U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    ZNF419 zinc finger protein 419 [ Homo sapiens (human) ]

    Gene ID: 79744, updated on 7-Apr-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    ZNF419provided by HGNC
    Official Full Name
    zinc finger protein 419provided by HGNC
    Primary source
    HGNC:HGNC:20648
    See related
    Ensembl:ENSG00000105136 MIM:617410; AllianceGenome:HGNC:20648
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ZAPHIR; ZNF419A
    Summary
    Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in thyroid (RPKM 5.2), spleen (RPKM 4.2) and 25 other tissues See more
    Orthologs
    all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    Location:
    19q13.43
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (57487750..57496098)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (60579865..60593144)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (57999118..58007466)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene vomeronasal 1 receptor 107 pseudogene Neighboring gene zinc finger protein 772 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr19:57988249-57989448 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:57998906-57999406 Neighboring gene zinc finger protein 773 Neighboring gene zinc finger protein 549

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. A polymorphism in the splice donor site of ZNF419 results in the novel renal cell carcinoma-associated minor histocompatibility antigen ZAPHIR. Broen K, et al. PLoS One, 2011. PMID 21738768, Free PMC Article
    2. Allele-specific splicing effects on DKKL1 and ZNF419 transcripts in HeLa cells. Martin G, et al. Gene, 2017 Jan 20. PMID 27826023
    3. Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions. Suzuki Y, et al. Genome Res, 2004 Sep. PMID 15342556, Free PMC Article
    4. Cullin 3 Exon 9 Deletion in Familial Hyperkalemic Hypertension Impairs Cullin3-Ring-E3 Ligase (CRL3) Dynamic Regulation and Cycling. Kouranti I, et al. Int J Mol Sci, 2022 May 5. PMID 35563538, Free PMC Article
    5. Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains. Haenig C, et al. Cell Rep, 2020 Aug 18. PMID 32814053

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. previously unreported alternative splicing patterns in the genes ZNF419 and DKKL1
      Title: Allele-specific splicing effects on DKKL1 and ZNF419 transcripts in HeLa cells.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    Phenotypes

    Go to the top of the page Help

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

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • FLJ23233

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    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 regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    zinc finger protein 419
    Names
    zinc finger protein 419A

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_054882.1 RefSeqGene

      Range
      5040..13388
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001098491.2 → NP_001091961.1  zinc finger protein 419 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC003005, AK026886, BC024259, DB004191
      Consensus CDS
      CCDS54325.1
      UniProtKB/Swiss-Prot
      Q96HQ0
      Related
      ENSP00000388864.1, ENST00000424930.6
      Conserved Domains (5) summary
      smart00349
      Location:28 → 88
      KRAB; krueppel associated box
      COG5048
      Location:262 → 418
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:262 → 282
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:28 → 67
      KRAB; KRAB box
      pfam13465
      Location:330 → 355
      zf-H2C2_2; Zinc-finger double domain

    2. NM_001098492.2 → NP_001091962.1  zinc finger protein 419 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.
      Source sequence(s)
      AC003005, AK026886, BC024259, DC315347
      Consensus CDS
      CCDS54327.1
      UniProtKB/Swiss-Prot
      Q96HQ0
      Related
      ENSP00000390916.1, ENST00000426954.6
      Conserved Domains (5) summary
      smart00349
      Location:15 → 75
      KRAB; krueppel associated box
      COG5048
      Location:249 → 405
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:249 → 269
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:15 → 54
      KRAB; KRAB box
      pfam13465
      Location:317 → 342
      zf-H2C2_2; Zinc-finger double domain

    3. NM_001098493.2 → NP_001091963.1  zinc finger protein 419 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an alternate in-frame exon and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in an isoform (4) that is shorter than isoform 1.
      Source sequence(s)
      AC003005, AK026886, BC024259, DC392630
      Consensus CDS
      CCDS54328.1
      UniProtKB/Swiss-Prot
      Q96HQ0
      Related
      ENSP00000414709.2, ENST00000442920.6
      Conserved Domains (5) summary
      smart00349
      Location:14 → 74
      KRAB; krueppel associated box
      COG5048
      Location:248 → 404
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:248 → 268
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:14 → 53
      KRAB; KRAB box
      pfam13465
      Location:316 → 341
      zf-H2C2_2; Zinc-finger double domain

    4. NM_001098494.2 → NP_001091964.1  zinc finger protein 419 isoform 5

      See identical proteins and their annotated locations for NP_001091964.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (5) that is shorter than isoform 1.
      Source sequence(s)
      AC003005, AK026886, BC024259
      Consensus CDS
      CCDS42637.1
      UniProtKB/Swiss-Prot
      Q96HQ0
      Related
      ENSP00000299860.9, ENST00000347466.10
      Conserved Domains (5) summary
      smart00349
      Location:28 → 69
      KRAB; krueppel associated box
      COG5048
      Location:229 → 385
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:229 → 249
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:28 → 67
      KRAB; KRAB box
      pfam13465
      Location:297 → 322
      zf-H2C2_2; Zinc-finger double domain

