U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

ZCCHC17 zinc finger CCHC-type containing 17 [ Homo sapiens (human) ]

Gene ID: 51538, updated on 3-Apr-2024

Summary

Go to the top of the page Help
Official Symbol
ZCCHC17provided by HGNC
Official Full Name
zinc finger CCHC-type containing 17provided by HGNC
Primary source
HGNC:HGNC:30246
See related
Ensembl:ENSG00000121766 MIM:619744; AllianceGenome:HGNC:30246
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PS1D; pNO40; HSPC251
Summary
Enables identical protein binding activity. Predicted to be involved in RNA stabilization. Predicted to be located in nucleolus. Predicted to be part of cytosolic large ribosomal subunit. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in heart (RPKM 23.1), brain (RPKM 18.8) and 24 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
1p35.2
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (31297032..31364936)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (31149209..31217206)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (31769879..31837783)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 566 Neighboring gene Sharpr-MPRA regulatory region 5533 Neighboring gene sodium/potassium transporting ATPase interacting 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:31671341-31671841 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:31688981-31689480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:31695101-31695601 Neighboring gene small nuclear ribonucleoprotein U5 subunit 40 Neighboring gene MPRA-validated peak156 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 641 Neighboring gene Sharpr-MPRA regulatory region 7682 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:31827736-31827903 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:31839312-31839494 Neighboring gene Sharpr-MPRA regulatory region 13821 Neighboring gene uncharacterized LOC124903892 Neighboring gene Sharpr-MPRA regulatory region 3310 Neighboring gene fatty acid binding protein 3 Neighboring gene uncharacterized LOC105378623

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. Ectopically expressed pNO40 suppresses ribosomal RNA synthesis by inhibiting UBF-dependent transcription activation. Lin YM, et al. Biochem Biophys Res Commun, 2019 Aug 20. PMID 31217076
  2. ZCCHC17 is a master regulator of synaptic gene expression in Alzheimer's disease. Tomljanovic Z, et al. Bioinformatics, 2018 Feb 1. PMID 29028963, Free PMC Article
  3. Molecular characterization of a novel nucleolar protein, pNO40. Chang WL, et al. Biochem Biophys Res Commun, 2003 Aug 1. PMID 12893261
  4. Identification of ribosomal proteins specific to higher eukaryotic organisms. Gueydan C, et al. J Biol Chem, 2002 Nov 22. PMID 12202495
  5. NKAIN1-SERINC2 is a functional, replicable and genome-wide significant risk gene region specific for alcohol dependence in subjects of European descent. Zuo L, et al. Drug Alcohol Depend, 2013 May 1. PMID 23455491, Free PMC Article

See all (57) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. ZCCHC17 Modulates Neuronal RNA Splicing and Supports Cognitive Resilience in Alzheimer's Disease.
    Title: ZCCHC17 Modulates Neuronal RNA Splicing and Supports Cognitive Resilience in Alzheimer's Disease.
  2. These results demonstrate the role of pNO40 in ribosomal RNA biosynthesis regulation by compromising UBF function in ribosomal DNA transcription activation with subsequent ribosomal RNA synthesis inhibition.
    Title: Ectopically expressed pNO40 suppresses ribosomal RNA synthesis by inhibiting UBF-dependent transcription activation.
  3. ZCCHC17 loss is an early driver of lower synaptic gene expression in Alzheimer's disease.
    Title: ZCCHC17 is a master regulator of synaptic gene expression in Alzheimer's disease.
  4. molecular cloning and characterization; it is localized to nucleoli of diverse cultured cells, with some concentration in the granular component of nucleoli
    Title: Molecular characterization of a novel nucleolar protein, pNO40.
Submit: New GeneRIF Correction

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
NKAIN1-SERINC2 is a functional, replicable and genome-wide significant risk gene region specific for alcohol dependence in subjects of European descent.
EBI GWAS Catalog

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)

