ZPR1 ZPR1 zinc finger [Homo sapiens (human)] - Gene

Summary

Official Symbol: ZPR1provided by HGNC
Official Full Name: ZPR1 zinc fingerprovided by HGNC
Primary source: HGNC:HGNC:13051
See related: Ensembl:ENSG00000109917 MIM:603901; AllianceGenome:HGNC:13051
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: GKAF; ZNF259
Summary: The protein encoded by this gene is found in the cytoplasm of quiescent cells but translocates to the nucleolus in proliferating cells. The encoded protein interacts with survival motor neuron protein (SMN1) to enhance pre-mRNA splicing and to induce neuronal differentiation and axonal growth. Defects in this gene or the SMN1 gene can cause spinal muscular atrophy. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2015]
Expression: Ubiquitous expression in testis (RPKM 14.8), bone marrow (RPKM 9.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11q23.3

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (116773799..116788023, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (116788425..116802647, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (116644515..116658739, complement)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Zinc finger 259 gene polymorphisms in Egyptian patients with metabolic syndrome and its association with dyslipidemia.
Title: Zinc finger 259 gene polymorphisms in Egyptian patients with metabolic syndrome and its association with dyslipidemia.
Kernel machine SNP set analysis finds the association of BUD13, ZPR1, and APOA5 variants with metabolic syndrome in Tehran Cardio-metabolic Genetics Study.
Title: Kernel machine SNP set analysis finds the association of BUD13, ZPR1, and APOA5 variants with metabolic syndrome in Tehran Cardio-metabolic Genetics Study.
The ZPR1 genotype predicts myocardial infarction in patients with familial hypercholesterolemia.
Title: The ZPR1 genotype predicts myocardial infarction in patients with familial hypercholesterolemia.
Implication between Genetic Variants from APOA5 and ZPR1 and NAFLD Severity in Patients with Hypertriglyceridemia.
Title: Implication between Genetic Variants from APOA5 and ZPR1 and NAFLD Severity in Patients with Hypertriglyceridemia.
ZPR1 prevents R-loop accumulation, upregulates SMN2 expression and rescues spinal muscular atrophy.
Title: ZPR1 prevents R-loop accumulation, upregulates SMN2 expression and rescues spinal muscular atrophy.
provide genetic and molecular evidence that a homozygous missense mutation in ZPR1 is associated with a rare and recognizable multisystem syndrome
Title: A ZPR1 mutation is associated with a novel syndrome of growth restriction, distinct craniofacial features, alopecia, and hypoplastic kidneys.
Identification of a relationship between a genetic variant in CETP and ZNF259 gene with coronary artery disease (CAD) and CAD and lipid profile, respectively. Further investigation in a larger population may help to investigate the value of emerging marker as a risk stratification marker in CAD and its risk factors.
Title: There is an association between a genetic polymorphism in the ZNF259 gene involved in lipid metabolism and coronary artery disease.
Results suggest that ZPR1 plays an important role in the etiology of type 2 diabetes mellitus, and this gene might be involved in abnormal glucose metabolism.
Title: Two-stage association study to identify the genetic susceptibility of a novel common variant of rs2075290 in ZPR1 to type 2 diabetes.
When the inter-dependence between alleles was examined using conditional models, five loci on BUD13, ZNF259, and ApoA5 showed possible independent associations.
Title: Multiple susceptibility loci at chromosome 11q23.3 are associated with plasma triglyceride in East Asians.
Single nucleotide polymorphisms (Rs964184, rs3317316, rs6589566) of ZNF259 protein did not increase the risk of CHD in the Chinese population.
Title: Effects of Polymorphisms in APOA4-APOA5-ZNF259-BUD13 Gene Cluster on Plasma Levels of Triglycerides and Risk of Coronary Heart Disease in a Chinese Han Population.

