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ZDHHC9 zinc finger DHHC-type palmitoyltransferase 9 [ Homo sapiens (human) ]

Gene ID: 51114, updated on 11-Apr-2024

Summary

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Official Symbol
ZDHHC9provided by HGNC
Official Full Name
zinc finger DHHC-type palmitoyltransferase 9provided by HGNC
Primary source
HGNC:HGNC:18475
See related
Ensembl:ENSG00000188706 MIM:300646; AllianceGenome:HGNC:18475
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
CGI89; DHHC9; MMSA1; MRXSR; MRXSZ; ZNF379; ZNF380; CXorf11; ZDHHC10
Summary
This gene encodes an integral membrane protein that is a member of the zinc finger DHHC domain-containing protein family. The encoded protein forms a complex with golgin subfamily A member 7 and functions as a palmitoyltransferase. This protein specifically palmitoylates HRAS and NRAS. Mutations in this gene are associated with X-linked cognitive disability. Alternate splicing results in multiple transcript variants that encode the same protein.[provided by RefSeq, May 2010]
Expression
Ubiquitous expression in brain (RPKM 17.9), kidney (RPKM 10.5) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
Xq26.1
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (129803288..129843886, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (128122064..128162666, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (128937264..128977862, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene X-prolyl aminopeptidase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:128889861-128890360 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29920 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29921 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:128902381-128902881 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29923 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29924 Neighboring gene uncharacterized LOC124905215 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29927 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29928 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29929 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29930 Neighboring gene SAM and SH3 domain containing 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:128983483-128984298 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:128984299-128985112 Neighboring gene spalt like transcription factor 4 pseudogene 2 Neighboring gene uncharacterized LOC105373335 Neighboring gene UTP14A small subunit processome component Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20979

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. Expanding the molecular basis and phenotypic spectrum of ZDHHC9-associated X-linked intellectual disability. Schirwani S, et al. Am J Med Genet A, 2018 May. PMID 29681091
  2. The first patient with sporadic X-linked intellectual disability with de novo ZDHHC9 mutation identified by targeted next-generation sequencing. Han JY, et al. Eur J Med Genet, 2017 Oct. PMID 28687527
  3. Global and Local Connectivity Differences Converge With Gene Expression in a Neurodevelopmental Disorder of Known Genetic Origin. Bathelt J, et al. Cereb Cortex, 2017 Jul 1. PMID 28168288, Free PMC Article
  4. Structural brain abnormalities in a single gene disorder associated with epilepsy, language impairment and intellectual disability. Bathelt J, et al. Neuroimage Clin, 2016. PMID 27747153, Free PMC Article
  5. Clinical application of whole-exome sequencing across clinical indications. Retterer K, et al. Genet Med, 2016 Jul. PMID 26633542

See all (42) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Involvement of ZDHHC9 in lung adenocarcinoma: regulation of PD-L1 stability via palmitoylation.
    Title: Involvement of ZDHHC9 in lung adenocarcinoma: regulation of PD-L1 stability via palmitoylation.
  2. DHHC9-mediated GLUT1 S-palmitoylation promotes glioblastoma glycolysis and tumorigenesis.
    Title: DHHC9-mediated GLUT1 S-palmitoylation promotes glioblastoma glycolysis and tumorigenesis.
  3. The results demonstrate that a mutation in a ZDHHC9 mutation impacts upon white matter organization across the whole-brain, but also shows regionally specific effects, according to variation in gene expression.
    Title: Global and Local Connectivity Differences Converge With Gene Expression in a Neurodevelopmental Disorder of Known Genetic Origin.
  4. studies suggest that ZDHHC9 may serve as a safe and effective target for developing therapies against NRAS-driven cancers
    Title: Palmitoylacyltransferase Zdhhc9 inactivation mitigates leukemogenic potential of oncogenic Nras.
  5. Data demonstrate that ZDHHC9 mutations are associated with reductions in cortical thickness and white matter microstructural integrity, particularly in regions and networks known to contribute to language function.
    Title: Structural brain abnormalities in a single gene disorder associated with epilepsy, language impairment and intellectual disability.
  6. De novo ZDHHC9 mutation was identified in a patient with X-linked intellectual disability.
    Title: The first patient with sporadic X-linked intellectual disability with de novo ZDHHC9 mutation identified by targeted next-generation sequencing.
  7. Report demonstrated that MMSA-1 is specifically expressed in multiple myeloma patients and its upregulation is associated with unfavorable clinical features and poor prognosis.
    Title: MMSA-1 expression pattern in multiple myeloma and its clinical significance.
  8. ZDHHC9 gene mutation is associated with Lujan-Fryns syndrome.
    Title: Tentative clinical diagnosis of Lujan-Fryns syndrome--A conglomeration of different genetic entities?
  9. Two missense mutation, R148W and P150S,of zDHHC9, affecting the autopalmitoylation is associated with the X-linked intellectual disability.
    Title: Mutations in the X-linked intellectual disability gene, zDHHC9, alter autopalmitoylation activity by distinct mechanisms.
  10. Data indicate that sp-Erf2/zDHHC9 palmitoylates Ras proteins in a highly selective manner in the trans-Golgi compartment to facilitate PM targeting via the trans-Golgi network, a role that is most certainly critical for Ras-driven tumorigenesis.
    Title: Regulation of Ras localization and cell transformation by evolutionarily conserved palmitoyltransferases.
Submit: New GeneRIF Correction See all GeneRIFs (14)

