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

Summary

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, Oct 2024]
Expression: Ubiquitous expression in heart (RPKM 23.1), brain (RPKM 18.8) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p35.2

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (31297032..31364936)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (31149209..31217206)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (31769879..31837783)

Chromosome 1 - NC_000001.11 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?

ZCCHC17 knockdown phenocopies Alzheimer's disease-related loss of synaptic proteins and hyperexcitability.
Title: ZCCHC17 knockdown phenocopies Alzheimer's disease-related loss of synaptic proteins and hyperexcitability.
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.
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.
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.
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.

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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

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 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)

HIV-1 interactions

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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

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-143051 (e-PCR)
- UniSTS:171777

SHGC-74490 (e-PCR)
- UniSTS:83035

D1S1430 (e-PCR)
- UniSTS:149626

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	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

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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)

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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_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. ...
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. ...
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 ...
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 ...
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. ...
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
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 ...
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 ...
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 ...
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 ...