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    ZNF462 zinc finger protein 462 [ Homo sapiens (human) ]

    Gene ID: 58499, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ZNF462provided by HGNC
    Official Full Name
    zinc finger protein 462provided by HGNC
    Primary source
    HGNC:HGNC:21684
    See related
    Ensembl:ENSG00000148143 MIM:617371; AllianceGenome:HGNC:21684
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    WSKA; ZFPIP; Zfp462
    Summary
    The protein encoded by this gene belongs to C2H2-type zinc finger family of proteins. It contains multiple C2H2-type zinc fingers and may be involved in transcriptional regulation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2016]
    Expression
    Ubiquitous expression in testis (RPKM 2.5), thyroid (RPKM 2.5) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZNF462 in Genome Data Viewer
    Location:
    9q31.2
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (106860158..107013634)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (119036267..119189919)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (109625447..109775915)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene COP1, E3 ubiquitin ligase pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28748 Neighboring gene uncharacterized LOC105376204 Neighboring gene RNA, 5S ribosomal pseudogene 292 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:109633482-109634681 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:109640709-109641456 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:109654807-109655306 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:109678392-109679591 Neighboring gene uncharacterized LOC340512 Neighboring gene ribosomal protein L7a pseudogene 44 Neighboring gene NANOG hESC enhancer GRCh37_chr9:109769611-109770112 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:109812053-109812571 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20155 Neighboring gene APAF1 interacting protein pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:109892664-109893478 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:109893479-109894291 Neighboring gene importin subunit alpha-1-like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Phenotypic spectrum in Weiss-Kruszka syndrome caused by ZNF462 variants: Three new patients and literature review. van der Laan L, et al. Eur J Med Genet, 2024 Oct. PMID 39069253
    2. Discovery of O-GlcNAc-6-phosphate modified proteins in large-scale phosphoproteomics data. Hahne H, et al. Mol Cell Proteomics, 2012 Oct. PMID 22826440, Free PMC Article
    3. Further characterization of the 9q31 microdeletion phenotype; delineation of a common region of overlap containing ZNF462. Brady L, et al. Mol Genet Genomic Med, 2023 Mar. PMID 36461789, Free PMC Article
    4. Haploinsufficiency of ZNF462 is associated with craniofacial anomalies, corpus callosum dysgenesis, ptosis, and developmental delay. Weiss K, et al. Eur J Hum Genet, 2017 Aug. PMID 28513610, Free PMC Article
    5. ZNF462 and KLF12 are disrupted by a de novo translocation in a patient with syndromic intellectual disability and autism spectrum disorder. Cosemans N, et al. Eur J Med Genet, 2018 Jul. PMID 29427787

    See all (57) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Phenotypic spectrum in Weiss-Kruszka syndrome caused by ZNF462 variants: Three new patients and literature review.
      Title: Phenotypic spectrum in Weiss-Kruszka syndrome caused by ZNF462 variants: Three new patients and literature review.
    2. Further characterization of the 9q31 microdeletion phenotype; delineation of a common region of overlap containing ZNF462.
      Title: Further characterization of the 9q31 microdeletion phenotype; delineation of a common region of overlap containing ZNF462.
    3. a multiple congenital anomaly syndrome associated with haploinsufficiency of ZNF462 that has distinct clinical characteristics and facial features, is reported.
      Title: Phenotype delineation of ZNF462 related syndrome.
    4. In the current study we describe a patient with a syndromic form of autism spectrum disorder and intellectual disability characterized by metopic craniosynostosis, ptosis and corpus callosum dysgenesis most likely caused by ZNF462 haploinsufficiency. The possible contribution of the disruption of KLF12 by one of the translocation breakpoints remains unclear.
      Title: ZNF462 and KLF12 are disrupted by a de novo translocation in a patient with syndromic intellectual disability and autism spectrum disorder.
    5. Loss of function variants in ZNF462 were identified in patients with ptosis, metopic ridging, craniosynostosis, dysgenesis of the corpus callosum, and developmental delay.
      Title: Haploinsufficiency of ZNF462 is associated with craniofacial anomalies, corpus callosum dysgenesis, ptosis, and developmental delay.
    6. Zinc finger protein 462 (ZNF462) is the first human O-GlcNAc-6-phosphate modified protein.
      Title: Discovery of O-GlcNAc-6-phosphate modified proteins in large-scale phosphoproteomics data.
    7. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    8. Observational study of gene-disease association. (HuGE Navigator)
      Title: The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Weiss-Kruszka syndrome
    MedGen: C5231429 OMIM: 618619 GeneReviews: Weiss-Kruszka Syndrome
    		not available