Genotypes

HIV-1 interactions

Go to the top of the page Help

Replication interactions

Interaction Pubs
Knockdown of zinc finger, CCHC domain containing 17 (ZCCHC17) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein 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 RNA stabilization IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of cytosolic large ribosomal subunit IEA
Inferred from Electronic Annotation
more info
  
located_in nucleolus IEA
Inferred from Electronic Annotation
more info
  

General protein information

Go to the top of the page Help
Preferred Names
zinc finger CCHC domain-containing protein 17
Names
nucleolar protein 40
nucleolar protein of 40 kDa
pnn-interacting nucleolar protein
putative S1 RNA binding domain protein
zinc finger, CCHC domain containing 17

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)

  1. NM_001282566.2 → NP_001269495.1  zinc finger CCHC domain-containing protein 17 isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AF247661, AK307478, BC050609, DC366453
    Consensus CDS
    CCDS72741.1
    UniProtKB/TrEMBL
    A0A087WXF8, B4DYA9
    Related
    ENSP00000480986.1, ENST00000615916.4
    Conserved Domains (1) summary
    cd05686
    Location:45 → 108
    S1_pNO40; S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. ...

  2. NM_001282567.2 → NP_001269496.1  zinc finger CCHC domain-containing protein 17 isoform b

    See identical proteins and their annotated locations for NP_001269496.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks a portion of the 5' UTR and 5' coding region, initiates translation at a downstream in-frame start codon, and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AF247661, AK302343, AK307478, BC050609, DC366453
    Consensus CDS
    CCDS60062.1
    UniProtKB/TrEMBL
    A0A0D9SEW3, B4DYA9
    Related
    ENSP00000486079.1, ENST00000627541.1
    Conserved Domains (1) summary
    cl09927
    Location:1 → 62
    S1_like; S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. ...

  3. NM_001282568.2 → NP_001269497.1  zinc finger CCHC domain-containing protein 17 isoform c

    See identical proteins and their annotated locations for NP_001269497.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and 5' coding region, and uses an alternate start codon, compared to variant 1. The encoded isoform (c) has a distinct and shorter N-terminus, compared to isoform a. Both variants 3 and 4 encode isoform c.
    Source sequence(s)
    AK302248, AK302343, AK307478, BC000685, BC050609, DC366453
    Consensus CDS
    CCDS341.1
    UniProtKB/Swiss-Prot
    B4DY38, D3DPN4, Q6PKH4, Q9NP64, Q9NYG4, Q9P0M8
    UniProtKB/TrEMBL
    B4DYA9
    Related
    ENSP00000362819.1, ENST00000373714.5
    Conserved Domains (1) summary
    cd05686
    Location:13 → 86
    S1_pNO40; pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was ...

  4. NM_001282569.2 → NP_001269498.1  zinc finger CCHC domain-containing protein 17 isoform d

    See identical proteins and their annotated locations for NP_001269498.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and 5' coding region, and uses an alternate start codon, compared to variant 1. The encoded isoform (d) has a distinct and shorter N-terminus, compared to isoform a.
    Source sequence(s)
    AK302248, AK307478, BC050609, DC366453
    Consensus CDS
    CCDS60061.1
    UniProtKB/TrEMBL
    B4DYA9
    Related
    ENSP00000444742.1, ENST00000546109.5
    Conserved Domains (1) summary
    cl09927
    Location:15 → 78
    S1_like; Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains ...

  5. NM_001282570.2 → NP_001269499.1  zinc finger CCHC domain-containing protein 17 isoform e

    See identical proteins and their annotated locations for NP_001269499.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) lacks a portion of the 5' UTR and 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (e) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AK307478, BC050609
    UniProtKB/TrEMBL
    B4DYA9
    Conserved Domains (1) summary
    cl09927
    Location:1 → 62
    S1_like; S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. ...

