SMPDL3B sphingomyelin phosphodiesterase acid like 3B [Homo sapiens (human)] - Gene

Summary

Official Symbol: SMPDL3Bprovided by HGNC
Official Full Name: sphingomyelin phosphodiesterase acid like 3Bprovided by HGNC
Primary source: HGNC:HGNC:21416
See related: Ensembl:ENSG00000130768 MIM:617737; AllianceGenome:HGNC:21416
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: ASML3B
Summary: Enables phosphoric diester hydrolase activity. Predicted to be involved in membrane lipid catabolic process; negative regulation of inflammatory response; and negative regulation of toll-like receptor signaling pathway. Located in extracellular exosome. [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in duodenum (RPKM 6.3), colon (RPKM 6.3) and 13 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p35.3

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (27935000..27959152)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (27776819..27800989)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (28261511..28285663)

Chromosome 1 - NC_000001.11 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?

SMPDL3B contributes to gastric adenocarcinoma cells progression by promoting the infiltration of M2 macrophages.
Title: SMPDL3B contributes to gastric adenocarcinoma cells progression by promoting the infiltration of M2 macrophages.
SMPDL3b modulates radiation-induced DNA damage response in renal podocytes.
Title: SMPDL3b modulates radiation-induced DNA damage response in renal podocytes.
Sphingomyelin Phosphodiesterase Acid-Like 3b is Essential for Toll-Like Receptor 3 Signaling in Human Podocytes.
Title: Sphingomyelin Phosphodiesterase Acid-Like 3b is Essential for Toll-Like Receptor 3 Signaling in Human Podocytes.
Phosphodiesterase SMPDL3B Gene Expression as Independent Outcome Prediction Marker in Localized Prostate Cancer.
Title: Phosphodiesterase SMPDL3B Gene Expression as Independent Outcome Prediction Marker in Localized Prostate Cancer.
Modulation of radiation-induced damage of human glomerular endothelial cells by SMPDL3B.
Title: Modulation of radiation-induced damage of human glomerular endothelial cells by SMPDL3B.
Study reports that SMPDL3b excess, as observed in podocytes in diabetic kidney disease, impairs insulin receptor isoform B-dependent pro-survival insulin signaling by interfering with insulin receptor isoforms binding to caveolin-1 in the plasma membrane.
Title: SMPDL3b modulates insulin receptor signaling in diabetic kidney disease.
Glomerular immunoreactivity and urinary excretion of SMPDL3b in proteinuric nephrotic syndrome patients decreased compared with controls.
Title: Urinary excretion of sphingomyelinase phosphodiesterase acid-like 3b in children with intractable nephrotic syndrome.
These results demonstrate that radiation injury induces early cytoskeletal remodeling, down-regulation of SMPDL3b, and elevation of cellular ceramide levels. Overexpression of SMPDL3b and pretreatment with rituximab confer a radioprotective effect in cultured podocytes.
Title: Sphingomyelinase-like phosphodiesterase 3b mediates radiation-induced damage of renal podocytes.

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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

EBI GWAS Catalog

Description
Identification of a candidate gene for astigmatism. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables hydrolase activity, acting on glycosyl bonds	IEA Inferred from Electronic Annotation more info
enables phosphoric diester hydrolase activity	IBA Inferred from Biological aspect of Ancestor more info
enables phosphoric diester hydrolase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables phosphoric diester hydrolase activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sphingomyelin phosphodiesterase activity	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in membrane lipid catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of inflammatory response	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of toll-like receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in sphingomyelin catabolic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular space	HDA more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in side of membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: acid sphingomyelinase-like phosphodiesterase 3b

Names: ASM-like phosphodiesterase 3b

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_001009568.3 → NP_001009568.1 acid sphingomyelinase-like phosphodiesterase 3b isoform 2 precursor

See identical proteins and their annotated locations for NP_001009568.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.

Source sequence(s)

AL512288, BC014444, BP284513, DC370191

Consensus CDS

CCDS30656.1

UniProtKB/Swiss-Prot

Q92485

Related

ENSP00000362995.4, ENST00000373888.8

Conserved Domains (1) summary

cd00842
Location:23 → 323

MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain
NM_001304579.2 → NP_001291508.1 acid sphingomyelinase-like phosphodiesterase 3b isoform 3

See identical proteins and their annotated locations for NP_001291508.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate splice junction at the 5' end of an internal exon compared to variant 1, which causes translation initiation at a downstream start codon. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.

Source sequence(s)

AK293566, AL512288, BP284513, CA425405

UniProtKB/TrEMBL

B4DEC6

Conserved Domains (1) summary

cl13995
Location:3 → 117

MPP_superfamily; metallophosphatase superfamily, metallophosphatase domain
NM_014474.4 → NP_055289.2 acid sphingomyelinase-like phosphodiesterase 3b isoform 1 precursor

See identical proteins and their annotated locations for NP_055289.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AK301349, AK316500, AL512288, CA425405

Consensus CDS

CCDS30655.1

UniProtKB/Swiss-Prot

B7ZB35, Q5T0Z0, Q92485, Q96CB7

UniProtKB/TrEMBL

B4DW34

Related

ENSP00000363001.3, ENST00000373894.8

Conserved Domains (2) summary

cd00842
Location:23 → 323

MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain

pfam00149
Location:82 → 281

Metallophos; Calcineurin-like phosphoesterase

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

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

27935000..27959152

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011541259.3 → XP_011539561.1 acid sphingomyelinase-like phosphodiesterase 3b isoform X1

UniProtKB/TrEMBL

B4DW34

Conserved Domains (2) summary

cd00842
Location:53 → 353

MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain

pfam00149
Location:112 → 311

Metallophos; Calcineurin-like phosphoesterase