Submit: New GeneRIF Correction See all GeneRIFs (22)

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
Growth restriction, hypoplastic kidneys, alopecia, and distinctive facies MedGen: C5543375 OMIM: 619321 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
A bivariate genome-wide approach to metabolic syndrome: STAMPEED consortium. EBI GWAS Catalog EBI GWAS CatalogPubMed
Amerindian-specific regions under positive selection harbour new lipid variants in Latinos. EBI GWAS Catalog EBI GWAS CatalogPubMed
An atlas of genetic influences on human blood metabolites. EBI GWAS Catalog EBI GWAS CatalogPubMed
Biological, clinical and population relevance of 95 loci for blood lipids. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common variants at 30 loci contribute to polygenic dyslipidemia. EBI GWAS Catalog EBI GWAS CatalogPubMed
Discovery and refinement of loci associated with lipid levels. EBI GWAS Catalog EBI GWAS CatalogPubMed
Eight genetic loci associated with variation in lipoprotein-associated phospholipase A2 mass and activity and coronary heart disease: meta-analysis of genome-wide association studies from five community-based studies. EBI GWAS Catalog EBI GWAS CatalogPubMed
Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemia. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic Loci Associated with Circulating Levels of Very Long-Chain Saturated Fatty Acids. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic variants influencing circulating lipid levels and risk of coronary artery disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies common variants associated with circulating vitamin E levels. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies genes for biomarkers of cardiovascular disease: serum urate and dyslipidemia. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies three common variants associated with serologic response to vitamin E supplementation in men. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of Lp-PLA(2) activity and mass in the Framingham Heart Study. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide characterization of shared and distinct genetic components that influence blood lipid levels in ethnically diverse human populations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide screen for metabolic syndrome susceptibility Loci reveals strong lipid gene contribution but no evidence for common genetic basis for clustering of metabolic syndrome traits. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Large-scale genome-wide association studies in East Asians identify new genetic loci influencing metabolic traits. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies for circulating phylloquinone concentrations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Newly identified loci that influence lipid concentrations and risk of coronary artery disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants. 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

