ZC3HC1 zinc finger C3HC-type containing 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ZC3HC1provided by HGNC
Official Full Name: zinc finger C3HC-type containing 1provided by HGNC
Primary source: HGNC:HGNC:29913
See related: Ensembl:ENSG00000091732 MIM:619746; AllianceGenome:HGNC:29913
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: NIPA; HSPC216
Summary: This gene encodes an F-box-containing protein that is a component of an SCF-type E3 ubiquitin ligase complex that regulates the onset of cell division. The G2/M transition in the cell cycle requires the interaction of the proteins cyclin B1 and cyclin-dependent kinase 1. The activated ubiquitin ligase complex targets the protein cyclin B1 for degradation, preventing this transition to mitosis. [provided by RefSeq, Aug 2013]
Expression: Ubiquitous expression in testis (RPKM 3.8), lymph node (RPKM 2.0) and 25 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 7q32.2

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (130018286..130051451, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (131331648..131364836, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (129658126..129691291, complement)

Chromosome 7 - NC_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

ZC3HC1 Is a Novel Inherent Component of the Nuclear Basket, Resident in a State of Reciprocal Dependence with TPR.
Title: ZC3HC1 Is a Novel Inherent Component of the Nuclear Basket, Resident in a State of Reciprocal Dependence with TPR.
Data show that common variants in A disintegrin and metalloproteinase with thrombospondin motifs 7 protein (ADAMTS7) and zinc finger, C3HC-type containing 1 protein (ZC3HC1) genes contribute to an increased risk for both coronary artery disease (CAD) and large artery ischemic stroke (LA atherosclerotic) IS.
Title: ADAMTS7 and ZC3HC1 Share Genetic Predisposition to Coronary Artery Disease and Large Artery Ischemic Stroke.
The Single Nucleotide Polymorphism of rs1464890 in ZC3HC1 is protective in hypertension.
Title: The genetic polymorphisms of ZC3HC1 and SMARCA4 are associated with hypertension risk.
Common nonsynonymous coding variant in ZC3HC1 (rs11556924) is associated with protection from coronary artery disease.
Title: Functional Validation of a Common Nonsynonymous Coding Variant in ZC3HC1 Associated With Protection From Coronary Artery Disease.
This study shows that the Coronary Artery Disease-associated coding polymorphism in ZC3HC1 alters the dynamics of cell-cycle regulation by NIPA.
Title: The Coronary Artery Disease-associated Coding Variant in Zinc Finger C3HC-type Containing 1 (ZC3HC1) Affects Cell Cycle Regulation.
ZC3HC1 rs11556924 polymorphism is associated with hypertension in a Finnish cohort.
Title: Association of Zinc Finger, C3HC-Type Containing 1 (ZC3HC1) rs11556924 Genetic Variant With Hypertension in a Finnish Population, the TAMRISK Study.
Results indicate that ZC3HC1 rs11556924 polymorphism is associated with subclinical atherosclerosis in rheumatoid arthritis.
Title: The ZC3HC1 rs11556924 polymorphism is associated with increased carotid intima-media thickness in patients with rheumatoid arthritis.
The NIPA protein is a human F-box-containing protein that defines an SCF-type E3 ligase (SCF(NIPA)) controlling mitotic entry.
Title: NIPA defines an SCF-type mammalian E3 ligase that regulates mitotic entry.
Data show that cell cycle-dependent phosphorylation of nuclear interaction partner of anaplastic lymphoma kinase (NIPA)is mediated by extracellular signal-regulated kinase 2 (ERK2).
Title: Extracellular signal-regulated kinase 2 (ERK2) mediates phosphorylation and inactivation of nuclear interaction partner of anaplastic lymphoma kinase (NIPA) at G2/M.
phosphorylated NIPA is degraded in late mitosis in an APC/C(Cdh1)-dependent manner
Title: APC/C(Cdh1)-mediated degradation of the F-box protein NIPA is regulated by its association with Skp1.

