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

Gene ID: 2531, updated on 5-Mar-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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Location:
18q21.33
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (63327726..63367206, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (63532776..63572250, complement)
105.20220307 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
  • 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. 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
  2. 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
  3. 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
  4. 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
  5. Sphingolipid dysregulation due to lack of functional KDSR impairs proplatelet formation causing thrombocytopenia. Bariana TK, et al. Haematologica, 2019 May. PMID 30467204, Free PMC Article

See all (38) 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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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
Erythrokeratodermia variabilis et progressiva 4
MedGen: C4479620 OMIM: 617526 GeneReviews: Not available
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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

  • 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 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 sphingolipid biosynthetic process IBA
Inferred from Biological aspect of Ancestor
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 precursor

    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_2023_10

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

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