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2020-01-16)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-01-16)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    A genome-wide association study of chemotherapy-induced alopecia in breast cancer patients.
    EBI GWAS Catalog
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog
    Many sequence variants affecting diversity of adult human height.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association data identifies two loci influencing age at menarche.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ14960, FLJ45904, KIAA1803, DKFZp686B2325, DKFZp762N2316

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein 462
    Names
    zinc finger PBX1-interacting protein

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_052913.1 RefSeqGene

      Range
      5070..155538
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001347997.2 → NP_001334926.1  zinc finger protein 462 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AL512593, AL590362, F13685
      Conserved Domains (2) summary
      sd00017
      Location:1162 → 1182
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13909
      Location:1218 → 1243
      zf-H2C2_5; C2H2-type zinc-finger domain

    2. NM_021224.6 → NP_067047.4  zinc finger protein 462 isoform 1

      See identical proteins and their annotated locations for NP_067047.4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL512593, BX648965, F13685
      Consensus CDS
      CCDS35096.1
      UniProtKB/Swiss-Prot
      Q5T0T4, Q8N408, Q96JM2
      UniProtKB/TrEMBL
      Q63HJ5
      Related
      ENSP00000277225.5, ENST00000277225.10
      Conserved Domains (1) summary
      sd00017
      Location:2027 → 2047
      ZF_C2H2; C2H2 Zn finger [structural motif]

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      106860158..107013634
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047423662.1 → XP_047279618.1  zinc finger protein 462 isoform X1

    2. XM_047423672.1 → XP_047279628.1  zinc finger protein 462 isoform X3

      UniProtKB/Swiss-Prot
      Q5T0T4, Q8N408, Q96JM2

    3. XM_047423680.1 → XP_047279636.1  zinc finger protein 462 isoform X4

    4. XM_047423685.1 → XP_047279641.1  zinc finger protein 462 isoform X6

    5. XM_006717212.5 → XP_006717275.1  zinc finger protein 462 isoform X1

      See identical proteins and their annotated locations for XP_006717275.1

      UniProtKB/TrEMBL
      Q63HJ5
      Conserved Domains (2) summary
      sd00017
      Location:2088 → 2108
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13909
      Location:2144 → 2169
      zf-H2C2_5; C2H2-type zinc-finger domain

    6. XM_047423669.1 → XP_047279625.1  zinc finger protein 462 isoform X2

    7. XM_047423676.1 → XP_047279632.1  zinc finger protein 462 isoform X3

      UniProtKB/Swiss-Prot
      Q5T0T4, Q8N408, Q96JM2

    8. XM_047423681.1 → XP_047279637.1  zinc finger protein 462 isoform X4

    9. XM_047423683.1 → XP_047279639.1  zinc finger protein 462 isoform X5

    10. XM_047423684.1 → XP_047279640.1  zinc finger protein 462 isoform X6

    11. XM_006717209.5 → XP_006717272.1  zinc finger protein 462 isoform X1

      See identical proteins and their annotated locations for XP_006717272.1

      UniProtKB/TrEMBL
      Q63HJ5
      Conserved Domains (2) summary
      sd00017
      Location:2088 → 2108
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13909
      Location:2144 → 2169
      zf-H2C2_5; C2H2-type zinc-finger domain