  6. NM_001282571.2 → NP_001269500.1  zinc finger CCHC domain-containing protein 17 isoform f

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) differs in the 5' UTR and 5' coding region, and uses an alternate start codon, compared to variant 1. The encoded isoform (f) has a distinct and shorter N-terminus, compared to isoform a.
    Source sequence(s)
    AK001929, AK302343, AK307478, BC050609, BP309837, BP371153, DC366453
    Consensus CDS
    CCDS72744.1
    UniProtKB/TrEMBL
    A0A087WYV3
    Related
    ENSP00000482122.1, ENST00000616393.4

  7. NM_001282572.2 → NP_001269501.1  zinc finger CCHC domain-containing protein 17 isoform g

    See identical proteins and their annotated locations for NP_001269501.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (8) differs in the 5' UTR and 5' coding region, uses an alternate start codon, and lacks two exons that result in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (g) has distinct N- and C-termini and is shorter than isoform a.
    Source sequence(s)
    AK001929, AK302343, AK307478, BC050609, BF309574
    UniProtKB/Swiss-Prot
    Q9NP64
    UniProtKB/TrEMBL
    B4DYA9
    Conserved Domains (1) summary
    cd05686
    Location:13 → 86
    S1_pNO40; pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was ...

  8. NM_001282573.2 → NP_001269502.1  zinc finger CCHC domain-containing protein 17 isoform h

    See identical proteins and their annotated locations for NP_001269502.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (9) differs in the 5' UTR and 5' coding region, uses an alternate start codon, and lacks two exons that result in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (h) has distinct N- and C-termini and is shorter than isoform a.
    Source sequence(s)
    AK001929, AK302343, AK307478, BC050609, DA737244
    Consensus CDS
    CCDS72743.1
    UniProtKB/TrEMBL
    A0A087WYF0
    Related
    ENSP00000481743.1, ENST00000616859.4
    Conserved Domains (1) summary
    cl09927
    Location:15 → 78
    S1_like; Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains ...

  9. NM_001282574.2 → NP_001269503.1  zinc finger CCHC domain-containing protein 17 isoform i

    See identical proteins and their annotated locations for NP_001269503.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (10) differs in the 5' UTR and 5' coding region, uses an alternate start codon, and lacks an exon that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (i) has distinct N- and C-termini and is shorter than isoform a.
    Source sequence(s)
    AK001929, AK302343, AK307478, BC050609, CN423139, DC366453
    Consensus CDS
    CCDS72742.1
    UniProtKB/TrEMBL
    A0A087WXU5
    Related
    ENSP00000481299.1, ENST00000618216.4
    Conserved Domains (1) summary
    cd05686
    Location:13 → 86
    S1_pNO40; pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was ...

  10. NM_016505.4 → NP_057589.2  zinc finger CCHC domain-containing protein 17 isoform c

    See identical proteins and their annotated locations for NP_057589.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and 5' coding region, and uses an alternate start codon, compared to variant 1. The encoded isoform (c) has a distinct and shorter N-terminus, compared to isoform a. Both variants 3 and 4 encode isoform c.
    Source sequence(s)
    AK001929, AK302343, AK307478, BC050609
    Consensus CDS
    CCDS341.1
    UniProtKB/Swiss-Prot
    B4DY38, D3DPN4, Q6PKH4, Q9NP64, Q9NYG4, Q9P0M8
    UniProtKB/TrEMBL
    B4DYA9
    Related
    ENSP00000343557.5, ENST00000344147.10
    Conserved Domains (1) summary
    cd05686
    Location:13 → 86
    S1_pNO40; pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was ...

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    31297032..31364936
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047422508.1 → XP_047278464.1  zinc finger CCHC domain-containing protein 17 isoform X1

    UniProtKB/Swiss-Prot
    B4DY38, D3DPN4, Q6PKH4, Q9NP64, Q9NYG4, Q9P0M8

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    31149209..31217206
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054336976.1 → XP_054192951.1  zinc finger CCHC domain-containing protein 17 isoform X1

    UniProtKB/Swiss-Prot
    B4DY38, D3DPN4, Q6PKH4, Q9NP64, Q9NYG4, Q9P0M8
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NP64.1 GenPept UniProtKB/Swiss-Prot:Q9NP64

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous