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

Summary

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

Location:: 16q22.1

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (68533479..68576506)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (74323667..74372339)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (68573194..68609975)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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 EBI GWAS CatalogPubMed
Genome-wide pharmacogenomic study of neurocognition as an indicator of antipsychotic treatment response in schizophrenia. EBI GWAS Catalog EBI GWAS CatalogPubMed
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 EBI GWAS CatalogPubMed
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D16S2533E (e-PCR)
- UniSTS:473345

RH66667 (e-PCR)
- UniSTS:39204

A002L44 (e-PCR)
- UniSTS:77148

RH68732 (e-PCR)
- UniSTS:20598

G29138 (e-PCR)
- UniSTS:48761

SHGC-60815 (e-PCR)
- UniSTS:4260

DBEST27813 (e-PCR)
- UniSTS:26546

SHGC-10922 (e-PCR)
- UniSTS:26547

D11S1908 (e-PCR)
- UniSTS:34232

D11S1889 (e-PCR), detects polymorphism
- UniSTS:14040

SHGC-7464 (e-PCR)
- UniSTS:9439

SHGC-10921 (e-PCR)
- UniSTS:60662

G20440 (e-PCR)
- UniSTS:42492

A005R23 (e-PCR)
- UniSTS:42493

RH68222 (e-PCR)
- UniSTS:18175

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)

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]
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
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
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
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
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

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
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
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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

68533479..68576506

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017022952.3 → XP_016878441.1 zinc finger protein 90 homolog isoform X1
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]
XM_047433640.1 → XP_047289596.1 zinc finger protein 90 homolog isoform X3
XM_047433641.1 → XP_047289597.1 zinc finger protein 90 homolog isoform X3
XM_047433639.1 → XP_047289595.1 zinc finger protein 90 homolog isoform X3
XM_047433642.1 → XP_047289598.1 zinc finger protein 90 homolog isoform X4

UniProtKB/TrEMBL

J3QKQ8
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]
XM_047433643.1 → XP_047289599.1 zinc finger protein 90 homolog isoform X5

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

74323667..74372339

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054379640.1 → XP_054235615.1 zinc finger protein 90 homolog isoform X6
XM_054379637.1 → XP_054235612.1 zinc finger protein 90 homolog isoform X1
XM_054379639.1 → XP_054235614.1 zinc finger protein 90 homolog isoform X2

UniProtKB/Swiss-Prot

B2RU00, B3KVE7, L7S2P3, Q49AD1, Q8TF47, Q96MQ6
XM_054379642.1 → XP_054235617.1 zinc finger protein 90 homolog isoform X3
XM_054379643.1 → XP_054235618.1 zinc finger protein 90 homolog isoform X3
XM_054379641.1 → XP_054235616.1 zinc finger protein 90 homolog isoform X3
XM_054379644.1 → XP_054235619.1 zinc finger protein 90 homolog isoform X4

UniProtKB/TrEMBL

J3QKQ8
XM_054379638.1 → XP_054235613.1 zinc finger protein 90 homolog isoform X2

UniProtKB/Swiss-Prot

B2RU00, B3KVE7, L7S2P3, Q49AD1, Q8TF47, Q96MQ6
XM_054379645.1 → XP_054235620.1 zinc finger protein 90 homolog isoform X5