GLMP

Summary

GLMP (glycosylated lysosomal membrane protein, HGNC:29436) is a protein-coding gene on chromosome 1q22, encoding Glycosylated lysosomal membrane protein (Q8WWB7). Required to protect lysosomal transporter MFSD1 from lysosomal proteolysis and for MFSD1 lysosomal localization.

Involved in positive regulation of transcription by RNA polymerase II. Located in cytosol; lysosome; and nucleus.

Source: NCBI Gene 112770 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 81 total
• MANE Select transcript: NM_144580

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29436
Approved symbol	GLMP
Name	glycosylated lysosomal membrane protein
Location	1q22
Locus type	gene with protein product
Status	Approved
Aliases	MGC31963, NCU-G1, lnc-UCID
Ensembl gene	ENSG00000198715
Ensembl biotype	protein_coding
OMIM	619958
Entrez	112770

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 8 protein_coding, 4 protein_coding_CDS_not_defined, 4 nonsense_mediated_decay, 3 retained_intron

ENST00000362007, ENST00000368264, ENST00000461597, ENST00000472870, ENST00000476177, ENST00000479084, ENST00000480968, ENST00000481050, ENST00000482579, ENST00000484214, ENST00000497831, ENST00000497955, ENST00000612353, ENST00000614643, ENST00000622703, ENST00000647767, ENST00000859553, ENST00000913480, ENST00000959456

RefSeq mRNA: 5 — MANE Select: NM_144580 NM_001256604, NM_001256605, NM_001256608, NM_001256609, NM_144580

CCDS: CCDS1139, CCDS72947, CCDS72948, CCDS72949

Canonical transcript exons

ENST00000362007 — 6 exons

Exon	Start	End
ENSE00001074976	156293320	156293576
ENSE00001074982	156295526	156295679
ENSE00003524836	156294018	156294236
ENSE00003538449	156292688	156293209
ENSE00003619057	156294365	156294565
ENSE00003707412	156294759	156295016

Expression profiles

Bgee: expression breadth ubiquitous, 239 present calls, max score 96.99.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 82.2847 / max 1019.4242, expressed in 1774 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
15101	82.2847	1774
15099	3.5002	1173

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right adrenal gland cortex	UBERON:0035827	96.99	gold quality
lower esophagus mucosa	UBERON:0035834	96.95	gold quality
right adrenal gland	UBERON:0001233	96.94	gold quality
left adrenal gland	UBERON:0001234	96.43	gold quality
left adrenal gland cortex	UBERON:0035825	96.37	gold quality
gall bladder	UBERON:0002110	95.82	gold quality
stromal cell of endometrium	CL:0002255	95.75	gold quality
adrenal cortex	UBERON:0001235	95.14	gold quality
adrenal gland	UBERON:0002369	94.92	gold quality
right lobe of liver	UBERON:0001114	94.84	gold quality
metanephros cortex	UBERON:0010533	94.82	gold quality
prostate gland	UBERON:0002367	94.67	gold quality
mucosa of stomach	UBERON:0001199	94.18	gold quality
minor salivary gland	UBERON:0001830	93.22	gold quality
right coronary artery	UBERON:0001625	93.21	gold quality
ectocervix	UBERON:0012249	93.02	gold quality
sural nerve	UBERON:0015488	92.93	gold quality
descending thoracic aorta	UBERON:0002345	92.91	gold quality
endocervix	UBERON:0000458	92.79	gold quality
omental fat pad	UBERON:0010414	92.71	gold quality
peritoneum	UBERON:0002358	92.65	gold quality
skin of abdomen	UBERON:0001416	92.63	gold quality
body of stomach	UBERON:0001161	92.54	gold quality
thoracic aorta	UBERON:0001515	92.54	gold quality
ascending aorta	UBERON:0001496	92.47	gold quality
esophagus mucosa	UBERON:0002469	92.47	gold quality
left coronary artery	UBERON:0001626	92.46	gold quality
adenohypophysis	UBERON:0002196	92.35	gold quality
cortex of kidney	UBERON:0001225	92.18	gold quality
smooth muscle tissue	UBERON:0001135	92.16	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-6678	yes	10.85
E-ANND-3	yes	8.02

