LAMP2 lysosomal associated membrane protein 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LAMP2provided by HGNC
Official Full Name: lysosomal associated membrane protein 2provided by HGNC
Primary source: HGNC:HGNC:6501
See related: Ensembl:ENSG00000005893 MIM:309060; AllianceGenome:HGNC:6501
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: DND; LAMPB; CD107b; LAMP-2; LGP-96; LGP110
Summary: The protein encoded by this gene is a member of a family of membrane glycoproteins. This glycoprotein provides selectins with carbohydrate ligands. It may play a role in tumor cell metastasis. It may also function in the protection, maintenance, and adhesion of the lysosome. Alternative splicing of this gene results in multiple transcript variants encoding distinct proteins. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in brain (RPKM 30.7), gall bladder (RPKM 27.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: Xq24

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (120426148..120469349, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (118801613..118844815, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (119560003..119603204, complement)

Chromosome X - NC_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Comparative study of the steady-state subcellular distribution of lysosome-associated membrane glycoprotein-2 (LAMP-2) isoforms with GYXXPhi-type tyrosine-based motifs that interact differently with four adaptor protein (AP) complexes.
Title: Comparative study of the steady-state subcellular distribution of lysosome-associated membrane glycoprotein-2 (LAMP-2) isoforms with GYXXΦ-type tyrosine-based motifs that interact differently with four adaptor protein (AP) complexes.
Altered Splicing of LAMP2 in a Multigenerational Family from Latvia Affected by Danon Disease.
Title: Altered Splicing of LAMP2 in a Multigenerational Family from Latvia Affected by Danon Disease.
Identification and functional analysis of a novel de novo missense mutation located in the initiation codon of LAMP2 associated with early onset female Danon disease.
Title: Identification and functional analysis of a novel de novo missense mutation located in the initiation codon of LAMP2 associated with early onset female Danon disease.
Danon Disease: Entire LAMP2 Gene Deletion with Unusual Clinical Presentation-Case Report and Review of the Literature.
Title: Danon Disease: Entire LAMP2 Gene Deletion with Unusual Clinical Presentation-Case Report and Review of the Literature.
Identification of a novel splicing-altering LAMP2 variant in a Chinese family with Danon disease.
Title: Identification of a novel splicing-altering LAMP2 variant in a Chinese family with Danon disease.
Lysosomal LAMP proteins regulate lysosomal pH by direct inhibition of the TMEM175 channel.
Title: Lysosomal LAMP proteins regulate lysosomal pH by direct inhibition of the TMEM175 channel.
Downregulation of Lysosome-Associated Membrane Protein-2A Contributes to the Pathogenesis of COPD.
Title: Downregulation of Lysosome-Associated Membrane Protein-2A Contributes to the Pathogenesis of COPD.
Metabolic Maturation Exaggerates Abnormal Calcium Handling in a Lamp2 Knockout Human Pluripotent Stem Cell-Derived Cardiomyocyte Model of Danon Disease.
Title: Metabolic Maturation Exaggerates Abnormal Calcium Handling in a Lamp2 Knockout Human Pluripotent Stem Cell-Derived Cardiomyocyte Model of Danon Disease.
[Clinical characteristics of Danon disease].
Title: [Clinical characteristics of Danon disease].
Chaperone-mediated Autophagy Regulates Cell Growth by Targeting SMAD3 in Glioma.
Title: Chaperone-mediated Autophagy Regulates Cell Growth by Targeting SMAD3 in Glioma.

Submit: New GeneRIF Correction See all GeneRIFs (116)

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
Danon disease MedGen: C0878677 OMIM: 300257 GeneReviews: Danon Disease	Compare labs

Copy number response

Description
Copy number response Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2021-02-09) ClinGen Genome Curation PagePubMed Triplosensitivity No evidence available (Last evaluated 2021-02-09) ClinGen Genome Curation Page

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
Nef	nef	Both HIV-1 Nef and Vpu downregulate the cell surface expression of lysosomal-associated membrane protein 2 (CD107b)	PubMed
	nef	HIV-1 Nef increases the production of exosomes and co-localizes with exosomal proteins CD63, AIP/Alix, AChE, Hsc70, LAMP2, and annexin A2 in HeLa cells	PubMed
Pr55(Gag)	gag	In Niemann-Pick type C-1 (NPC1)-deficient (NPCD) cells, HIV-1 Gag co-localizes with CD63 and LAMP2 in late endosomal/lysosomal (LE/L) compartments	PubMed
Tat	tat	HIV-1 Tat associates with lysosomal-associated membrane protein 2 in neuronal cells	PubMed
Vpr	vpr	HIV-1 Vpr reduces co-localization of LAMP2 colocalization with HIV-1 MA (p17) in monocyte-derived macropaphages	PubMed
Vpu	vpu	Both HIV-1 Nef and Vpu downregulate the cell surface expression of lysosomal-associated membrane protein 2 (CD107b)	PubMed
	vpu	HIV-1 Vpu co-localizes with the lysosomal marker LAMP2 during HIV-1 protein expression	PubMed
capsid	gag	HIV-1 CA-stimulated CD8+ T cells upregulate CD107 expression compared to unstimulated cells	PubMed
matrix	gag	HIV-1 MA (p17) colocalizes with LAMP2 in the absense of Vpr in monocyte-derived macrophages	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

KAL1 (e-PCR)
- UniSTS:480269

RH79207 (e-PCR)
- UniSTS:78613

WI-13810 (e-PCR)
- UniSTS:60949

G19741 (e-PCR)
- UniSTS:17433

A001X10 (e-PCR)
- UniSTS:17434

DXS7521 (e-PCR)
- UniSTS:28957

G20613 (e-PCR)
- UniSTS:15910

A005Z05 (e-PCR)
- UniSTS:15911

STS-AA009802 (e-PCR)
- UniSTS:6965

WI-11028 (e-PCR)
- UniSTS:76088

RH124059 (e-PCR)
- UniSTS:138836

RH36081 (e-PCR)
- UniSTS:25695

GDB:574059 (e-PCR)
- UniSTS:157792

DXS7032E (e-PCR)
- UniSTS:44133

STS-N63463 (e-PCR)
- UniSTS:32884

RH78986 (e-PCR)
- UniSTS:52101

STS-G07303 (e-PCR)
- UniSTS:46988

AL008932 (e-PCR)
- UniSTS:78994

A006D20 (e-PCR)
- UniSTS:61076

G32325 (e-PCR)
- UniSTS:116918

DXS8328 (e-PCR)
- UniSTS:63686

DXS7878 (e-PCR)
- UniSTS:34292

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables ion channel inhibitor activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in autophagosome maturation	IBA Inferred from Biological aspect of Ancestor more info
involved_in autophagosome maturation	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to starvation	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular response to starvation	ISS Inferred from Sequence or Structural Similarity more info
involved_in chaperone-mediated autophagy	IDA Inferred from Direct Assay more info	PubMed
involved_in chaperone-mediated autophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chaperone-mediated autophagy	ISS Inferred from Sequence or Structural Similarity more info
involved_in lysosomal lumen acidification	IDA Inferred from Direct Assay more info	PubMed
involved_in lysosomal protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in muscle cell cellular homeostasis	IEA Inferred from Electronic Annotation more info
involved_in protein import	TAS Traceable Author Statement more info	PubMed
involved_in protein stabilization	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein targeting	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein targeting to lysosome involved in chaperone-mediated autophagy	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein targeting to lysosome involved in chaperone-mediated autophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein targeting to lysosome involved in chaperone-mediated autophagy	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of protein stability	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in autolysosome	IDA Inferred from Direct Assay more info	PubMed
is_active_in autophagosome membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in autophagosome membrane	IEA Inferred from Electronic Annotation more info
located_in azurophil granule membrane	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular exosome	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
located_in ficolin-1-rich granule membrane	TAS Traceable Author Statement more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in late endosome	IDA Inferred from Direct Assay more info	PubMed
is_active_in late endosome membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in late endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in lysosomal lumen	TAS Traceable Author Statement more info	PubMed
located_in lysosomal membrane	HDA more info	PubMed
is_active_in lysosomal membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in lysosomal membrane	IDA Inferred from Direct Assay more info	PubMed
located_in lysosomal membrane	IDA Inferred from Direct Assay more info	PubMed
located_in lysosome	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
colocalizes_with membrane microdomain	TAS Traceable Author Statement more info	PubMed
located_in phagocytic vesicle membrane	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in platelet dense granule membrane	IDA Inferred from Direct Assay more info	PubMed
located_in platelet dense granule membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: lysosome-associated membrane glycoprotein 2

Names: CD107 antigen-like family member B

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

NG_007995.1 RefSeqGene

Range

5001..48202

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_749

mRNA and Protein(s)

NM_001122606.1 → NP_001116078.1 lysosome-associated membrane glycoprotein 2 isoform C precursor

See identical proteins and their annotated locations for NP_001116078.1

Status: REVIEWED

Description

Transcript Variant: This variant (C) results from alternative splicing of exon 9 and results in a shorter transcript, but longer protein, as compared to variant A. Variant C encodes isoform C.

Source sequence(s)

AC002476, AY561849, BC040653

Consensus CDS

CCDS48159.1

UniProtKB/TrEMBL

B4E2S7

Related

ENSP00000408411.2, ENST00000434600.6

Conserved Domains (1) summary

pfam01299
Location:110 → 411

Lamp; Lysosome-associated membrane glycoprotein (Lamp)
NM_002294.3 → NP_002285.1 lysosome-associated membrane glycoprotein 2 isoform A precursor

See identical proteins and their annotated locations for NP_002285.1

Status: REVIEWED

Description

Transcript Variant: This variant (A) is the longest and predominant form of this gene. Variant A encodes isoform A.

Source sequence(s)

AC002476, BC040653, X77196

Consensus CDS

CCDS14599.1

UniProtKB/Swiss-Prot

A8K4X5, D3DTF0, P13473, Q16641, Q6Q3G8, Q96J30, Q99534, Q9UD93

UniProtKB/TrEMBL

B4E2S7

Related

ENSP00000200639.4, ENST00000200639.9

Conserved Domains (1) summary

pfam01299
Location:110 → 410

Lamp; Lysosome-associated membrane glycoprotein (Lamp)
NM_013995.2 → NP_054701.1 lysosome-associated membrane glycoprotein 2 isoform B precursor

See identical proteins and their annotated locations for NP_054701.1

Status: REVIEWED

Description

Transcript Variant: This variant (B) results from alternative splicing of exon 9 and results in a shorter transcript, but not protein, as compared to variant A. Transcript variant B is over-expressed in muscle and encodes isoform B.

Source sequence(s)

AC002476, BP386088, DA405328, S79873

Consensus CDS

CCDS14600.1

UniProtKB/TrEMBL

B4E2S7

Related

ENSP00000360386.4, ENST00000371335.4

Conserved Domains (1) summary

pfam01299
Location:110 → 410

Lamp; Lysosome-associated membrane glycoprotein (Lamp)