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SGPL1 sphingosine-1-phosphate lyase 1 [ Homo sapiens (human) ]

Gene ID: 8879, updated on 5-May-2024

Summary

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Official Symbol
SGPL1provided by HGNC
Official Full Name
sphingosine-1-phosphate lyase 1provided by HGNC
Primary source
HGNC:HGNC:10817
See related
Ensembl:ENSG00000166224 MIM:603729; AllianceGenome:HGNC:10817
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
SPL; RENI; S1PL; NPHS14
Summary
Enables sphinganine-1-phosphate aldolase activity. Involved in apoptotic signaling pathway; fatty acid metabolic process; and sphingolipid metabolic process. Located in endoplasmic reticulum. Implicated in nephrotic syndrome type 14. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in urinary bladder (RPKM 14.9), skin (RPKM 13.8) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
10q22.1
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (70815948..70881184)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (71685701..71750988)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (72575704..72640941)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72536007-72536834 Neighboring gene thymus, brain and testes associated Neighboring gene ribosomal protein S26 pseudogene 40 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2451 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2452 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2453 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2454 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2455 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2456 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2457 Neighboring gene pterin-4 alpha-carbinolamine dehydratase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72663371-72663919 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:72677493-72677667 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:72678259-72678439 Neighboring gene long intergenic non-protein coding RNA 2622

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. SGPL1 Deficiency: Nephrotic Syndrome with Lymphopenia. Tran P, et al. J Clin Immunol, 2023 Jan. PMID 36050428
  2. A rare cause of nephrotic syndrome-sphingosine-1-phosphate lyase (SGPL1) deficiency: 6 cases and a review of the literature. Tastemel Ozturk T, et al. Pediatr Nephrol, 2023 Mar. PMID 35748945
  3. Sphingosine Phosphate Lyase Insufficiency Syndrome. Adam MP, et al. , 1993. PMID 33074640
  4. S1P Lyase siRNA Dampens Malignancy of DLD-1 Colorectal Cancer Cells. Faqar-Uz-Zaman WF, et al. Lipids, 2021 Mar. PMID 32971566
  5. SGPL1(321) mutation: one main trigger for invasiveness of pediatric alveolar rhabdomyosarcoma. Adamus A, et al. Cancer Gene Ther, 2020 Aug. PMID 31455837, Free PMC Article

See all (119) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Loss of S1P Lyase Expression in Human Podocytes Causes a Reduction in Nephrin Expression That Involves PKCdelta Activation.
    Title: Loss of S1P Lyase Expression in Human Podocytes Causes a Reduction in Nephrin Expression That Involves PKCδ Activation.
  2. SGPL1 Deficiency: Nephrotic Syndrome with Lymphopenia.
    Title: SGPL1 Deficiency: Nephrotic Syndrome with Lymphopenia.
  3. A rare cause of nephrotic syndrome-sphingosine-1-phosphate lyase (SGPL1) deficiency: 6 cases and a review of the literature.
    Title: A rare cause of nephrotic syndrome-sphingosine-1-phosphate lyase (SGPL1) deficiency: 6 cases and a review of the literature.
  4. Influenza A virus NS1 induces degradation of sphingosine 1-phosphate lyase to obstruct the host innate immune response.
    Title: Influenza A virus NS1 induces degradation of sphingosine 1-phosphate lyase to obstruct the host innate immune response.
  5. S1P Lyase siRNA Dampens Malignancy of DLD-1 Colorectal Cancer Cells.
    Title: S1P Lyase siRNA Dampens Malignancy of DLD-1 Colorectal Cancer Cells.
  6. SGPL1321 mutation: one main trigger for invasiveness of pediatric alveolar rhabdomyosarcoma.
    Title: SGPL1(321) mutation: one main trigger for invasiveness of pediatric alveolar rhabdomyosarcoma.
  7. S1P Lyase Regulates Intestinal Stem Cell Quiescence via Ki-67 and FOXO3.
    Title: S1P Lyase Regulates Intestinal Stem Cell Quiescence via Ki-67 and FOXO3.
  8. Neurodegeneration Caused by S1P-Lyase Deficiency Involves Calcium-Dependent Tau Pathology and Abnormal Histone Acetylation.
    Title: Neurodegeneration Caused by S1P-Lyase Deficiency Involves Calcium-Dependent Tau Pathology and Abnormal Histone Acetylation.
  9. Heterogenous Nuclear Ribonucleoprotein H1 Promotes Colorectal Cancer Progression through the Stabilization of mRNA of Sphingosine-1-Phosphate Lyase 1.
    Title: Heterogenous Nuclear Ribonucleoprotein H1 Promotes Colorectal Cancer Progression through the Stabilization of mRNA of Sphingosine-1-Phosphate Lyase 1.
  10. SGPL1 Deficiency is associated with Primary Adrenal Insufficiency.
    Title: SGPL1 Deficiency: A Rare Cause of Primary Adrenal Insufficiency.
Submit: New GeneRIF Correction See all GeneRIFs (39)

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

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

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Vpu vpu HIV-1 Vpu is identified to have a physical interaction with sphingosine-1-phosphate lyase 1 (SGPL1) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

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

  • FLJ13811, KIAA1252

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables pyridoxal phosphate binding IEA
Inferred from Electronic Annotation
more info
  
enables sphinganine-1-phosphate aldolase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables sphinganine-1-phosphate aldolase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables sphinganine-1-phosphate aldolase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables sphinganine-1-phosphate aldolase activity NAS
Non-traceable Author Statement
more info
 PubMed 
enables sphinganine-1-phosphate aldolase activity TAS
Traceable Author Statement
more info
  
Process Evidence Code Pubs
involved_in Leydig cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in androgen metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in apoptotic signaling pathway IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in ceramide metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in estrogen metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in face morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in fatty acid metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in fibroblast migration IEA
Inferred from Electronic Annotation
more info
  
involved_in hemopoiesis IEA
Inferred from Electronic Annotation
more info
  
involved_in kidney development IEA
Inferred from Electronic Annotation
more info
  
involved_in luteinization IEA
Inferred from Electronic Annotation
more info
  
involved_in platelet-derived growth factor receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in post-embryonic development IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of multicellular organism growth IEA
Inferred from Electronic Annotation
more info
  
involved_in roof of mouth development IEA
Inferred from Electronic Annotation
more info
  
involved_in skeletal system morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in spermatogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in sphingolipid catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in sphingolipid catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in sphingolipid catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in sphingolipid catabolic process NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in sphingolipid catabolic process TAS
Traceable Author Statement
more info
  
involved_in vasculogenesis IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
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 NAS
Non-traceable Author Statement
more info
 PubMed 
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
sphingosine-1-phosphate lyase 1
Names
SP-lyase 1
SPL 1
hSPL
sphingosine-1-phosphate aldolase
NP_003892.2
XP_005270320.1
XP_011538618.1
XP_011538619.1
XP_011538620.1
XP_047281937.1
XP_047281938.1
XP_054223076.1
XP_054223077.1
XP_054223078.1
XP_054223079.1
XP_054223080.1
XP_054223081.1

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.

mRNA and Protein(s)

  1. NM_003901.4 → NP_003892.2  sphingosine-1-phosphate lyase 1

    See identical proteins and their annotated locations for NP_003892.2

    Status: VALIDATED

    Source sequence(s)
    AC073176, BC052991, BP314104
    Consensus CDS
    CCDS31216.1
    UniProtKB/Swiss-Prot
    B2RBD4, O95470, Q7Z732, Q9ULG8, Q9UN89
    Related
    ENSP00000362298.3, ENST00000373202.8
    Conserved Domains (1) summary
    cd06450
    Location:144 → 507
    DOPA_deC_like; DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to DOPA/tyrosine decarboxylase (DDC), histidine decarboxylase (HDC), and ...

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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    70815948..70881184
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047425981.1 → XP_047281937.1  sphingosine-1-phosphate lyase 1 isoform X1

    UniProtKB/Swiss-Prot
    B2RBD4, O95470, Q7Z732, Q9ULG8, Q9UN89

  2. XM_011540316.3 → XP_011538618.1  sphingosine-1-phosphate lyase 1 isoform X1

    See identical proteins and their annotated locations for XP_011538618.1

    UniProtKB/Swiss-Prot
    B2RBD4, O95470, Q7Z732, Q9ULG8, Q9UN89
    Conserved Domains (1) summary
    cd06450
    Location:144 → 507
    DOPA_deC_like; DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to DOPA/tyrosine decarboxylase (DDC), histidine decarboxylase (HDC), and ...

  3. XM_011540318.2 → XP_011538620.1  sphingosine-1-phosphate lyase 1 isoform X2

    See identical proteins and their annotated locations for XP_011538620.1

    UniProtKB/TrEMBL
    A0A8V8TN35
    Related
    ENSP00000513481.1, ENST00000697927.1
    Conserved Domains (1) summary
    cd06450
    Location:64 → 427
    DOPA_deC_like; DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to DOPA/tyrosine decarboxylase (DDC), histidine decarboxylase (HDC), and ...

  4. XM_047425982.1 → XP_047281938.1  sphingosine-1-phosphate lyase 1 isoform X3

  5. XM_005270263.2 → XP_005270320.1  sphingosine-1-phosphate lyase 1 isoform X1

    See identical proteins and their annotated locations for XP_005270320.1

    UniProtKB/Swiss-Prot
    B2RBD4, O95470, Q7Z732, Q9ULG8, Q9UN89
    Related
    ENSP00000513485.1, ENST00000697931.1
    Conserved Domains (1) summary
    cd06450
    Location:144 → 507
    DOPA_deC_like; DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to DOPA/tyrosine decarboxylase (DDC), histidine decarboxylase (HDC), and ...

  6. XM_011540317.2 → XP_011538619.1  sphingosine-1-phosphate lyase 1 isoform X1

    See identical proteins and their annotated locations for XP_011538619.1

    UniProtKB/Swiss-Prot
    B2RBD4, O95470, Q7Z732, Q9ULG8, Q9UN89
    Related
    ENSP00000513486.1, ENST00000697932.1
    Conserved Domains (1) summary
    cd06450
    Location:144 → 507
    DOPA_deC_like; DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to DOPA/tyrosine decarboxylase (DDC), histidine decarboxylase (HDC), and ...

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    71685701..71750988
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054367103.1 → XP_054223078.1  sphingosine-1-phosphate lyase 1 isoform X1

    UniProtKB/Swiss-Prot
    B2RBD4, O95470, Q7Z732, Q9ULG8, Q9UN89

  2. XM_054367104.1 → XP_054223079.1  sphingosine-1-phosphate lyase 1 isoform X1

    UniProtKB/Swiss-Prot
    B2RBD4, O95470, Q7Z732, Q9ULG8, Q9UN89

  3. XM_054367105.1 → XP_054223080.1  sphingosine-1-phosphate lyase 1 isoform X2

    UniProtKB/TrEMBL
    A0A8V8TN35

  4. XM_054367106.1 → XP_054223081.1  sphingosine-1-phosphate lyase 1 isoform X3

  5. XM_054367102.1 → XP_054223077.1  sphingosine-1-phosphate lyase 1 isoform X1

    UniProtKB/Swiss-Prot
    B2RBD4, O95470, Q7Z732, Q9ULG8, Q9UN89

  6. XM_054367101.1 → XP_054223076.1  sphingosine-1-phosphate lyase 1 isoform X1

    UniProtKB/Swiss-Prot
    B2RBD4, O95470, Q7Z732, Q9ULG8, Q9UN89
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O95470.3 GenPept UniProtKB/Swiss-Prot:O95470

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