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
Syndromic X-linked intellectual disability Raymond type
MedGen: C3275406 OMIM: 300799 GeneReviews: Not available
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Copy number response

Description
Copy number response
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2021-10-12)

ClinGen Genome Curation PagePubMed
Triplosensitivity

No evidence available (Last evaluated 2021-10-12)

ClinGen Genome Curation Page

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables Ras palmitoyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables palmitoyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-cysteine S-palmitoyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein-cysteine S-palmitoyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein-cysteine S-palmitoyltransferase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables protein-cysteine S-palmitoyltransferase activity TAS
Traceable Author Statement
more info
  
Process Evidence Code Pubs
involved_in MAPK cascade TAS
Traceable Author Statement
more info
  
involved_in peptidyl-L-cysteine S-palmitoylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in peptidyl-L-cysteine S-palmitoylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in peptidyl-L-cysteine S-palmitoylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation by host of viral process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation by host of viral process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of cGAS/STING signaling pathway IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein palmitoylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein targeting to membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in Golgi membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in Golgi membrane TAS
Traceable Author Statement
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
is_active_in endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in endoplasmic reticulum-Golgi intermediate compartment membrane IC
Inferred by Curator
more info
 PubMed 
part_of palmitoyltransferase complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
palmitoyltransferase ZDHHC9
Names
Asp-His-His-Cys domain containing protein 9
antigen MMSA-1
zinc finger DHHC-type containing 9
zinc finger protein 379
zinc finger protein 380
zinc finger, DHHC domain containing 10
NP_001008223.1
NP_057116.2
XP_011529650.1
XP_047298107.1
XP_054183140.1
XP_054183141.1

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_021387.1 RefSeqGene

    Range
    5049..45647
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001008222.3 → NP_001008223.1  palmitoyltransferase ZDHHC9

    See identical proteins and their annotated locations for NP_001008223.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an alternate 5' UTR and encodes the same protein, as compared to variant 1.
    Source sequence(s)
    AL034405, AL359542, BC000035, DA768650
    Consensus CDS
    CCDS35395.1
    UniProtKB/Swiss-Prot
    B4F6G2, D3DTF9, Q59EK4, Q5JSW5, Q8WWS7, Q9BPY4, Q9NSP0, Q9NVL0, Q9NVR6, Q9Y397
    UniProtKB/TrEMBL
    B3KM45
    Related
    ENSP00000360103.3, ENST00000371064.7
    Conserved Domains (1) summary
    pfam01529
    Location:138 → 261
    DHHC; DHHC palmitoyltransferase

  2. NM_016032.4 → NP_057116.2  palmitoyltransferase ZDHHC9

    See identical proteins and their annotated locations for NP_057116.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) is the longer transcript and both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AL359542, BC003128, DA493628
    Consensus CDS
    CCDS35395.1
    UniProtKB/Swiss-Prot
    B4F6G2, D3DTF9, Q59EK4, Q5JSW5, Q8WWS7, Q9BPY4, Q9NSP0, Q9NVL0, Q9NVR6, Q9Y397
    UniProtKB/TrEMBL
    B3KM45
    Related
    ENSP00000349689.6, ENST00000357166.11
    Conserved Domains (1) summary
    pfam01529
    Location:138 → 261
    DHHC; DHHC palmitoyltransferase

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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    129803288..129843886 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047442151.1 → XP_047298107.1  palmitoyltransferase ZDHHC9 isoform X1

  2. XM_011531348.4 → XP_011529650.1  palmitoyltransferase ZDHHC9 isoform X2

    Conserved Domains (1) summary
    cl19890
    Location:17 → 170
    zf-DHHC; DHHC palmitoyltransferase

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    128122064..128162666 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054327165.1 → XP_054183140.1  palmitoyltransferase ZDHHC9 isoform X1

  2. XM_054327166.1 → XP_054183141.1  palmitoyltransferase ZDHHC9 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y397.2 GenPept UniProtKB/Swiss-Prot:Q9Y397

Gene LinkOut

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

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