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting GLMP, 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-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-7162-3P	99.89	68.16	1682
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-451B	99.55	68.28	1380
HSA-MIR-4696	99.48	67.48	1040
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-3911	99.38	66.95	1087
HSA-MIR-4297	98.77	66.95	2013
HSA-MIR-147A	98.33	66.40	795
HSA-MIR-6793-3P	97.66	65.78	1084
HSA-MIR-5189-3P	97.52	66.33	487
HSA-MIR-4524B-3P	95.52	64.12	964

Literature-anchored findings (GeneRIF, showing 2)

• NCU-G1 is a dual-function protein capable of functioning as a transcription factor as well as a nuclear receptor co-activator. (PMID:18021396)
• N4-acetylcytidine-dependent GLMP mRNA stabilization by NAT10 promotes head and neck squamous cell carcinoma metastasis and remodels tumor microenvironment through MAPK/ERK signaling pathway. (PMID:37914704)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	glmp	ENSDARG00000059354
mus_musculus	Glmp	ENSMUSG00000001418
rattus_norvegicus	Glmp	ENSRNOG00000019281

Protein

Protein identifiers

Glycosylated lysosomal membrane protein — Q8WWB7 (reviewed: Q8WWB7)

Alternative names: Lysosomal protein NCU-G1

All UniProt accessions (7): Q8WWB7, A0A087WV34, A0A087X0W3, V9GXZ9, V9GYX8, V9GYY1, V9GYZ8

UniProt curated annotations — full annotation on UniProt →

Function. Required to protect lysosomal transporter MFSD1 from lysosomal proteolysis and for MFSD1 lysosomal localization.

Subunit / interactions. Interacts (via lumenal domain) with lysosomal protein MFSD1; the interaction starts while both proteins are still in the endoplasmic reticulum and is required for stabilization of MFSD1 in lysosomes but has no direct effect on its targeting to lysosomes or transporter activity.

Subcellular location. Lysosome membrane.

Post-translational modifications. Highly N-glycosylated. N-glycosylation is essential for GLMP stability and for MFSD1 lysosomal localization.

Induction. Transcription is activated by TFEB.

Similarity. Belongs to the GLMP family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8WWB7-1	1	yes
Q8WWB7-2	2

RefSeq proteins (5): NP_001243533, NP_001243534, NP_001243537, NP_001243538, NP_653181* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029382	GLMP	Family

Pfam: PF15065

UniProt features (15 total): glycosylation site 5, sequence variant 3, topological domain 2, signal peptide 1, chain 1, splice variant 1, transmembrane region 1, short sequence motif 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WWB7-F1	86.37	0.66

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 (5): 230, 65, 134, 159, 187

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 107 (showing top): GOCC_VACUOLAR_MEMBRANE, GOZGIT_ESR1_TARGETS_DN, GOBP_PROTEIN_LOCALIZATION_TO_LYSOSOME, GOBP_PROTEIN_LOCALIZATION_TO_VACUOLE, GOBP_PROTEIN_STABILIZATION, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, GOBP_REGULATION_OF_PROTEIN_STABILITY, chr1q22, BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_TRANS, DODD_NASOPHARYNGEAL_CARCINOMA_UP, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, BURTON_ADIPOGENESIS_9, TCANNTGAY_SREBP1_01, MIKKELSEN_MCV6_LCP_WITH_H3K4ME3, MIKKELSEN_MEF_LCP_WITH_H3K4ME3

GO Biological Process (3): positive regulation of transcription by RNA polymerase II (GO:0045944), protein stabilization (GO:0050821), protein localization to lysosome (GO:0061462)

GO Molecular Function (0):

GO Cellular Component (5): nucleus (GO:0005634), lysosome (GO:0005764), lysosomal membrane (GO:0005765), cytosol (GO:0005829), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
positive regulation of DNA-templated transcription	1
regulation of protein stability	1
protein localization to vacuole	1
intracellular membrane-bounded organelle	1
lytic vacuole	1
lysosome	1
lytic vacuole membrane	1
cytoplasm	1

