPVEGPKDPSCPKDSGLTSVGTDTFRL
Sequence length 3703
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Signaling pathways regulating pluripotency of stem cells   RUNX3 regulates CDKN1A transcription
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
185
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Moyamoya angiopathy Likely pathogenic rs2038723552 RCV004704490
Neurodevelopmental disorder Likely pathogenic; Pathogenic rs2144074254, rs775876705, rs2507406125, rs2143405085, rs869312913 RCV002471723
RCV002471769
RCV002471781
RCV002471835
RCV004786565
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Acute myeloid leukemia Conflicting classifications of pathogenicity rs148383343 RCV005898589
Adrenocortical carcinoma, hereditary Conflicting classifications of pathogenicity rs143351192 RCV005912232
Atrial fibrillation, familial, 8 risk factor rs12931021 RCV003444097
Autism spectrum disorder Likely benign rs2507195645, rs2035877112 RCV003127350
RCV003128052
Associations from Text MiningDisease associations identified through Pubtator
Disease Name Relationship Type References
Adenocarcinoma Associate 36103249
Adenoma Associate 28713972
Alzheimer Disease Associate 30598117
Anxiety Associate 35577822
Apraxia oculomotor Cogan type Associate 38035881
Atrial Fibrillation Associate 19597491, 19597492, 21107608, 21760908, 22384221, 22726630, 22776031, 23132824, 23428961, 24239840, 24910551, 24983873, 25539802, 26267381, 26272656
View all (12 more)
Atrial Standstill Associate 28381281
Autism Spectrum Disorder Associate 38412861
Autoimmune Diseases of the Nervous System Associate 39615603
Brachydactyly Associate 38412861