SPPL3 signal peptide peptidase like 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SPPL3provided by HGNC
Official Full Name: signal peptide peptidase like 3provided by HGNC
Primary source: HGNC:HGNC:30424
See related: Ensembl:ENSG00000157837 MIM:608240; AllianceGenome:HGNC:30424
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: IMP2; PSH1; PSL4; PRO4332; MDHV1887
Summary: Enables aspartic endopeptidase activity, intramembrane cleaving and protein homodimerization activity. Involved in T cell receptor signaling pathway; membrane protein proteolysis; and positive regulation of calcineurin-NFAT signaling cascade. Located in Golgi-associated vesicle membrane; endoplasmic reticulum; and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]
Expression: Ubiquitous expression in skin (RPKM 21.6), testis (RPKM 17.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12q24.31

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (120762510..120904358, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (120751646..120893446, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (121200313..121342161, complement)

Chromosome 12 - NC_000012.12 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

N-terminome analyses underscore the prevalence of SPPL3-mediated intramembrane proteolysis among Golgi-resident enzymes and its role in Golgi enzyme secretion.
Title: N-terminome analyses underscore the prevalence of SPPL3-mediated intramembrane proteolysis among Golgi-resident enzymes and its role in Golgi enzyme secretion.
SPPL3-dependent downregulation of the synthesis of (neo)lacto-series glycosphingolipid is required for the staining of cell surface CD59.
Title: SPPL3-dependent downregulation of the synthesis of (neo)lacto-series glycosphingolipid is required for the staining of cell surface CD59.
The SPPL3-Defined Glycosphingolipid Repertoire Orchestrates HLA Class I-Mediated Immune Responses.
Title: The SPPL3-Defined Glycosphingolipid Repertoire Orchestrates HLA Class I-Mediated Immune Responses.
Data suggest that activation of the metalloproteinase ADAM10 by signal peptide peptidase-like 3 (SPPL3) triggered by mutant BRAF(V600E) was a critical transformation event.
Title: Multiepitope tissue analysis reveals SPPL3-mediated ADAM10 activation as a key step in the transformation of melanocytes.
Secretome analysis identifies novel signal Peptide peptidase-like 3 substrates and reveals a role of Sppl3 in multiple Golgi glycosylation pathways
Title: Secretome analysis identifies novel signal Peptide peptidase-like 3 (Sppl3) substrates and reveals a role of Sppl3 in multiple Golgi glycosylation pathways.
Authors demonstrate that SPPL3 alters the pattern of cellular N-glycosylation by triggering the proteolytic release of active site-containing ectodomains of glycosidases and glycosyltransferases.
Title: Shedding of glycan-modifying enzymes by signal peptide peptidase-like 3 (SPPL3) regulates cellular N-glycosylation.
SPPL3 substrates identified on a proteome-wide scale in human and murine cells include numerous glycan-modifying enzymes residing in the Golgi network and implicated in distinct glycosylation pathways, including N-glycosylation, mucin-type O-glycosylation, O-mannosylation and glycosaminoglycan biosynthesis.
Title: Secretome analysis identifies novel signal Peptide peptidase-like 3 (Sppl3) substrates and reveals a role of Sppl3 in multiple Golgi glycosylation pathways.
SPPL3 cleaves Golgi type II membrane proteins leading to their secretion. SPPL3 substrates include Golgi glycosyltransferases MGAT5, B4GALT1, and B3GNT1. By facilitating disengagement of these glycosyltransferases from their membrane anchors, SPPL3 causes their premature secretion and consequently orchestrates the extent of N-glycosylation on human and murine cells.
Title: Shedding of glycan-modifying enzymes by signal peptide peptidase-like 3 (SPPL3) regulates cellular N-glycosylation.
SPPL3 enhances the signal-induced association of stromal interaction molecule 1
Title: A protease-independent function for SPPL3 in NFAT activation.
human SPPL3 is the first GxGD-type aspartyl protease shown to be capable of acting like a sheddase, similar to members of the rhomboid family, which belong to the class of intramembrane-cleaving serine proteases.
Title: Foamy virus envelope protein is a substrate for signal peptide peptidase-like 3 (SPPL3).

Submit: New GeneRIF Correction See all GeneRIFs (13)

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
Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae. 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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Markers

D11S2560 (e-PCR)
- UniSTS:37928

A006Q41 (e-PCR)
- UniSTS:15920

D8S2279 (e-PCR)
- UniSTS:473907

RH66303 (e-PCR)
- UniSTS:56900

D12S2073 (e-PCR), detects polymorphism
- UniSTS:57157

NoName (e-PCR)
- UniSTS:483686

RH93199 (e-PCR)
- UniSTS:88684

D1S1423 (e-PCR)
- UniSTS:149619

SGC34924 (e-PCR)
- UniSTS:55193

RH103879 (e-PCR)
- UniSTS:98204

D4S2372 (e-PCR)
- UniSTS:24744

RH44592 (e-PCR)
- UniSTS:15846

RH75805 (e-PCR)
- UniSTS:92138

Clone Names

MGC90402, MGC126674, MGC126676, DKFZp586C1324

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables aspartic endopeptidase activity, intramembrane cleaving	IBA Inferred from Biological aspect of Ancestor more info
enables aspartic endopeptidase activity, intramembrane cleaving	IDA Inferred from Direct Assay more info	PubMed
enables aspartic endopeptidase activity, intramembrane cleaving	IEA Inferred from Electronic Annotation more info
enables aspartic endopeptidase activity, intramembrane cleaving	IMP Inferred from Mutant Phenotype more info	PubMed
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables peptidase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables protein homodimerization activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in T cell receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in T cell receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in T cell receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
NOT involved_in membrane protein ectodomain proteolysis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in membrane protein proteolysis	IBA Inferred from Biological aspect of Ancestor more info
involved_in membrane protein proteolysis	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of calcineurin-NFAT signaling cascade	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of calcineurin-NFAT signaling cascade	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cytosolic calcium ion concentration	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cytosolic calcium ion concentration	ISS Inferred from Sequence or Structural Similarity more info
involved_in proteolysis	IEA Inferred from Electronic Annotation more info
involved_in signal peptide processing	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
is_active_in Golgi-associated vesicle membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in Golgi-associated vesicle membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytoplasmic side of endoplasmic reticulum membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasmic side of endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasmic side of endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum-Golgi intermediate compartment membrane	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum-Golgi intermediate compartment membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in lumenal side of endoplasmic reticulum membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in lumenal side of endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
located_in lumenal side of endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IDA Inferred from Direct Assay more info
located_in rough endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: signal peptide peptidase-like 3

Names: SPP-like 3; intramembrane protease 2; presenilin homologous protein 1; presenilin-like protein 4

NP_620584.2

EC 3.4.23.-

XP_011536227.1

EC 3.4.23.-

XP_054227100.1

EC 3.4.23.-

XP_054227101.1

EC 3.4.23.-

XP_054227102.1

EC 3.4.23.-

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_139015.5 → NP_620584.2 signal peptide peptidase-like 3

See identical proteins and their annotated locations for NP_620584.2

Status: VALIDATED

Source sequence(s)

AC069214, AC069234

Consensus CDS

CCDS9208.1

UniProtKB/Swiss-Prot

Q3MJ04, Q8TAU4, Q8TCT6, Q96DD9

UniProtKB/TrEMBL

Q53EP9

Related

ENSP00000288680.4, ENST00000353487.7

Conserved Domains (1) summary

pfam04258
Location:61 → 374

Peptidase_A22B; Signal peptide peptidase

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_000012.12 Reference GRCh38.p14 Primary Assembly

Range

120762510..120904358 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011537925.3 → XP_011536227.1 signal peptide peptidase-like 3 isoform X1

UniProtKB/TrEMBL

Q53EP9

Conserved Domains (1) summary

pfam04258
Location:61 → 374

Peptidase_A22B; Signal peptide peptidase

Alternate T2T-CHM13v2.0

Genomic

NC_060936.1 Alternate T2T-CHM13v2.0

Range

120751646..120893446 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054371127.1 → XP_054227102.1 signal peptide peptidase-like 3 isoform X3

UniProtKB/TrEMBL

A8K546
XM_054371126.1 → XP_054227101.1 signal peptide peptidase-like 3 isoform X1

UniProtKB/TrEMBL

Q53EP9
XM_054371125.1 → XP_054227100.1 signal peptide peptidase-like 3 isoform X2

UniProtKB/TrEMBL

Q53EP9