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    DHX38 DEAH-box helicase 38 [ Homo sapiens (human) ]

    Gene ID: 9785, updated on 9-Jun-2024

    Summary

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    Official Symbol
    DHX38provided by HGNC
    Official Full Name
    DEAH-box helicase 38provided by HGNC
    Primary source
    HGNC:HGNC:17211
    See related
    Ensembl:ENSG00000140829 MIM:605584; AllianceGenome:HGNC:17211
    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
    RP84; DDX38; PRP16; PRPF16
    Summary
    DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. The protein encoded by this gene is a member of the DEAD/H box family of splicing factors. This protein resembles yeast Prp16 more closely than other DEAD/H family members. It is an ATPase and essential for the catalytic step II in pre-mRNA splicing process. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in spleen (RPKM 15.5), bone marrow (RPKM 15.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DHX38 in Genome Data Viewer
    Location:
    16q22.2
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (72093847..72112912)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (77910161..77929227)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (72127746..72146811)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene haptoglobin Neighboring gene haptoglobin-related protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11089 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11090 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11091 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:72132901-72133401 Neighboring gene thioredoxin like 4B Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:72141414-72142613 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11093 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11092 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:72159455-72159956 Neighboring gene NANOG hESC enhancer GRCh37_chr16:72162293-72163093 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:72163923-72164424 Neighboring gene polyamine modulated factor 1 binding protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:72171124-72171624 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11094 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11095 Neighboring gene uncharacterized LOC105371341 Neighboring gene VISTA enhancer hs22 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:72257113-72258312 Neighboring gene uncharacterized LOC124903720 Neighboring gene MYC binding protein pseudogene

    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. Retinitis pigmentosa-linked mutation in DHX38 modulates its splicing activity. Obuća M, et al. PLoS One, 2022. PMID 35385551, Free PMC Article
    2. The splicing factor DHX38/PRP16 is required for ovarian clear cell carcinoma tumorigenesis, as revealed by a CRISPR-Cas9 screen. Cona B, et al. FEBS Open Bio, 2022 Mar. PMID 34965029, Free PMC Article
    3. Confirmation of the Role of DHX38 in the Etiology of Early-Onset Retinitis Pigmentosa. Latif Z, et al. Invest Ophthalmol Vis Sci, 2018 Sep 4. PMID 30208423, Free PMC Article
    4. A missense mutation in the splicing factor gene DHX38 is associated with early-onset retinitis pigmentosa with macular coloboma. Ajmal M, et al. J Med Genet, 2014 Jul. PMID 24737827
    5. PRP16 is an RNA-dependent ATPase that interacts transiently with the spliceosome. Schwer B, et al. Nature, 1991 Feb 7. PMID 1825134

    See all (97) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. DHX38 enhances proliferation, metastasis, and EMT progression in NSCLC through the G3BP1-mediated MAPK pathway.
      Title: DHX38 enhances proliferation, metastasis, and EMT progression in NSCLC through the G3BP1-mediated MAPK pathway.
    2. DHX38 restricts chemoresistance by regulating the alternative pre-mRNA splicing of RELL2 in pancreatic ductal adenocarcinoma.
      Title: DHX38 restricts chemoresistance by regulating the alternative pre-mRNA splicing of RELL2 in pancreatic ductal adenocarcinoma.
    3. Retinitis pigmentosa-linked mutation in DHX38 modulates its splicing activity.
      Title: Retinitis pigmentosa-linked mutation in DHX38 modulates its splicing activity.
    4. The splicing factor DHX38/PRP16 is required for ovarian clear cell carcinoma tumorigenesis, as revealed by a CRISPR-Cas9 screen.
      Title: The splicing factor DHX38/PRP16 is required for ovarian clear cell carcinoma tumorigenesis, as revealed by a CRISPR-Cas9 screen.
    5. We identified a second deleterious DHX38 variant that segregates with arRP in two families, providing additional evidence that DHX38 is involved in RP etiology. DHX38 encodes for pre-mRNA splicing factor PRP16, which is important in catalyzing pre-mRNA splicing.
      Title: Confirmation of the Role of DHX38 in the Etiology of Early-Onset Retinitis Pigmentosa.
    6. DHX38 is the first pre-mRNA splicing gene that is putatively associated with autosomal-recessive inherited retinitis pigmentosa.
      Title: A missense mutation in the splicing factor gene DHX38 is associated with early-onset retinitis pigmentosa with macular coloboma.
    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

    Associated conditions

    Description Tests
    Retinitis pigmentosa 84
    MedGen: C4748725 OMIM: 618220 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Biological, clinical and population relevance of 95 loci for blood lipids.
    EBI GWAS Catalog
    Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.
    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)

    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

    Clone Names

    • KIAA0224

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 3'-5' RNA helicase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding HDA PubMed 
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA helicase activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA splicing, via spliceosome IC
    Inferred by Curator
    more info
    		 PubMed 
    involved_in mRNA splicing, via spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in mRNA splicing, via spliceosome TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    part_of catalytic step 2 spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in intracellular anatomical structure IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane HDA PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of spliceosomal complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16
    Names
    ATP-dependent RNA helicase DHX38
    DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 38
    DEAH (Asp-Glu-Ala-His) box polypeptide 38
    DEAH box protein 38
    PRP16 homolog of S.cerevisiae
    pre-mRNA processing factor 16
    NP_054722.2
    XP_011521786.1
    XP_016879402.1
    XP_047290941.1
    XP_047290942.1
    XP_054170516.1
    XP_054170517.1
    XP_054170518.1

    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_034207.1 RefSeqGene

      Range
      5132..24197
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_014003.4 → NP_054722.2  pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16

      See identical proteins and their annotated locations for NP_054722.2

      Status: REVIEWED

      Source sequence(s)
      AA126451, BC008340, BG719187, BM473438
      Consensus CDS
      CCDS10907.1
      UniProtKB/Swiss-Prot
      B4DVG8, D3DWS7, O75212, Q92620, Q96HN7
      UniProtKB/TrEMBL
      A8K6G9
      Related
      ENSP00000268482.3, ENST00000268482.8
      Conserved Domains (1) summary
      COG1643
      Location:515 → 1146
      HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      72093847..72112912
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011523484.3 → XP_011521786.1  pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 isoform X1

      See identical proteins and their annotated locations for XP_011521786.1

      UniProtKB/Swiss-Prot
      B4DVG8, D3DWS7, O75212, Q92620, Q96HN7
      UniProtKB/TrEMBL
      A8K6G9
      Conserved Domains (1) summary
      COG1643
      Location:515 → 1146
      HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]

    2. XM_017023913.3 → XP_016879402.1  pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 isoform X2

      UniProtKB/TrEMBL
      A8K6G9
      Conserved Domains (5) summary
      smart00490
      Location:723 → 826
      HELICc; helicase superfamily c-terminal domain
      smart00487
      Location:491 → 678
      DEXDc; DEAD-like helicases superfamily
      smart00847
      Location:895 → 977
      HA2; Helicase associated domain (HA2) Add an annotation
      cd00046
      Location:516 → 652
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      pfam07717
      Location:1028 → 1111
      OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold

    3. XM_047434985.1 → XP_047290941.1  pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 isoform X1

      UniProtKB/Swiss-Prot
      B4DVG8, D3DWS7, O75212, Q92620, Q96HN7
      UniProtKB/TrEMBL
      A8K6G9

    4. XM_047434986.1 → XP_047290942.1  pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      77910161..77929227
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314541.1 → XP_054170516.1  pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 isoform X1

      UniProtKB/Swiss-Prot
      B4DVG8, D3DWS7, O75212, Q92620, Q96HN7
      UniProtKB/TrEMBL
      A8K6G9

    2. XM_054314542.1 → XP_054170517.1  pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 isoform X2

      UniProtKB/TrEMBL
      A8K6G9

    3. XM_054314543.1 → XP_054170518.1  pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q92620.2 GenPept UniProtKB/Swiss-Prot:Q92620

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