ZNF408 zinc finger protein 408 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ZNF408provided by HGNC
Official Full Name: zinc finger protein 408provided by HGNC
Primary source: HGNC:HGNC:20041
See related: Ensembl:ENSG00000175213 MIM:616454; AllianceGenome:HGNC:20041
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: EVR6; RP72
Summary: The protein encoded by this gene contains ten tandem zinc fingers and an N-terminal SET domain, so it is likely a DNA binding protein that interacts with other proteins. In adults, the encoded protein is expressed most highly in retina. Consequently, defects in this gene have been associated with familial exudative vitreoretinopathy (FEVR) and retinitis pigmentosa (RP). [provided by RefSeq, Dec 2016]
Expression: Ubiquitous expression in bone marrow (RPKM 5.1), ovary (RPKM 3.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11p11.2

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (46701031..46705912)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (46857047..46861916)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (46722581..46727462)

Chromosome 11 - NC_000011.10 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
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?

Genetic and clinical characteristics of ZNF408-related familial exudative vitreoretinopathy.
Title: Genetic and clinical characteristics of ZNF408-related familial exudative vitreoretinopathy.
p.H455Y ZNF408 has reduced DNA-binding ability, as compared to the wild-type protein. The fact that the p.H455Y mutation disrupts the expression of genes important for the development of vasculature sheds further light on the molecular mechanisms underlying ZNF408-associated familial exudative vitreoretinopathy.
Title: An FEVR-associated mutation in ZNF408 alters the expression of genes involved in the development of vasculature.
In a Pakistani family with retinal degeneration, whole-exome sequencing identified 2 homozygous missense variants: c.1304G>A; p.Arg435Gln in ZNF408 (NM_024741) and c.902G>A; p.Gly301Asp in C1QTNF4 (NM_031909). Both segregated with the retinal phenotype in this family and were absent in ethnically matched control chromosomes.
Title: Whole-Exome Sequencing Identifies Novel Variants that Co-segregates with Autosomal Recessive Retinal Degeneration in a Pakistani Pedigree.
This is the first study to report a group of patients with digenic familial exudative vitreoretinopathy (FEVR). In most affected eyes, the stage was more severe than stage 3. We speculate that the phenotype of FEVR is more severe in patients with digenic rather than monogenic variants of FEVR-related genes.
Title: The characteristics of digenic familial exudative vitreoretinopathy.
In conclusion, we report a novel mutation in ZNF408 causing autosomal recessive retinitis pigmentosa with vitreal alterations in three members of a Tunisian family, which further accentuates the role of this new gene in the susceptibility to retinitis pigmentosa.
Title: Exome sequencing confirms ZNF408 mutations as a cause of familial retinitis pigmentosa.
Several novel mutations (missense, non-stop and insertion) were detected in the coding regions of FZD4, TSPAN12 and ZNF408 genes among the unrelated vitreoretinopathy probands.
Title: Mutation spectrum of the FZD-4, TSPAN12 AND ZNF408 genes in Indian FEVR patients.
ZNF408, previously associated with Familial Exudative Vitreoretinopathy (FEVR), is a new gene causing autosomal recessive rtinitis pigmentosa.
Title: Whole-exome sequencing reveals ZNF408 as a new gene associated with autosomal recessive retinitis pigmentosa with vitreal alterations.
Data indicate ZNF408 missense variant (p.Ser126Asn) in 132 familial exudative vitreoretinopathy (FEVR) individuals in a Japanese family.
Title: ZNF408 is mutated in familial exudative vitreoretinopathy and is crucial for the development of zebrafish retinal vasculature.

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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
Exudative vitreoretinopathy 6 MedGen: C4225316 OMIM: 616468 GeneReviews: Not available	Compare labs
Retinitis pigmentosa 72 MedGen: C4225315 OMIM: 616469 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. EBI GWAS Catalog EBI GWAS CatalogPubMed
Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies. 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

RH36421 (e-PCR)
- UniSTS:29847

RH11922 (e-PCR)
- UniSTS:23257

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 identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
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
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: zinc finger protein 408

Names: PR domain zinc finger protein 17

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

NG_052967.1 RefSeqGene

Range

5265..10146

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001184751.2 → NP_001171680.1 zinc finger protein 408 isoform 2

See identical proteins and their annotated locations for NP_001171680.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.

Source sequence(s)

AC115088, AK022889, AK302180, AW246726, BC015708

UniProtKB/TrEMBL

B4DXY4

Conserved Domains (3) summary

COG5048
Location:300 → 508

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:403 → 423

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam13465
Location:474 → 499

zf-H2C2_2; Zinc-finger double domain
NM_024741.3 → NP_079017.1 zinc finger protein 408 isoform 1

See identical proteins and their annotated locations for NP_079017.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AK022889, AW246726, BC015708

Consensus CDS

CCDS7923.1

UniProtKB/Swiss-Prot

Q9H9D4

Related

ENSP00000309606.2, ENST00000311764.3

Conserved Domains (3) summary

COG5048
Location:308 → 516

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:411 → 431

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam13465
Location:482 → 507

zf-H2C2_2; Zinc-finger double domain