    12. XM_047423668.1 → XP_047279624.1  zinc finger protein 462 isoform X2

    13. XM_047423679.1 → XP_047279635.1  zinc finger protein 462 isoform X4

    14. XM_047423682.1 → XP_047279638.1  zinc finger protein 462 isoform X5

    15. XM_047423661.1 → XP_047279617.1  zinc finger protein 462 isoform X1

    16. XM_006717215.5 → XP_006717278.1  zinc finger protein 462 isoform X2

      UniProtKB/TrEMBL
      Q63HJ5
      Conserved Domains (1) summary
      sd00017
      Location:2087 → 2107
      ZF_C2H2; C2H2 Zn finger [structural motif]

    17. XM_006717216.5 → XP_006717279.1  zinc finger protein 462 isoform X3

      See identical proteins and their annotated locations for XP_006717279.1

      UniProtKB/Swiss-Prot
      Q5T0T4, Q8N408, Q96JM2
      UniProtKB/TrEMBL
      Q63HJ5
      Conserved Domains (1) summary
      sd00017
      Location:2027 → 2047
      ZF_C2H2; C2H2 Zn finger [structural motif]

    18. XM_047423663.1 → XP_047279619.1  zinc finger protein 462 isoform X1

    19. XM_047423664.1 → XP_047279620.1  zinc finger protein 462 isoform X1

    20. XM_047423677.1 → XP_047279633.1  zinc finger protein 462 isoform X3

      UniProtKB/Swiss-Prot
      Q5T0T4, Q8N408, Q96JM2

    21. XM_017014998.3 → XP_016870487.1  zinc finger protein 462 isoform X6

      Conserved Domains (2) summary
      sd00017
      Location:1162 → 1182
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13909
      Location:1218 → 1243
      zf-H2C2_5; C2H2-type zinc-finger domain

    22. XM_017014996.3 → XP_016870485.1  zinc finger protein 462 isoform X1

      UniProtKB/TrEMBL
      Q63HJ5
      Conserved Domains (2) summary
      sd00017
      Location:2088 → 2108
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13909
      Location:2144 → 2169
      zf-H2C2_5; C2H2-type zinc-finger domain

    23. XM_047423670.1 → XP_047279626.1  zinc finger protein 462 isoform X2

    24. XM_047423673.1 → XP_047279629.1  zinc finger protein 462 isoform X3

      UniProtKB/Swiss-Prot
      Q5T0T4, Q8N408, Q96JM2

    25. XM_024447629.1 → XP_024303397.1  zinc finger protein 462 isoform X1

      UniProtKB/TrEMBL
      Q63HJ5
      Conserved Domains (2) summary
      sd00017
      Location:2088 → 2108
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13909
      Location:2144 → 2169
      zf-H2C2_5; C2H2-type zinc-finger domain

    26. XM_047423675.1 → XP_047279631.1  zinc finger protein 462 isoform X3

      UniProtKB/Swiss-Prot
      Q5T0T4, Q8N408, Q96JM2

    27. XM_017014997.3 → XP_016870486.1  zinc finger protein 462 isoform X1

      UniProtKB/TrEMBL
      Q63HJ5
      Conserved Domains (2) summary
      sd00017
      Location:2088 → 2108
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13909
      Location:2144 → 2169
      zf-H2C2_5; C2H2-type zinc-finger domain