ECD01530 (e-PCR)
- UniSTS:282633

ECD15189 (e-PCR)
- UniSTS:296206

ECD14448 (e-PCR)
- UniSTS:295469

SHGC-30085 (e-PCR)
- UniSTS:81743

ECD13451 (e-PCR)
- UniSTS:294481

REN73108 (e-PCR)
- UniSTS:397908

REN73109 (e-PCR)
- UniSTS:397909

REN73110 (e-PCR)
- UniSTS:397910

REN73111 (e-PCR)
- UniSTS:397911

REN73112 (e-PCR)
- UniSTS:397912

REN73113 (e-PCR)
- UniSTS:397913

REN73114 (e-PCR)
- UniSTS:397914

REN73115 (e-PCR)
- UniSTS:397915

REN73116 (e-PCR)
- UniSTS:397916

REN73117 (e-PCR)
- UniSTS:397917

REN73118 (e-PCR)
- UniSTS:397918

REN73119 (e-PCR)
- UniSTS:397919

REN73120 (e-PCR)
- UniSTS:397920

REN73121 (e-PCR)
- UniSTS:397921

REN73122 (e-PCR)
- UniSTS:397922

REN73123 (e-PCR)
- UniSTS:397923

REN73124 (e-PCR)
- UniSTS:397924

REN73125 (e-PCR)
- UniSTS:397925

REN73126 (e-PCR)
- UniSTS:397926

ECD18612 (e-PCR)
- UniSTS:299622

REN73127 (e-PCR)
- UniSTS:397927

REN73128 (e-PCR)
- UniSTS:397928

REN73129 (e-PCR)
- UniSTS:397929

REN73130 (e-PCR)
- UniSTS:397930

ECD13220 (e-PCR)
- UniSTS:294250

REN73131 (e-PCR)
- UniSTS:397931

REN73132 (e-PCR)
- UniSTS:397932

REN73133 (e-PCR)
- UniSTS:397933

REN73134 (e-PCR)
- UniSTS:397934

REN73135 (e-PCR)
- UniSTS:397935

REN73136 (e-PCR)
- UniSTS:397936

REN73137 (e-PCR)
- UniSTS:397937

REN73138 (e-PCR)
- UniSTS:397938

REN73139 (e-PCR)
- UniSTS:397939

stSG601767 (e-PCR)
- UniSTS:444531

REN73140 (e-PCR)
- UniSTS:397940

REN73141 (e-PCR)
- UniSTS:397941

REN73142 (e-PCR)
- UniSTS:397942

REN73143 (e-PCR)
- UniSTS:397943

REN73144 (e-PCR)
- UniSTS:397944

REN73145 (e-PCR)
- UniSTS:397945

REN73146 (e-PCR)
- UniSTS:397946

REN73147 (e-PCR)
- UniSTS:397947

REN73148 (e-PCR)
- UniSTS:397948

REN73149 (e-PCR)
- UniSTS:397949

REN73150 (e-PCR)
- UniSTS:397950

REN73151 (e-PCR)
- UniSTS:397951

REN73152 (e-PCR)
- UniSTS:397952

REN73153 (e-PCR)
- UniSTS:397953

ECD14547 (e-PCR)
- UniSTS:295567

ECD11205 (e-PCR)
- UniSTS:292241

ECD04011 (e-PCR)
- UniSTS:285090

ECD00655 (e-PCR)
- UniSTS:281764

D11S1169 (e-PCR)
- UniSTS:4539

ECD03802 (e-PCR)
- UniSTS:284882

AL008751 (e-PCR)
- UniSTS:94689

ECD16192 (e-PCR)
- UniSTS:297207

ECD14402 (e-PCR)
- UniSTS:295423

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein folding chaperone	ISS Inferred from Sequence or Structural Similarity more info
enables receptor tyrosine kinase binding	IEA Inferred from Electronic Annotation more info
enables translation initiation factor binding	IBA Inferred from Biological aspect of Ancestor more info
enables translation initiation factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in Cajal body organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in Cajal body organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in DNA endoreduplication	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within_positive_effect DNA replication	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in RNA splicing	IEA Inferred from Electronic Annotation more info
involved_in apoptotic process involved in development	ISS Inferred from Sequence or Structural Similarity more info
involved_in axon development	IBA Inferred from Biological aspect of Ancestor more info
involved_in axon development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in axon development	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to epidermal growth factor stimulus	IDA Inferred from Direct Assay more info	PubMed
involved_in inner cell mass cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in microtubule cytoskeleton organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of motor neuron apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of RNA splicing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of growth	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of protein import into nucleus	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of protein import into nucleus	IDA Inferred from Direct Assay more info	PubMed
involved_in pre-mRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein folding	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of myelination	ISS Inferred from Sequence or Structural Similarity more info
involved_in signal transduction	TAS Traceable Author Statement more info	PubMed
involved_in spinal cord development	ISS Inferred from Sequence or Structural Similarity more info
involved_in trophectodermal cell proliferation	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in Cajal body	IBA Inferred from Biological aspect of Ancestor more info
located_in Cajal body	IDA Inferred from Direct Assay more info	PubMed
located_in Gemini of coiled bodies	IDA Inferred from Direct Assay more info	PubMed
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in axon	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in growth cone	ISS Inferred from Sequence or Structural Similarity more info
located_in neuronal cell body	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in perikaryon	ISS Inferred from Sequence or Structural Similarity more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: zinc finger protein ZPR1

Names: zinc finger protein 259

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_001317086.2 → NP_001304015.1 zinc finger protein ZPR1 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' end compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AP006216, BC017349, CD359945, CD365951, CR975994

UniProtKB/TrEMBL

H7C0E5

Related

ENSP00000394495.1, ENST00000429220.5

Conserved Domains (2) summary

smart00709
Location:203 → 362

Zpr1; Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins

pfam03367
Location:58 → 152

zf-ZPR1; ZPR1 zinc-finger domain
NM_003904.5 → NP_003895.1 zinc finger protein ZPR1 isoform 1

See identical proteins and their annotated locations for NP_003895.1

Status: REVIEWED

Description

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

Source sequence(s)

AP006216, BC017349, CD365951

Consensus CDS

CCDS8375.1

UniProtKB/Swiss-Prot

O75312, Q2TAA0

UniProtKB/TrEMBL

H7BZM7

Related

ENSP00000227322.3, ENST00000227322.8

Conserved Domains (2) summary

smart00709
Location:257 → 416

Zpr1; Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins

pfam03367
Location:49 → 206

zf-ZPR1; ZPR1 zinc-finger domain