Submit: New GeneRIF Correction See all GeneRIFs (11)

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

EBI GWAS Catalog

Description
Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. 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

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)

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

RH69855 (e-PCR)
- UniSTS:23581

G32457 (e-PCR)
- UniSTS:117042

A009D40 (e-PCR)
- UniSTS:69233

ZC3HC1 (e-PCR)
- UniSTS:503675

RH12411 (e-PCR)
- UniSTS:60872

RH103940 (e-PCR)
- UniSTS:98265

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase 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 cell division	IEA Inferred from Electronic Annotation more info
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in nuclear membrane	IDA Inferred from Direct Assay more info
part_of nuclear pore nuclear basket	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info

General protein information

Go to the top of the page Help

Preferred Names: zinc finger C3HC-type protein 1

Names: hematopoietic stem/progenitor cell protein 216; nuclear interacting partner of anaplastic lymphoma kinase (ALK); nuclear-interacting partner of ALK

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.

mRNA and Protein(s)

NM_001282190.2 → NP_001269119.1 zinc finger C3HC-type protein 1 isoform 2

See identical proteins and their annotated locations for NP_001269119.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, contains an alternate exon in the 5' coding region, and initiates translation at an alternate start codon compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

AC073320, AF151050, AK001317, BC011551

Consensus CDS

CCDS64767.1

UniProtKB/TrEMBL

A4D1L4

Conserved Domains (2) summary

pfam07967
Location:52 → 180

zf-C3HC; C3HC zinc finger-like

pfam08600
Location:227 → 317

Rsm1; Rsm1-like
NM_001282191.1 → NP_001269120.1 zinc finger C3HC-type protein 1 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an in-frame exon in the coding region compared to variant 1. The encoded isoform (3) is shorter than isoform 1.

Source sequence(s)

AC073320, AC087071, AF151050, BC011551, BI830062, BM013594

Consensus CDS

CCDS75659.1

UniProtKB/TrEMBL

A0AAQ5BHH3

Related

ENSP00000353933.5, ENST00000360708.9

Conserved Domains (2) summary

pfam07967
Location:73 → 201

zf-C3HC; C3HC zinc finger-like

pfam08600
Location:248 → 395

Rsm1; Rsm1-like
NM_001363701.1 → NP_001350630.1 zinc finger C3HC-type protein 1 isoform 4

Status: REVIEWED

Source sequence(s)

AC073320, AC087071

Consensus CDS

CCDS87546.1

UniProtKB/TrEMBL

A0AAQ5BHH3, C9J0I9

Related

ENSP00000418533.1, ENST00000481503.5

Conserved Domains (2) summary

pfam07967
Location:73 → 201

zf-C3HC; C3HC zinc finger-like

pfam08600
Location:376 → 423

Rsm1; Rsm1-like
NM_016478.5 → NP_057562.3 zinc finger C3HC-type protein 1 isoform 1

See identical proteins and their annotated locations for NP_057562.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AC073320, AC087071

Consensus CDS

CCDS34753.1

UniProtKB/Swiss-Prot

A6NH66, Q75MF3, Q75MF4, Q86WB0, Q8N330, Q96F75, Q9HA34, Q9NVX4, Q9P0R0

UniProtKB/TrEMBL

A0AAQ5BHH3

Related

ENSP00000351052.4, ENST00000358303.9

Conserved Domains (2) summary

pfam07967
Location:73 → 201

zf-C3HC; C3HC zinc finger-like

pfam08600
Location:248 → 338

Rsm1; Rsm1-like

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_000007.14 Reference GRCh38.p14 Primary Assembly

Range

130018286..130051451 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047420454.1 → XP_047276410.1 zinc finger C3HC-type protein 1 isoform X4
XM_005250403.4 → XP_005250460.1 zinc finger C3HC-type protein 1 isoform X3

Conserved Domains (2) summary

pfam07967
Location:14 → 77

zf-C3HC; C3HC zinc finger-like

pfam08600
Location:124 → 214

Rsm1; Rsm1-like
XM_047420453.1 → XP_047276409.1 zinc finger C3HC-type protein 1 isoform X2
XM_011516288.4 → XP_011514590.1 zinc finger C3HC-type protein 1 isoform X1

UniProtKB/TrEMBL

A4D1L4

Conserved Domains (2) summary

pfam07967
Location:56 → 134

zf-C3HC; C3HC zinc finger-like

pfam08600
Location:181 → 271

Rsm1; Rsm1-like
XM_011516290.3 → XP_011514592.1 zinc finger C3HC-type protein 1 isoform X5

Conserved Domains (2) summary

pfam07967
Location:1 → 33

zf-C3HC; C3HC zinc finger-like

pfam08600
Location:80 → 170

Rsm1; Rsm1-like
XM_017012288.2 → XP_016867777.1 zinc finger C3HC-type protein 1 isoform X5

Conserved Domains (2) summary

pfam07967
Location:1 → 33

zf-C3HC; C3HC zinc finger-like

pfam08600
Location:80 → 170

Rsm1; Rsm1-like