    28. XM_047423671.1 → XP_047279627.1  zinc finger protein 462 isoform X2

    29. XM_047423678.1 → XP_047279634.1  zinc finger protein 462 isoform X3

      UniProtKB/Swiss-Prot
      Q5T0T4, Q8N408, Q96JM2

    30. XM_047423667.1 → XP_047279623.1  zinc finger protein 462 isoform X1

    31. XM_047423666.1 → XP_047279622.1  zinc finger protein 462 isoform X1

    32. XM_047423674.1 → XP_047279630.1  zinc finger protein 462 isoform X3

      UniProtKB/Swiss-Prot
      Q5T0T4, Q8N408, Q96JM2

    33. XM_047423665.1 → XP_047279621.1  zinc finger protein 462 isoform X1

    34. XM_006717211.5 → XP_006717274.1  zinc finger protein 462 isoform X1

      See identical proteins and their annotated locations for XP_006717274.1

      UniProtKB/TrEMBL
      Q63HJ5
      Conserved Domains (2) summary
      sd00017
      Location:2088 → 2108
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13909
      Location:2144 → 2169
      zf-H2C2_5; C2H2-type zinc-finger domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      119036267..119189919
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054363457.1 → XP_054219432.1  zinc finger protein 462 isoform X3

    2. XM_054363438.1 → XP_054219413.1  zinc finger protein 462 isoform X1

    3. XM_054363447.1 → XP_054219422.1  zinc finger protein 462 isoform X2

    4. XM_054363464.1 → XP_054219439.1  zinc finger protein 462 isoform X6

    5. XM_054363460.1 → XP_054219435.1  zinc finger protein 462 isoform X4

    6. XM_054363462.1 → XP_054219437.1  zinc finger protein 462 isoform X5

    7. XM_054363451.1 → XP_054219426.1  zinc finger protein 462 isoform X3

    8. XM_054363435.1 → XP_054219410.1  zinc finger protein 462 isoform X1

    9. XM_054363465.1 → XP_054219440.1  zinc finger protein 462 isoform X6

    10. XM_054363459.1 → XP_054219434.1  zinc finger protein 462 isoform X4

    11. XM_054363434.1 → XP_054219409.1  zinc finger protein 462 isoform X1

    12. XM_054363445.1 → XP_054219420.1  zinc finger protein 462 isoform X2

    13. XM_054363458.1 → XP_054219433.1  zinc finger protein 462 isoform X4

    14. XM_054363461.1 → XP_054219436.1  zinc finger protein 462 isoform X5

    15. XM_054363456.1 → XP_054219431.1  zinc finger protein 462 isoform X3

    16. XM_054363446.1 → XP_054219421.1  zinc finger protein 462 isoform X2

    17. XM_054363450.1 → XP_054219425.1  zinc finger protein 462 isoform X3

    18. XM_054363436.1 → XP_054219411.1  zinc finger protein 462 isoform X1

    19. XM_054363439.1 → XP_054219414.1  zinc finger protein 462 isoform X1

    20. XM_054363440.1 → XP_054219415.1  zinc finger protein 462 isoform X1

    21. XM_054363448.1 → XP_054219423.1  zinc finger protein 462 isoform X2

    22. XM_054363452.1 → XP_054219427.1  zinc finger protein 462 isoform X3

    23. XM_054363463.1 → XP_054219438.1  zinc finger protein 462 isoform X6

    24. XM_054363443.1 → XP_054219418.1  zinc finger protein 462 isoform X1

    25. XM_054363454.1 → XP_054219429.1  zinc finger protein 462 isoform X3

    26. XM_054363437.1 → XP_054219412.1  zinc finger protein 462 isoform X1

    27. XM_054363449.1 → XP_054219424.1  zinc finger protein 462 isoform X2

    28. XM_054363455.1 → XP_054219430.1  zinc finger protein 462 isoform X3

    29. XM_054363444.1 → XP_054219419.1  zinc finger protein 462 isoform X1

    30. XM_054363453.1 → XP_054219428.1  zinc finger protein 462 isoform X3

    31. XM_054363442.1 → XP_054219417.1  zinc finger protein 462 isoform X1

    32. XM_054363441.1 → XP_054219416.1  zinc finger protein 462 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96JM2.3 GenPept UniProtKB/Swiss-Prot:Q96JM2

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