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ZFP90 ZFP90 zinc finger protein [ Homo sapiens (human) ]

Gene ID: 146198, updated on 11-Apr-2024

Summary

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Official Symbol
ZFP90provided by HGNC
Official Full Name
ZFP90 zinc finger proteinprovided by HGNC
Primary source
HGNC:HGNC:23329
See related
Ensembl:ENSG00000184939 MIM:609451; AllianceGenome:HGNC:23329
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
FIK; NK10; ZNF756; zfp-90
Summary
This gene encodes a member of the zinc finger protein family that modulates gene expression. The encoded protein derepresses the transcription of certain fetal cardiac genes and may contribute to the genetic reprogramming that occurs during the development of heart failure. Genome wide association studies have identified this gene among ulcerative colitis risk loci. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Mar 2015]
Expression
Ubiquitous expression in ovary (RPKM 6.9), brain (RPKM 6.4) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
16q22.1
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (68533479..68576506)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (74323667..74372339)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (68573194..68609975)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ribosomal protein L35a pseudogene 33 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68541928-68542428 Neighboring gene uncharacterized LOC105371321 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11019 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11020 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11021 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11022 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11023 Neighboring gene RNA, U4 small nuclear 36, pseudogene Neighboring gene small nucleolar RNA U109 Neighboring gene uncharacterized LOC124903809

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
  • 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. Assessing the Function of the ZFP90 Variant rs1170426 in SLE and the Association Between SLE Drug Target and Susceptibility Genes. Zhu T, et al. Front Immunol, 2021. PMID 33796098, Free PMC Article
  2. A 16q22.1 variant confers susceptibility to colorectal cancer as a distal regulator of ZFP90. Yu CY, et al. Oncogene, 2020 Feb. PMID 31641208, Free PMC Article
  3. Spastic paraplegia, optic atrophy, and neuropathy is linked to chromosome 11q13. Macedo-Souza LI, et al. Ann Neurol, 2005 May. PMID 15852396
  4. Zinc-finger protein 90 negatively regulates neuron-restrictive silencer factor-mediated transcriptional repression of fetal cardiac genes. Hata L, et al. J Mol Cell Cardiol, 2011 Jun. PMID 21284946
  5. Developmentally regulated mouse gene NK10 encodes a zinc finger repressor protein with differential DNA-binding domains. Lange R, et al. DNA Cell Biol, 1995 Nov. PMID 7576184

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Assessing the Function of the ZFP90 Variant rs1170426 in SLE and the Association Between SLE Drug Target and Susceptibility Genes.
    Title: Assessing the Function of the ZFP90 Variant rs1170426 in SLE and the Association Between SLE Drug Target and Susceptibility Genes.
  2. A 16q22.1 variant confers susceptibility to colorectal cancer as a distal regulator of ZFP90.
    Title: A 16q22.1 variant confers susceptibility to colorectal cancer as a distal regulator of ZFP90.
  3. 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

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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

EBI GWAS Catalog

Description
Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region.
EBI GWAS Catalog
Genome-wide pharmacogenomic study of neurocognition as an indicator of antipsychotic treatment response in schizophrenia.
EBI GWAS Catalog
Genomewide association study for determinants of HIV-1 acquisition and viral set point in HIV-1 serodiscordant couples with quantified virus exposure.
EBI GWAS Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
EBI GWAS Catalog
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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 DNA-binding transcription repressor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase II transcription 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 negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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

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Preferred Names
zinc finger protein 90 homolog
Names
FOXP3-interacting KRAB domain-containing protein
zinc finger protein 476
zinc finger protein 756

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.

mRNA and Protein(s)

  1. NM_001305203.2 → NP_001292132.1  zinc finger protein 90 homolog isoform 1

    See identical proteins and their annotated locations for NP_001292132.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein (isoform 1).
    Source sequence(s)
    AC009162, AC126773
    Consensus CDS
    CCDS42183.1
    UniProtKB/Swiss-Prot
    B2RU00, B3KVE7, L7S2P3, Q49AD1, Q8TF47, Q96MQ6
    Related
    ENSP00000454418.2, ENST00000563169.7
    Conserved Domains (3) summary
    smart00349
    Location:14 → 74
    KRAB; krueppel associated box
    COG5048
    Location:336 → 632
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:555 → 575
    ZF_C2H2; C2H2 Zn finger [structural motif]

  2. NM_001305204.2 → NP_001292133.1  zinc finger protein 90 homolog isoform 2

    See identical proteins and their annotated locations for NP_001292133.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate 3' terminal exon, compared to variant 1. It encodes isoform 2 which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC009162, AC126773, AW135652
    Consensus CDS
    CCDS76892.1
    UniProtKB/TrEMBL
    I3L0X7
    Related
    ENSP00000480309.1, ENST00000611381.4
    Conserved Domains (1) summary
    smart00349
    Location:14 → 74
    KRAB; krueppel associated box

  3. NM_001305206.2 → NP_001292135.1  zinc finger protein 90 homolog isoform 3

    See identical proteins and their annotated locations for NP_001292135.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and uses an alternate splice site in the 3' coding region, compared to variant 1. It encodes isoform 3 which is shorter and has a distinct C-terminus, compared to isoform 1. Both variants 4 and 5 encode the same protein (isoform 3).
    Source sequence(s)
    AC009162, AC126773
    Consensus CDS
    CCDS82003.1
    UniProtKB/TrEMBL
    H3BVC6, J3QKQ8
    Conserved Domains (1) summary
    smart00349
    Location:14 → 74
    KRAB; krueppel associated box

  4. NM_001305207.2 → NP_001292136.1  zinc finger protein 90 homolog isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and uses an alternate splice site in the 3' coding region, compared to variant 1. It encodes isoform 4 which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC009162, AC126773
    UniProtKB/TrEMBL
    H3BVC6
    Conserved Domains (1) summary
    smart00349
    Location:14 → 74
    KRAB; krueppel associated box

  5. NM_001305208.2 → NP_001292137.1  zinc finger protein 90 homolog isoform 3

    See identical proteins and their annotated locations for NP_001292137.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate splice site in the 3' coding region, compared to variant 1. It encodes isoform 3 which is shorter and has a distinct C-terminus, compared to isoform 1. Both variants 4 and 5 encode the same protein (isoform 3).
    Source sequence(s)
    AC009162, AC126773
    Consensus CDS
    CCDS82003.1
    UniProtKB/TrEMBL
    H3BVC6, J3QKQ8
    Related
    ENSP00000463193.1, ENST00000564323.5
    Conserved Domains (1) summary
    smart00349
    Location:14 → 74
    KRAB; krueppel associated box

  6. NM_133458.4 → NP_597715.2  zinc finger protein 90 homolog isoform 1

    See identical proteins and their annotated locations for NP_597715.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest protein. Both variants 1 and 2 encode the same protein (isoform 1).
    Source sequence(s)
    AC009162, AC126773
    Consensus CDS
    CCDS42183.1
    UniProtKB/Swiss-Prot
    B2RU00, B3KVE7, L7S2P3, Q49AD1, Q8TF47, Q96MQ6
    Related
    ENSP00000460547.1, ENST00000570495.5
    Conserved Domains (3) summary
    smart00349
    Location:14 → 74
    KRAB; krueppel associated box
    COG5048
    Location:336 → 632
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:555 → 575
    ZF_C2H2; C2H2 Zn finger [structural motif]

RNA

  1. NR_130976.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) uses an alternate splice sites in the 5'-most exon and an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC009162, AC126773
    Related
    ENST00000564558.5

  2. NR_130977.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) uses an alternate splice sites in the 5'-most exon and an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC009162, AC126773

  3. NR_130978.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) uses an alternate splice sites in the 5'-most exon and an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC009162, AC126773

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    68533479..68576506
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017022952.3 → XP_016878441.1  zinc finger protein 90 homolog isoform X1

  2. XM_024450159.2 → XP_024305927.1  zinc finger protein 90 homolog isoform X2

    UniProtKB/Swiss-Prot
    B2RU00, B3KVE7, L7S2P3, Q49AD1, Q8TF47, Q96MQ6
    Related
    ENSP00000381304.2, ENST00000398253.6
    Conserved Domains (3) summary
    smart00349
    Location:14 → 74
    KRAB; krueppel associated box
    COG5048
    Location:336 → 632
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:555 → 575
    ZF_C2H2; C2H2 Zn finger [structural motif]

  3. XM_047433640.1 → XP_047289596.1  zinc finger protein 90 homolog isoform X3

  4. XM_047433641.1 → XP_047289597.1  zinc finger protein 90 homolog isoform X3

  5. XM_047433639.1 → XP_047289595.1  zinc finger protein 90 homolog isoform X3

  6. XM_047433642.1 → XP_047289598.1  zinc finger protein 90 homolog isoform X4

    UniProtKB/TrEMBL
    J3QKQ8

  7. XM_005255804.3 → XP_005255861.1  zinc finger protein 90 homolog isoform X2

    See identical proteins and their annotated locations for XP_005255861.1

    UniProtKB/Swiss-Prot
    B2RU00, B3KVE7, L7S2P3, Q49AD1, Q8TF47, Q96MQ6
    Conserved Domains (3) summary
    smart00349
    Location:14 → 74
    KRAB; krueppel associated box
    COG5048
    Location:336 → 632
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:555 → 575
    ZF_C2H2; C2H2 Zn finger [structural motif]

  8. XM_047433643.1 → XP_047289599.1  zinc finger protein 90 homolog isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    74323667..74372339
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054379640.1 → XP_054235615.1  zinc finger protein 90 homolog isoform X6

  2. XM_054379637.1 → XP_054235612.1  zinc finger protein 90 homolog isoform X1

  3. XM_054379639.1 → XP_054235614.1  zinc finger protein 90 homolog isoform X2

    UniProtKB/Swiss-Prot
    B2RU00, B3KVE7, L7S2P3, Q49AD1, Q8TF47, Q96MQ6

  4. XM_054379642.1 → XP_054235617.1  zinc finger protein 90 homolog isoform X3

  5. XM_054379643.1 → XP_054235618.1  zinc finger protein 90 homolog isoform X3

  6. XM_054379641.1 → XP_054235616.1  zinc finger protein 90 homolog isoform X3

  7. XM_054379644.1 → XP_054235619.1  zinc finger protein 90 homolog isoform X4

    UniProtKB/TrEMBL
    J3QKQ8

  8. XM_054379638.1 → XP_054235613.1  zinc finger protein 90 homolog isoform X2

    UniProtKB/Swiss-Prot
    B2RU00, B3KVE7, L7S2P3, Q49AD1, Q8TF47, Q96MQ6

  9. XM_054379645.1 → XP_054235620.1  zinc finger protein 90 homolog isoform X5

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TF47.2 GenPept UniProtKB/Swiss-Prot:Q8TF47

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