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    KDSR 3-ketodihydrosphingosine reductase [ Homo sapiens (human) ]

    Gene ID: 2531, updated on 2-Nov-2024

    Summary

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    Official Symbol
    KDSRprovided by HGNC
    Official Full Name
    3-ketodihydrosphingosine reductaseprovided by HGNC
    Primary source
    HGNC:HGNC:4021
    See related
    Ensembl:ENSG00000119537 MIM:136440; AllianceGenome:HGNC:4021
    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
    DHSR; FVT1; EKVP4; SDR35C1
    Summary
    The protein encoded by this gene catalyzes the reduction of 3-ketodihydrosphingosine to dihydrosphingosine. The putative active site residues of the encoded protein are found on the cytosolic side of the endoplasmic reticulum membrane. A chromosomal rearrangement involving this gene is a cause of follicular lymphoma, also known as type II chronic lymphatic leukemia. The mutation of a conserved residue in the bovine ortholog causes spinal muscular atrophy. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in ovary (RPKM 14.9), skin (RPKM 11.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See KDSR in Genome Data Viewer
    Location:
    18q21.33
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (63327726..63367206, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (63532776..63572250, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (60994959..61034439, complement)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13442 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13441 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13444 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13445 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13446 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:60805026-60805892 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13448 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13449 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:60813108-60813608 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:60813609-60814109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13451 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13452 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13453 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13454 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13455 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13456 Neighboring gene BCL2 apoptosis regulator Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13458 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13457 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13459 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13461 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13462 Neighboring gene uncharacterized LOC124904379 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13463 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:60881329-60881829 Neighboring gene Sharpr-MPRA regulatory region 13227 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13466 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9522 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9523 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9524 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9525 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13467 Neighboring gene uncharacterized LOC124904317 Neighboring gene Sharpr-MPRA regulatory region 13815 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:61033863-61034810 Neighboring gene KDSR divergent transcript Neighboring gene uncharacterized LOC124904316 Neighboring gene vacuolar protein sorting 4 homolog B

    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 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. B-cell non-Hodgkin's lymphoma cell line (Karpas 1106) with complex translocation involving 18q21.3 but lacking BCL2 rearrangement and expression. Nacheva E, et al. Blood, 1994 Nov 15. PMID 7949096
    2. Uterine tumor resembling ovarian sex cord tumor: report of a case with t(X;6)(p22.3;q23.1) and t(4;18)(q21.1;q21.3). Wang J, et al. Diagn Mol Pathol, 2003 Sep. PMID 12960700
    3. Formation of keto-type ceramides in palmoplantar keratoderma based on biallelic KDSR mutations in patients. Pilz R, et al. Hum Mol Genet, 2022 Mar 31. PMID 34686882
    4. Expression of the follicular lymphoma variant translocation 1 gene in diffuse large B-cell lymphoma correlates with subtype and clinical outcome. Czuchlewski DR, et al. Am J Clin Pathol, 2008 Dec. PMID 19019774, Free PMC Article
    5. FVT-1, a novel human transcription unit affected by variant translocation t(2;18)(p11;q21) of follicular lymphoma. Rimokh R, et al. Blood, 1993 Jan 1. PMID 8417785

    See all (44) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Formation of keto-type ceramides in palmoplantar keratoderma based on biallelic KDSR mutations in patients.
      Title: Formation of keto-type ceramides in palmoplantar keratoderma based on biallelic KDSR mutations in patients.
    2. Depletion of kdsr causes thrombocytopenia due to impaired proplatelet formation and sphingolipid dysregulation.
      Title: Sphingolipid dysregulation due to lack of functional KDSR impairs proplatelet formation causing thrombocytopenia.
    3. mutations in KDSR (3-ketodihydrosphingosine reductase), encoding an enzyme in the ceramide synthesis pathway, lead to a previously undescribed recessive Mendelian disorder in the progressive symmetric erythrokeratoderma spectrum.
      Title: Mutations in KDSR Cause Recessive Progressive Symmetric Erythrokeratoderma.
    4. FVT1 is significantly underexpressed by germinal center-type diffuse large B-cell lymphoma compared with non-germinal center-type DLBCL, follicular lymphoma, & normal tonsil control samples. Increased expression of FVT1 correlated with decreased survival.
      Title: Expression of the follicular lymphoma variant translocation 1 gene in diffuse large B-cell lymphoma correlates with subtype and clinical outcome.
    5. Data show that mutations in FVT1 do not contribute significantly to the cause of motor neuron diseases in the human population.
      Title: Candidate screening of the bovine and feline spinal muscular atrophy genes reveals no evidence for involvement in human motor neuron disorders.
    6. Observational study of gene-disease association. (HuGE Navigator)
      Title: Common genetic variation in multiple metabolic pathways influences susceptibility to low HDL-cholesterol and coronary heart disease.
    7. Describes an Ala-175 to Thr mutation in the bovine ortholog that causes spinal muscular atrophy. This residue is conserved in several species, including human.
      Title: A missense mutation in the 3-ketodihydrosphingosine reductase FVT1 as candidate causal mutation for bovine spinal muscular atrophy.
    8. FVT-1 is a mammalian 3-ketodihydrosphingosine reductase with an active site that faces the cytosolic side of the endoplasmic reticulum membrane
      Title: FVT-1 is a mammalian 3-ketodihydrosphingosine reductase with an active site that faces the cytosolic side of the endoplasmic reticulum membrane.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Erythrokeratodermia variabilis et progressiva 4
    MedGen: C4479620 OMIM: 617526 GeneReviews: Not available
    		not available

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    • FLJ36555, FLJ92680

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 3-dehydrosphinganine reductase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables 3-dehydrosphinganine reductase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables 3-dehydrosphinganine reductase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables 3-dehydrosphinganine reductase activity TAS
    Traceable Author Statement
    more info
    		  
    enables NADPH binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in 3-keto-sphinganine metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within 3-keto-sphinganine metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in 3-keto-sphinganine metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in sphingolipid biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in sphingolipid biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in sphingolipid biosynthetic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in sphingolipid biosynthetic process TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular space TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in membrane HDA PubMed 

    General protein information

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    Preferred Names
    3-ketodihydrosphingosine reductase
    Names
    3-dehydrosphinganine reductase
    FVT-1
    KDS reductase
    follicular lymphoma variant translocation 1
    follicular variant translocation protein 1
    short chain dehydrogenase/reductase family 35C member 1
    NP_002026.1

    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_028249.1 RefSeqGene

      Range
      5068..44548
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1196

    mRNA and Protein(s)

    1. NM_002035.4 → NP_002026.1  3-ketodihydrosphingosine reductase

      See identical proteins and their annotated locations for NP_002026.1

      Status: REVIEWED

      Source sequence(s)
      AC021803, X63657
      Consensus CDS
      CCDS11982.1
      UniProtKB/Swiss-Prot
      B2R5Y1, B4DMX0, Q06136
      UniProtKB/TrEMBL
      K7ERC8
      Related
      ENSP00000494352.1, ENST00000645214.2
      Conserved Domains (1) summary
      cd08939
      Location:32 → 268
      KDSR-like_SDR_c; 3-ketodihydrosphingosine reductase (KDSR) and related proteins, classical (c) SDR

    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_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      63327726..63367206 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      63532776..63572250 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q06136.1 GenPept UniProtKB/Swiss-Prot:Q06136

    Gene LinkOut

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

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