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KHNYN KH and NYN domain containing [ Homo sapiens (human) ]

Gene ID: 23351, updated on 10-Dec-2024

Summary

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Official Symbol
KHNYNprovided by HGNC
Official Full Name
KH and NYN domain containingprovided by HGNC
Primary source
HGNC:HGNC:20166
See related
Ensembl:ENSG00000100441 MIM:619579; AllianceGenome:HGNC:20166
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
KIAA0323
Summary
The protein encoded by this gene contains a ribonuclease NYN domain and belongs to the N4BP1 family. The protein is a cofactor for the zinc finger antiviral protein (ZAP protein) which targets viral RNA for degradation and restricts SARS-CoV-2 infection. [provided by RefSeq, Sep 2021]
Expression
Ubiquitous expression in stomach (RPKM 18.8), small intestine (RPKM 18.4) and 25 other tissues See more
Orthologs
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Genomic context

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See KHNYN in Genome Data Viewer
Location:
14q12
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (24423165..24441843)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (18621854..18640575)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (24898492..24911049)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903292 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5642 Neighboring gene NYN domain and retroviral integrase containing Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5643 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8217 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:24899891-24900454 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:24900455-24901016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:24901017-24901578 Neighboring gene cerebellin 3 precursor Neighboring gene uncharacterized LOC101927045 Neighboring gene short chain dehydrogenase/reductase family 39U member 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:24949129-24949670 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:24976080-24977279 Neighboring gene chymase 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Crystallization and biochemical studies of the NYN domain of human KHNYN. Hong S, et al. Acta Crystallogr F Struct Biol Commun, 2024 Mar 1. PMID 38376822,
  2. CGIN1: a retroviral contribution to mammalian genomes. Marco A, et al. Mol Biol Evol, 2009 Oct. PMID 19561090
  3. A Nuclear Export Signal in KHNYN Required for Its Antiviral Activity Evolved as ZAP Emerged in Tetrapods. Lista MJ, et al. J Virol, 2023 Jan 31. PMID 36633408, Free PMC Article
  4. KHNYN is essential for the zinc finger antiviral protein (ZAP) to restrict HIV-1 containing clustered CpG dinucleotides. Ficarelli M, et al. Elife, 2019 Jul 9. PMID 31284899, Free PMC Article
  5. SARS-CoV-2 Is Restricted by Zinc Finger Antiviral Protein despite Preadaptation to the Low-CpG Environment in Humans. Nchioua R, et al. mBio, 2020 Oct 16. PMID 33067384, Free PMC Article

See all (35) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Crystallization and biochemical studies of the NYN domain of human KHNYN.
    Title: Crystallization and biochemical studies of the NYN domain of human KHNYN.
  2. KHNYN as a novel cofactor for ZAP to target CpG-containing retroviral RNA for degradation.
    Title: KHNYN is essential for the zinc finger antiviral protein (ZAP) to restrict HIV-1 containing clustered CpG dinucleotides.
  3. Observational study of gene-disease association. (HuGE Navigator)
    Title: Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study.
Submit: New GeneRIF Correction

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
Biological, clinical and population relevance of 95 loci for blood lipids.
EBI GWAS Catalog

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

Homology

Clone Names

  • KIAA0323

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA endonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables molecular_function ND
No biological Data available
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
Component Evidence Code Pubs
is_active_in cellular_component ND
No biological Data available
more info
  
is_active_in cytoplasmic ribonucleoprotein granule IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
protein KHNYN

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

  1. NG_034018.2 RefSeqGene

    Range
    11791..23680
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001290256.2 → NP_001277185.1  protein KHNYN isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and initiates translation at an alternate start codon, compared to variant 1. The encoded protein (isoform 2) has a longer N-terminus, compared to isoform 1.
    Source sequence(s)
    AA493312, AB002321, AL132800, BX161465
    UniProtKB/TrEMBL
    A8K6L5
    Conserved Domains (1) summary
    pfam11977
    Location:477 → 630
    RNase_Zc3h12a; Zc3h12a-like Ribonuclease NYN domain

  2. NM_001290257.2 → NP_001277186.1  protein KHNYN isoform 1

    See identical proteins and their annotated locations for NP_001277186.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Variants 1 and 3 encode the same protein (isoform 1).
    Source sequence(s)
    AA493312, AB002321, AK291680, AL132800, BX161465
    Consensus CDS
    CCDS32058.1
    UniProtKB/Swiss-Prot
    O15037, Q86TZ6, Q8IUQ2, Q96BA9
    UniProtKB/TrEMBL
    A8K6L5
    Related
    ENSP00000451106.1, ENST00000556842.5
    Conserved Domains (1) summary
    pfam11977
    Location:436 → 589
    RNase_Zc3h12a; Zc3h12a-like Ribonuclease NYN domain

  3. NM_015299.3 → NP_056114.1  protein KHNYN isoform 1

    See identical proteins and their annotated locations for NP_056114.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes isoform 1. Variants 1 and 3 encode the same protein.
    Source sequence(s)
    AL132800, BC015780, BX161465, CB115247, DA674601
    Consensus CDS
    CCDS32058.1
    UniProtKB/Swiss-Prot
    O15037, Q86TZ6, Q8IUQ2, Q96BA9
    UniProtKB/TrEMBL
    A8K6L5
    Related
    ENSP00000450799.1, ENST00000553935.6
    Conserved Domains (1) summary
    pfam11977
    Location:436 → 589
    RNase_Zc3h12a; Zc3h12a-like Ribonuclease NYN domain

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

  1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    24423165..24441843
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011536590.3 → XP_011534892.1  protein KHNYN isoform X1

    UniProtKB/TrEMBL
    A8K6L5
    Conserved Domains (1) summary
    pfam11977
    Location:479 → 632
    RNase_Zc3h12a; Zc3h12a-like Ribonuclease NYN domain

  2. XM_047431169.1 → XP_047287125.1  protein KHNYN isoform X4

  3. XM_047431168.1 → XP_047287124.1  protein KHNYN isoform X3

  4. XM_047431167.1 → XP_047287123.1  protein KHNYN isoform X3

  5. XM_005267474.6 → XP_005267531.1  protein KHNYN isoform X2

    See identical proteins and their annotated locations for XP_005267531.1

    UniProtKB/Swiss-Prot
    O15037, Q86TZ6, Q8IUQ2, Q96BA9
    UniProtKB/TrEMBL
    A8K6L5
    Conserved Domains (1) summary
    pfam11977
    Location:436 → 589
    RNase_Zc3h12a; Zc3h12a-like Ribonuclease NYN domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    18621854..18640575
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054375713.1 → XP_054231688.1  protein KHNYN isoform X1

    UniProtKB/TrEMBL
    A8K6L5

  2. XM_054375716.1 → XP_054231691.1  protein KHNYN isoform X3

  3. XM_054375715.1 → XP_054231690.1  protein KHNYN isoform X3

  4. XM_054375717.1 → XP_054231692.1  protein KHNYN isoform X4

  5. XM_054375714.1 → XP_054231689.1  protein KHNYN isoform X2

    UniProtKB/TrEMBL
    A8K6L5
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O15037.3 GenPept UniProtKB/Swiss-Prot:O15037

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