LAMP5

Summary

LAMP5 (lysosome associated membrane protein 5, HGNC:16097) is a protein-coding gene on chromosome 20p12.2, encoding Lysosome-associated membrane glycoprotein 5 (Q9UJQ1). Plays a role in short-term synaptic plasticity in a subset of GABAergic neurons in the brain.

Predicted to be involved in establishment of protein localization to organelle. Located in endoplasmic reticulum-Golgi intermediate compartment membrane; endosome membrane; and plasma membrane.

Source: NCBI Gene 24141 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 49 total
• MANE Select transcript: NM_012261

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16097
Approved symbol	LAMP5
Name	lysosome associated membrane protein 5
Location	20p12.2
Locus type	gene with protein product
Status	Approved
Aliases	dJ1119D9.3, BAD-LAMP, UNC-46
Ensembl gene	ENSG00000125869
Ensembl biotype	protein_coding
OMIM	614641
Entrez	24141

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000246070, ENST00000427562, ENST00000903197, ENST00000903198, ENST00000903199, ENST00000949036

RefSeq mRNA: 2 — MANE Select: NM_012261 NM_001199897, NM_012261

CCDS: CCDS13106, CCDS56177

Canonical transcript exons

ENST00000246070 — 6 exons

Exon	Start	End
ENSE00000859075	9515453	9515625
ENSE00000859076	9516000	9516131
ENSE00000859077	9516256	9516361
ENSE00000859078	9518040	9518228
ENSE00001102486	9529642	9530524
ENSE00001937636	9514590	9514916

Expression profiles

Bgee: expression breadth ubiquitous, 191 present calls, max score 97.64.

FANTOM5 (CAGE): breadth broad, TPM avg 5.3018 / max 671.1288, expressed in 316 samples.

FANTOM5 promoters (14 alternative TSS)

Promoter ID	TPM avg	Samples expressed
183494	2.1341	205
183495	0.9443	180
183489	0.6967	102
183486	0.4603	106
183493	0.2360	108
183496	0.2115	106
183498	0.1314	66
183492	0.1207	68
183485	0.1172	45
183490	0.0919	30

Top tissues by expression

278 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
nucleus accumbens	UBERON:0001882	97.64	gold quality
middle temporal gyrus	UBERON:0002771	97.64	gold quality
caudate nucleus	UBERON:0001873	96.32	gold quality
putamen	UBERON:0001874	95.90	gold quality
amygdala	UBERON:0001876	92.28	gold quality
pons	UBERON:0000988	91.29	gold quality
temporal lobe	UBERON:0001871	90.32	gold quality
right frontal lobe	UBERON:0002810	89.98	gold quality
anterior cingulate cortex	UBERON:0009835	89.79	gold quality
cingulate cortex	UBERON:0003027	89.70	gold quality
Brodmann (1909) area 9	UBERON:0013540	89.47	gold quality
telencephalon	UBERON:0001893	89.12	gold quality
prefrontal cortex	UBERON:0000451	88.63	gold quality
Brodmann (1909) area 23	UBERON:0013554	88.49	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	88.25	gold quality
Ammon’s horn	UBERON:0001954	87.99	gold quality
right uterine tube	UBERON:0001302	87.98	gold quality
frontal cortex	UBERON:0001870	87.68	gold quality
primary visual cortex	UBERON:0002436	87.30	gold quality
neocortex	UBERON:0001950	87.18	gold quality
entorhinal cortex	UBERON:0002728	86.95	gold quality
cerebral cortex	UBERON:0000956	86.84	gold quality
forebrain	UBERON:0001890	86.49	gold quality
orbitofrontal cortex	UBERON:0004167	85.53	gold quality
superior frontal gyrus	UBERON:0002661	85.13	gold quality
postcentral gyrus	UBERON:0002581	85.07	gold quality
occipital lobe	UBERON:0002021	84.62	gold quality
Brodmann (1909) area 46	UBERON:0006483	84.34	gold quality
brain	UBERON:0000955	83.76	gold quality
parietal lobe	UBERON:0001872	83.71	gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-HCAD-56	yes	997.77
E-MTAB-10485	yes	827.65
E-GEOD-98556	yes	484.71
E-MTAB-8495	yes	206.35
E-MTAB-8498	yes	12.77
E-GEOD-110499	no	978.17
E-ANND-3	no	2.44

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

51 targeting LAMP5, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-302A-3P	99.89	71.23	1777
HSA-MIR-302B-3P	99.89	71.23	1777
HSA-MIR-302C-3P	99.89	71.20	1778
HSA-MIR-302D-3P	99.89	71.25	1777
HSA-MIR-3140-3P	99.88	68.47	2069
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-4503	99.85	71.45	1869
HSA-MIR-373-3P	99.84	70.68	1668
HSA-MIR-520E-3P	99.84	70.55	1698
HSA-MIR-372-3P	99.83	70.58	1691
HSA-MIR-520A-3P	99.83	70.59	1687
HSA-MIR-520B-3P	99.83	70.56	1699
HSA-MIR-520C-3P	99.83	70.56	1699
HSA-MIR-520D-3P	99.83	70.78	1676
HSA-MIR-520F-3P	99.82	71.32	1216
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-377-5P	99.70	65.28	712
HSA-MIR-6086	99.70	65.38	699
HSA-MIR-549A-3P	99.54	68.17	825
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-4519	99.48	66.10	859

Literature-anchored findings (GeneRIF, showing 3)

• BAD-LAMP (LAMP5)-silencing enhances TLR9 retention in endolysosome compartment and consequent downstream signalling events. (PMID:29030552)
• High LAMP5 expression is associated with Leukemia. (PMID:30651276)
• Lysosomal-associated membrane protein family member 5 promotes the metastatic potential of gastric cancer cells. (PMID:35226222)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
		ENSDARG00000101098
mus_musculus	Lamp5	ENSMUSG00000027270
rattus_norvegicus	Lamp5	ENSRNOG00000005457
drosophila_melanogaster	CG32225	FBGN0052225

Paralogs (3): LAMP2 (ENSG00000005893), CD68 (ENSG00000129226), LAMP1 (ENSG00000185896)

Protein

Protein identifiers

Lysosome-associated membrane glycoprotein 5 — Q9UJQ1 (reviewed: Q9UJQ1)

Alternative names: Brain and dendritic cell-associated LAMP, Brain-associated LAMP-like protein, Lysosome-associated membrane protein 5

All UniProt accessions (1): Q9UJQ1

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in short-term synaptic plasticity in a subset of GABAergic neurons in the brain.

Subcellular location. Cell membrane. Cytoplasmic vesicle. Secretory vesicle. Synaptic vesicle membrane. Endoplasmic reticulum-Golgi intermediate compartment membrane. Endosome membrane. Cytoplasmic vesicle membrane. Cell projection. Dendrite. Growth cone membrane. Early endosome membrane. Recycling endosome.

Tissue specificity. Expressed in plasmocytoid dendritic cells. Expressed in suprabasal skin keratinocytes and squamous cells (at protein level). Expressed in the brain and weakly in spleen and skin. Expressed in plasmocytoid dendritic cells.

Post-translational modifications. Glycosylated.

Induction. Up-regulated upon CpG dinucleotides activation. Down-regulated upon activation by Toll-like receptor (TLR) ligands.

Miscellaneous. Appears to be a novel specific biomarker for blastic plasmocytoid dendritic cells neoplasia.

Similarity. Belongs to the LAMP family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9UJQ1-1	1	yes
Q9UJQ1-2	2

RefSeq proteins (2): NP_001186826, NP_036393* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002000	Lysosome-assoc_membr_glycop	Family
IPR048528	Lamp2-like_luminal	Domain

Pfam: PF01299

UniProt features (15 total): sequence variant 4, glycosylation site 3, topological domain 2, signal peptide 1, chain 1, mutagenesis site 1, sequence conflict 1, transmembrane region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UJQ1-F1	86.55	0.68

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (3): 35, 53, 127

Mutagenesis-validated functional residues (1):

Position	Phenotype
276	cell surface localization.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 171 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_UP, VERHAAK_AML_WITH_NPM1_MUTATED_DN, BENPORATH_ES_WITH_H3K27ME3, GOCC_VACUOLAR_MEMBRANE, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_CELL_CELL_SIGNALING, ROSS_LEUKEMIA_WITH_MLL_FUSIONS, TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_UP, OCT1_07, GOBP_SYNAPTIC_SIGNALING, AACTTT_UNKNOWN, USF_02, GOCC_NEURON_PROJECTION, MULLIGHAN_NPM1_SIGNATURE_3_DN, RFX1_02

GO Biological Process (2): establishment of protein localization to organelle (GO:0072594), presynaptic modulation of chemical synaptic transmission (GO:0099171)

GO Molecular Function (0):

GO Cellular Component (22): lysosomal membrane (GO:0005765), plasma membrane (GO:0005886), endosome membrane (GO:0010008), cytoplasmic vesicle membrane (GO:0030659), synaptic vesicle membrane (GO:0030672), early endosome membrane (GO:0031901), late endosome membrane (GO:0031902), growth cone membrane (GO:0032584), dendrite membrane (GO:0032590), endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116), recycling endosome membrane (GO:0055038), GABA-ergic synapse (GO:0098982), lysosome (GO:0005764), endosome (GO:0005768), late endosome (GO:0005770), synaptic vesicle (GO:0008021), membrane (GO:0016020), dendrite (GO:0030425), cytoplasmic vesicle (GO:0031410), cell projection (GO:0042995), synapse (GO:0045202), recycling endosome (GO:0055037)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
endosome membrane	3
cellular anatomical structure	3
presynapse	2
endosome	2
bounding membrane of organelle	2
cytoplasmic vesicle	2
establishment of protein localization	1
modulation of chemical synaptic transmission	1
lysosome	1
lytic vacuole membrane	1
membrane	1
cell periphery	1
cytoplasmic vesicle membrane	1
vesicle membrane	1
synaptic vesicle	1
exocytic vesicle membrane	1
early endosome	1
late endosome	1
plasma membrane	1
growth cone	1
dendrite	1
neuron projection membrane	1
endoplasmic reticulum-Golgi intermediate compartment	1
recycling endosome	1
synapse	1
lytic vacuole	1
endomembrane system	1
exocytic vesicle	1
neuron projection	1
dendritic tree	1
cytoplasm	1
intracellular vesicle	1

Protein interactions and networks

STRING

1196 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LAMP5	RORB	Q92753	602
LAMP5	SLC32A1	Q9H598	575
LAMP5	CHODL	Q9H9P2	558
LAMP5	SNCG	O76070	540
LAMP5	NDNF	Q8TB73	540
LAMP5	SST	P01166	513
LAMP5	LHX6	Q9UPM6	480
LAMP5	C1orf198	Q9H425	474
LAMP5	FREM3	P0C091	467
LAMP5	SLX4IP	Q5VYV7	432
LAMP5	SLC17A7	Q9P2U7	431
LAMP5	CUX2	O14529	417
LAMP5	FEZF2	Q8TBJ5	394
LAMP5	CPLX3	Q8WVH0	391
LAMP5	UTS2B	Q765I0	390

IntAct

5 interactions, top by confidence:

A	B	Type	Score
LAMP5	SMPD2	psi-mi:“MI:0915”(physical association)	0.400
LAMP5	LTB4R2	psi-mi:“MI:0915”(physical association)	0.370
C8orf33	TSPY2	psi-mi:“MI:0914”(association)	0.350
LAMP5	ABHD2	psi-mi:“MI:0914”(association)	0.350

BioGRID (12): LAMP5 (Two-hybrid), LAMP5 (Affinity Capture-MS), TMEM186 (Affinity Capture-MS), MBOAT2 (Affinity Capture-MS), ABHD2 (Affinity Capture-MS), AGTRAP (Affinity Capture-MS), LMBRD2 (Affinity Capture-MS), SMPD2 (Affinity Capture-MS), LAMP5 (Affinity Capture-MS), LAMP5 (Cross-Linking-MS (XL-MS)), LAMP5 (Cross-Linking-MS (XL-MS)), LAMP5 (Affinity Capture-RNA)

ESM2 similar proteins: A1L2K1, A4FV27, A4IGL3, A7E2Z9, A8WFR0, B0S5G3, L7VG99, O14525, O43556, O54715, O70258, O70367, O75829, O77049, O77770, O88823, P05300, P13473, P17046, P17047, P17404, P40682, P49130, Q15904, Q29S03, Q4R5B1, Q5PPI4, Q5R5V2, Q5RAP2, Q5VW38, Q61137, Q6AXF6, Q6Q3F5, Q6YAT4, Q6ZQE4, Q8BXN9, Q8NBN3, Q8VDA1, Q90617, Q9D387

Diamond homologs: A4FV27, A4IGL3, A8WFR0, Q5PPI4, Q5R5V2, Q9D387, Q9UJQ1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

49 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	39
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

847 predictions. Top by Δscore:

Variant	Effect	Δscore
20:9515451:A:AG	acceptor_gain	1.0000
20:9515452:G:GG	acceptor_gain	1.0000
20:9515623:GAT:G	donor_gain	1.0000
20:9516359:GTG:G	donor_gain	1.0000
20:9529641:GA:G	acceptor_gain	1.0000
20:9514912:GTTCC:G	donor_gain	0.9900
20:9514917:G:GG	donor_gain	0.9900
20:9515447:CCGCA:C	acceptor_loss	0.9900
20:9515449:GCAGA:G	acceptor_loss	0.9900
20:9515450:CA:C	acceptor_loss	0.9900
20:9515451:A:T	acceptor_loss	0.9900
20:9515452:GA:G	acceptor_gain	0.9900
20:9515452:GAT:G	acceptor_gain	0.9900
20:9515452:GATA:G	acceptor_gain	0.9900
20:9515452:GATAC:G	acceptor_gain	0.9900
20:9515626:G:GG	donor_gain	0.9900
20:9516358:AGTGG:A	donor_loss	0.9900
20:9516359:GTGGT:G	donor_loss	0.9900
20:9516361:GGTGA:G	donor_loss	0.9900
20:9516362:G:A	donor_loss	0.9900
20:9516362:G:GG	donor_gain	0.9900
20:9516364:GA:G	donor_loss	0.9900
20:9518038:A:AG	acceptor_gain	0.9900
20:9518038:AGCTG:A	acceptor_gain	0.9900
20:9518039:G:GG	acceptor_gain	0.9900
20:9518039:GCT:G	acceptor_gain	0.9900
20:9518039:GCTGG:G	acceptor_gain	0.9900
20:9518079:T:TA	acceptor_gain	0.9900
20:9518229:G:GA	donor_loss	0.9900
20:9518230:T:G	donor_loss	0.9900

AlphaMissense

1858 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:9516294:G:C	W136C	0.998
20:9516294:G:T	W136C	0.998
20:9518108:T:A	C182S	0.998
20:9518109:G:C	C182S	0.998
20:9516292:T:A	W136R	0.997
20:9516292:T:C	W136R	0.997
20:9518108:T:C	C182R	0.997
20:9518195:T:C	F211L	0.997
20:9518197:T:A	F211L	0.997
20:9518197:T:G	F211L	0.997
20:9515561:T:C	L58P	0.996
20:9515566:G:C	A60P	0.996
20:9518193:C:A	P210H	0.996
20:9529650:T:A	C225S	0.996
20:9529650:T:C	C225R	0.996
20:9529651:G:C	C225S	0.996
20:9515573:T:C	F62S	0.995
20:9516057:T:A	C99S	0.995
20:9516058:G:C	C99S	0.995
20:9516314:T:C	F143S	0.995
20:9518196:T:G	F211C	0.995
20:9518220:T:G	F219C	0.995
20:9515557:T:A	C57S	0.994
20:9515557:T:C	C57R	0.994
20:9515558:G:C	C57S	0.994
20:9515579:C:A	A64D	0.994
20:9518219:T:C	F219L	0.994
20:9518221:C:A	F219L	0.994
20:9518221:C:G	F219L	0.994
20:9518193:C:G	P210R	0.993

dbSNP variants (sampled 300 via entrez): RS1000012847 (20:9515070 C>T), RS1000018646 (20:9530286 T>A,C), RS1000266415 (20:9528832 A>C), RS1000373734 (20:9518677 C>A,T), RS1000489403 (20:9517845 C>A,T), RS1000551729 (20:9519123 TG>T), RS1000603690 (20:9513900 T>C), RS1000820613 (20:9522976 T>C), RS1000922242 (20:9522647 C>A), RS1000970728 (20:9528955 T>A), RS1001191762 (20:9530128 A>G), RS1001411597 (20:9522609 C>A,T), RS1001495223 (20:9528694 T>C), RS1001700591 (20:9524270 G>A), RS1001711098 (20:9517778 A>G)

Disease associations

OMIM: gene MIM:614641 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST006956_15	Erectile dysfunction	7.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	3
Tretinoin	decreases expression, increases expression	2
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
arsenite	increases methylation	1
sulforaphane	decreases expression	1
perfluorooctanoic acid	decreases expression	1
2,2’,4,4’,5-brominated diphenyl ether	decreases expression	1
abrine	increases expression	1
MRK 003	decreases expression	1
Arsenic Trioxide	decreases expression	1
Allergens	increases expression	1
Atrazine	increases expression	1
Benzo(a)pyrene	affects methylation	1
Diethylhexyl Phthalate	decreases expression	1
Iron	decreases expression	1
Tunicamycin	decreases expression	1
Aflatoxin B1	decreases methylation	1
Thapsigargin	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.