    5. NM_001098495.2 → NP_001091965.1  zinc finger protein 419 isoform 6

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) lacks two alternate in-frame exons in the 5' coding region, compared to variant 1, resulting in an isoform (6) that is shorter than isoform 1.
      Source sequence(s)
      AC003005, AK026886, BC024259, BP336834, DC407547
      UniProtKB/Swiss-Prot
      Q96HQ0
      Conserved Domains (5) summary
      smart00349
      Location:15 → 56
      KRAB; krueppel associated box
      COG5048
      Location:216 → 372
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:216 → 236
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:15 → 54
      KRAB; KRAB box
      pfam13465
      Location:284 → 309
      zf-H2C2_2; Zinc-finger double domain

    6. NM_001098496.2 → NP_001091966.1  zinc finger protein 419 isoform 7

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) lacks two alternate in-frame exons and and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in an isoform (7) that is shorter than isoform 1.
      Source sequence(s)
      AC003005, AK026886, BC024259, DC315347, DC425209
      Consensus CDS
      CCDS46211.1
      UniProtKB/Swiss-Prot
      Q96HQ0
      Related
      ENSP00000392129.2, ENST00000415379.6
      Conserved Domains (5) summary
      smart00349
      Location:14 → 55
      KRAB; krueppel associated box
      COG5048
      Location:215 → 371
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:215 → 235
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:14 → 53
      KRAB; KRAB box
      pfam13465
      Location:283 → 308
      zf-H2C2_2; Zinc-finger double domain

    7. NM_001291743.2 → NP_001278672.1  zinc finger protein 419 isoform 8

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8) uses an alternate in-frame splice site and lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (8) that is shorter than isoform 1.
      Source sequence(s)
      AC003005, AK026886, BC008297, CT002615, DC315347
      UniProtKB/Swiss-Prot
      Q96HQ0
      Conserved Domains (5) summary
      smart00349
      Location:27 → 68
      KRAB; krueppel associated box
      COG5048
      Location:228 → 384
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:228 → 248
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:27 → 66
      KRAB; KRAB box
      pfam13465
      Location:296 → 321
      zf-H2C2_2; Zinc-finger double domain

    8. NM_001291744.2 → NP_001278673.1  zinc finger protein 419 isoform 9

      Status: VALIDATED

      Description
      Transcript Variant: This variant (9) uses an alternate splice site and it thus differs in its 5' UTR and initiates translation at a downstream in-frame start codon, and it also lacks an in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (9) is shorter at the N-terminus, compared to isoform 1.
      Source sequence(s)
      AC003005, AK026886, BC008297, DA548110, DC315347
      UniProtKB/Swiss-Prot
      Q96HQ0
      Conserved Domains (3) summary
      COG5048
      Location:173 → 329
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:173 → 193
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:241 → 266
      zf-H2C2_2; Zinc-finger double domain

    9. NM_001291745.2 → NP_001278674.1  zinc finger protein 419 isoform 10

      Status: VALIDATED

      Description
      Transcript Variant: This variant (10) lacks an alternate in-frame exon in the 5' coding region, and it uses an alternate splice site in its 3' terminal exon and thus differs in the 3' coding region, compared to variant 1. The encoded isoform (10) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      BC008297, BF110540, DC315347
      UniProtKB/Swiss-Prot
      Q96HQ0
      Conserved Domains (2) summary
      smart00349
      Location:15 → 75
      KRAB; krueppel associated box
      pfam01352
      Location:15 → 54
      KRAB; KRAB box

    10. NM_024691.4 → NP_078967.3  zinc finger protein 419 isoform 2

      See identical proteins and their annotated locations for NP_078967.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
      Source sequence(s)
      AC003005, AK026886, BC024259, BP336834
      Consensus CDS
      CCDS54326.1
      UniProtKB/Swiss-Prot
      B4DXU7, B4E348, B7ZA41, E9PCP4, E9PED0, E9PET3, E9PFX9, Q96HQ0, Q9H5P0
      Related
      ENSP00000221735.7, ENST00000221735.12
      Conserved Domains (5) summary
      smart00349
      Location:27 → 87
      KRAB; krueppel associated box
      COG5048
      Location:261 → 417
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:261 → 281
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam01352
      Location:27 → 66
      KRAB; KRAB box
      pfam13465
      Location:329 → 354
      zf-H2C2_2; Zinc-finger double domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      57487750..57496098
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      60579865..60593144
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322177.1 → XP_054178152.1  zinc finger protein 419 isoform X3

    2. XM_054322176.1 → XP_054178151.1  zinc finger protein 419 isoform X3

    3. XM_054322178.1 → XP_054178153.1  zinc finger protein 419 isoform X4

    4. XM_054322175.1 → XP_054178150.1  zinc finger protein 419 isoform X2

    5. XM_054322174.1 → XP_054178149.1  zinc finger protein 419 isoform X1

    6. XM_054322179.1 → XP_054178154.1  zinc finger protein 419 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96HQ0.2 GenPept UniProtKB/Swiss-Prot:Q96HQ0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous