CNBP CCHC-type zinc finger nucleic acid binding protein [Homo sapiens (human)] - Gene

Summary

Official Symbol: CNBPprovided by HGNC
Official Full Name: CCHC-type zinc finger nucleic acid binding proteinprovided by HGNC
Primary source: HGNC:HGNC:13164
See related: Ensembl:ENSG00000169714 MIM:116955; AllianceGenome:HGNC:13164
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: DM2; ZNF9; CNBP1; PROMM; RNF163; ZCCHC22
Summary: This gene encodes a nucleic-acid binding protein with seven zinc-finger domains. The protein has a preference for binding single stranded DNA and RNA. The protein functions in cap-independent translation of ornithine decarboxylase mRNA, and may also function in sterol-mediated transcriptional regulation. A CCTG expansion from <30 repeats to 75-11000 repeats in the first intron of this gene results in myotonic dystrophy type 2. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2016]
Expression: Ubiquitous expression in ovary (RPKM 93.4), heart (RPKM 89.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q21.3

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (129167827..129183896, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (131912733..131928791, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (128886670..128902739, complement)

Chromosome 3 - NC_000003.12 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?

The transcription of the main gene associated with Treacher-Collins syndrome (TCOF1) is regulated by G-quadruplexes and cellular nucleic acid binding protein (CNBP).
Title: The transcription of the main gene associated with Treacher-Collins syndrome (TCOF1) is regulated by G-quadruplexes and cellular nucleic acid binding protein (CNBP).
Cellular nucleic acid-binding protein restricts SARS-CoV-2 by regulating interferon and disrupting RNA-protein condensates.
Title: Cellular nucleic acid-binding protein restricts SARS-CoV-2 by regulating interferon and disrupting RNA-protein condensates.
CircPACRGL promoted cell proliferation, migration and invasion as well as inhibited cell apoptosis in colorectal cancer via regulation of the miR-330-3p/CNBP axis.
Title: CircPACRGL promoted cell proliferation, migration and invasion as well as inhibited cell apoptosis in colorectal cancer via regulation of the miR-330-3p/CNBP axis.
Circ-HuR serves as a tumor suppressor to inhibit CNBP-facilitated HuR expression and gastric cancer progression, indicating a potential therapeutic target for gastric cancer.
Title: Circ-HuR suppresses HuR expression and gastric cancer progression by inhibiting CNBP transactivation.
CNBP controls transcription by unfolding DNA G-quadruplex structures.
Title: CNBP controls transcription by unfolding DNA G-quadruplex structures.
The abnormal expansion of CTG repeats in the 3'-UTR of the DMPK gene elicits Myotonic Dystrophy 1, whereas elongated CCTG repeats in intron 1 of ZNF9 triggers Myotonic Dystrophy 2.
Title: Quantitative Methods to Monitor RNA Biomarkers in Myotonic Dystrophy.
The authors report a previously unknown long noncoding RNA which, together with CNBP, is involved in the fine-tuned regulation of CCND1 mRNA stability, without which CCND1 exhibits, at most, partial expression.
Title: LAST, a c-Myc-inducible long noncoding RNA, cooperates with CNBP to promote CCND1 mRNA stability in human cells.
[CCTG]n repeat expansion, differently from the DM1 mutation, does not influence the methylation status of the CNBP gene and other molecular mechanisms are involved in the pathogenesis of Myotonic Dystrophy type 2..
Title: Expanded [CCTG]n repetitions are not associated with abnormal methylation at the CNBP locus in myotonic dystrophy type 2 (DM2) patients.
RNA sequence preferences of unconventional RNA-binding proteins, Nudt21 and CNBP, has been described.
Title: RNAcompete methodology and application to determine sequence preferences of unconventional RNA-binding proteins.
A second point is that DM mutations, although located in noncoding regions, may reduce the expression of mutant alleles, raising questions whether loss-of-function may contribute to the phenotype, or possibly impose a safety limit on knockdown therapies that create or aggravate a DMPK or CNBP deficiency state
Title: Myotonic dystrophy: approach to therapy.

Submit: New GeneRIF Correction See all GeneRIFs (39)

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
Myotonic dystrophy type 2 MedGen: C2931689 OMIM: 602668 GeneReviews: Myotonic Dystrophy Type 2	Compare labs

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

Cnbp (e-PCR), detects polymorphism
- UniSTS:141362

D8S2279 (e-PCR)
- UniSTS:473907

D3S2800E (e-PCR)
- UniSTS:150838

A008K17 (e-PCR)
- UniSTS:36670

PMC15869P1 (e-PCR)
- UniSTS:271437

SHGC-77307 (e-PCR)
- UniSTS:25935

D3S1541 (e-PCR), detects polymorphism
- UniSTS:63314

Cnbp (e-PCR), detects polymorphism
- UniSTS:547432

D10S16 (e-PCR)
- UniSTS:155756

D3S1589 (e-PCR), detects polymorphism
- UniSTS:48783

RH47204 (e-PCR)
- UniSTS:55456

RH98983 (e-PCR)
- UniSTS:87486

SHGC-32794 (e-PCR)
- UniSTS:45771

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables G-quadruplex DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	HDA more info	PubMed
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables single-stranded RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables translation regulator activity	IBA Inferred from Biological aspect of Ancestor more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in G-quadruplex DNA formation	IDA Inferred from Direct Assay more info	PubMed
involved_in cholesterol homeostasis	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell population proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cytoplasmic translation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of DNA-templated transcription	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	TAS Traceable Author Statement more info
located_in endoplasmic reticulum	ISS Inferred from Sequence or Structural Similarity more info
NOT located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: CCHC-type zinc finger nucleic acid binding protein

Names: cellular nucleic acid-binding protein; erythroid differentiation-related; sterol regulatory element-binding protein; zinc finger protein 273; zinc finger protein 9 (a cellular retroviral nucleic acid binding protein)

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_011902.1 RefSeqGene

Range

5072..21141

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001127192.2 → NP_001120664.1 CCHC-type zinc finger nucleic acid binding protein isoform 1

See identical proteins and their annotated locations for NP_001120664.1

Status: REVIEWED

Description

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

Source sequence(s)

AC108673, AK292119, BU616793

Consensus CDS

CCDS46906.1

UniProtKB/Swiss-Prot

P62633

Related

ENSP00000410769.2, ENST00000441626.6

Conserved Domains (1) summary

PTZ00368
Location:54 → 173

PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional
NM_001127193.2 → NP_001120665.1 CCHC-type zinc finger nucleic acid binding protein isoform 2

See identical proteins and their annotated locations for NP_001120665.1

Status: REVIEWED

Description

Transcript Variant: This variant, also known as alpha variant 1, uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in a shorter protein (isoform 2).

Source sequence(s)

AC108673, BU616793, DQ091187

Consensus CDS

CCDS46907.1

UniProtKB/Swiss-Prot

P62633

Related

ENSP00000399488.2, ENST00000451728.6

Conserved Domains (1) summary

PTZ00368
Location:54 → 172

PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional
NM_001127194.2 → NP_001120666.1 CCHC-type zinc finger nucleic acid binding protein isoform 4

See identical proteins and their annotated locations for NP_001120666.1

Status: REVIEWED

Description

Transcript Variant: This variant, also known as beta variant 2, uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in a shorter protein (isoform 4).

Source sequence(s)

AC108673, BU616793, DQ092367

Consensus CDS

CCDS46908.1

UniProtKB/Swiss-Prot

P62633

Related

ENSP00000400444.2, ENST00000446936.6

Conserved Domains (1) summary

PTZ00368
Location:47 → 166

PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional
NM_001127195.2 → NP_001120667.1 CCHC-type zinc finger nucleic acid binding protein isoform 5

See identical proteins and their annotated locations for NP_001120667.1

Status: REVIEWED

Description

Transcript Variant: This variant, also known as beta variant 1, uses two alternate in-frame splice sites in the 5' and central coding regions, compared to variant 1, resulting in a shorter protein (isoform 5).

Source sequence(s)

AC108673, BU616793, DQ092366

UniProtKB/Swiss-Prot

P62633

Conserved Domains (1) summary

PTZ00368
Location:47 → 165

PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional
NM_001127196.2 → NP_001120668.1 CCHC-type zinc finger nucleic acid binding protein isoform 6

See identical proteins and their annotated locations for NP_001120668.1

Status: REVIEWED

Description

Transcript Variant: This variant uses two alternate in-frame splice sites in the 5' and central coding regions, compared to variant 1, resulting in a shorter protein (isoform 6).

Source sequence(s)

AC108673, BC014911, BU616793, DB027227

Consensus CDS

CCDS54637.1

UniProtKB/TrEMBL

A0A0S2Z4Q3

Related

ENSP00000421323.1, ENST00000502976.5

Conserved Domains (1) summary

PTZ00368
Location:47 → 164

PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional
NM_003418.5 → NP_003409.1 CCHC-type zinc finger nucleic acid binding protein isoform 3

See identical proteins and their annotated locations for NP_003409.1

Status: REVIEWED

Description

Transcript Variant: This variant uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in a shorter protein (isoform 3).

Source sequence(s)

AC108673, BC093058, BU616793, DB027227

Consensus CDS

CCDS3056.1

UniProtKB/Swiss-Prot

A8K7V4, B2RAV9, B4DP17, D3DNB9, D3DNC0, D3DNC1, E9PDR7, P20694, P62633, Q4JGY0, Q4JGY1, Q5QJR0, Q5U0E9, Q6PJI7, Q96NV3

UniProtKB/TrEMBL

A0A0S2Z4K2

Related

ENSP00000410619.3, ENST00000422453.7

Conserved Domains (1) summary

PTZ00368
Location:54 → 171

PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional