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

Summary

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; 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: mouse all
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Genomic context

Location:: 10q22.1

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (70815948..70881184)
RS_2023_03	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_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
SGPL1 Deficiency: Nephrotic Syndrome with Lymphopenia.
Title: SGPL1 Deficiency: Nephrotic Syndrome with Lymphopenia.
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.
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.
S1P Lyase siRNA Dampens Malignancy of DLD-1 Colorectal Cancer Cells.
Title: S1P Lyase siRNA Dampens Malignancy of DLD-1 Colorectal Cancer Cells.
SGPL1321 mutation: one main trigger for invasiveness of pediatric alveolar rhabdomyosarcoma.
Title: SGPL1(321) mutation: one main trigger for invasiveness of pediatric alveolar rhabdomyosarcoma.
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.
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.
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.
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

Associated conditions

Description	Tests
Charcot-Marie-Tooth disease MedGen: C0007959 GeneReviews: Charcot-Marie-Tooth Hereditary Neuropathy Overview	Compare labs
Nephrotic syndrome 14 MedGen: C4540559 OMIM: 617575 GeneReviews: Sphingosine Phosphate Lyase Insufficiency Syndrome	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-33649 (e-PCR)
- UniSTS:54537

WI-14267 (e-PCR)
- UniSTS:6476

RH27225 (e-PCR)
- UniSTS:88916

G32525 (e-PCR)
- UniSTS:117110

SHGC-36893 (e-PCR)
- UniSTS:4019

A009G12 (e-PCR)
- UniSTS:456

RH44692 (e-PCR)
- UniSTS:46807

Homology

Homologs of the SGPL1 gene: The SGPL1 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, C.elegans, S.cerevisiae, K.lactis, M.oryzae, N.crassa, A.thaliana, rice, and frog.
Orthologs from Annotation Pipeline: 504 organisms have orthologs with human gene SGPL1
Orthologs

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	PubMed
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 biosynthetic process	TAS Traceable Author Statement more info
involved_in sphingolipid catabolic process	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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 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	PubMed
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

EC 4.1.2.27

XP_005270320.1

EC 4.1.2.27

XP_011538618.1

EC 4.1.2.27

XP_011538619.1

EC 4.1.2.27

XP_011538620.1

EC 4.1.2.27

XP_047281937.1

EC 4.1.2.27

XP_047281938.1

EC 4.1.2.27

XP_054223076.1

EC 4.1.2.27

XP_054223077.1

EC 4.1.2.27

XP_054223078.1

EC 4.1.2.27

XP_054223079.1

EC 4.1.2.27

XP_054223080.1

EC 4.1.2.27

XP_054223081.1

EC 4.1.2.27

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)

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

O95470, 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_03

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000010.11 Reference GRCh38.p14 Primary Assembly

Range

70815948..70881184

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

Q9UN89
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

O95470, 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 ...
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 ...
XM_047425982.1 → XP_047281938.1 sphingosine-1-phosphate lyase 1 isoform X3
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

O95470, 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 ...
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

O95470, 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 ...