Protein interactions and networks

STRING

654 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GLMP	CHST13	Q8NET6	440
GLMP	SNX29	Q8TEQ0	417
GLMP	PGS1	Q32NB8	374
GLMP	DIP2A	Q14689	370
GLMP	NSG1	P42857	357
GLMP	PMAIP1	Q13794	348
GLMP	BCL2L11	O43521	348
GLMP	ALG14	Q96F25	316
GLMP	FDX2	Q6P4F2	313
GLMP	SNX7	Q9UNH6	308
GLMP	GM2A	P17900	300
GLMP	MTHFD2L	Q9H903	286
GLMP	RPL14	P50914	275
GLMP	MCOLN3	Q8TDD5	268
GLMP	DYNLT1	P63172	259

IntAct

10 interactions, top by confidence:

A	B	Type	Score
PRKAG1	PRKAB2	psi-mi:“MI:0914”(association)	0.940
DHRS9	MFSD4B	psi-mi:“MI:0914”(association)	0.530
	VPS37C	psi-mi:“MI:0914”(association)	0.350
	NPC1	psi-mi:“MI:0914”(association)	0.350
ST14	LIPT2	psi-mi:“MI:0914”(association)	0.350
GLMP	RTL8C	psi-mi:“MI:0914”(association)	0.350
C5AR2	UBXN8	psi-mi:“MI:0914”(association)	0.350
VDR	TPP2	psi-mi:“MI:0914”(association)	0.350
yscR	GLMP	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (133): C1orf85 (Affinity Capture-MS), C1orf85 (Affinity Capture-MS), C1orf85 (Affinity Capture-MS), C1orf85 (Affinity Capture-MS), TUBB1 (Affinity Capture-MS), SFXN3 (Affinity Capture-MS), FAM118B (Affinity Capture-MS), MTG2 (Affinity Capture-MS), TUBB8 (Affinity Capture-MS), DEPDC1 (Affinity Capture-MS), SFXN5 (Affinity Capture-MS), SLC25A15 (Affinity Capture-MS), PEX16 (Affinity Capture-MS), TUBA4A (Affinity Capture-MS), SLC25A20 (Affinity Capture-MS)

ESM2 similar proteins: A0A8M9PDM1, A2RU67, A4IGL3, A8WH34, B5DFM7, C0HBB2, E1B9E5, E9Q9F6, F1QNV4, O54715, O75787, P0DP43, P81134, Q0P5L7, Q0VA04, Q12769, Q1LXZ7, Q2HJH8, Q3UZZ4, Q3V5L5, Q5FVF4, Q5I0R4, Q5R563, Q5RBU0, Q5SY80, Q66HW4, Q68FQ4, Q68FV6, Q6AX53, Q6AXS4, Q6P7C7, Q765H6, Q86XM0, Q8CC70, Q8IUK5, Q8R0G9, Q8WWB7, Q90372, Q91ZV7, Q95JI2

Diamond homologs: A8WH34, C0HBB2, Q0P5L7, Q5RBU0, Q66HW4, Q68FV6, Q6AX53, Q8WWB7, Q9JHJ3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	63
Likely benign	4
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1134 predictions. Top by Δscore:

Variant	Effect	Δscore
1:156291383:A:AG	acceptor_gain	1.0000
1:156291383:AGGCT:A	acceptor_gain	1.0000
1:156291384:G:GG	acceptor_gain	1.0000
1:156291384:GGCT:G	acceptor_gain	1.0000
1:156291384:GGCTG:G	acceptor_gain	1.0000
1:156293208:ACCTA:A	acceptor_loss	1.0000
1:156293210:C:CA	acceptor_loss	1.0000
1:156294237:CTAG:C	acceptor_loss	1.0000
1:156294361:TTA:T	donor_loss	1.0000
1:156294362:TA:T	donor_loss	1.0000
1:156294363:A:AC	donor_gain	1.0000
1:156294363:AC:A	donor_gain	1.0000
1:156294364:C:CC	donor_gain	1.0000
1:156294364:CC:C	donor_gain	1.0000
1:156294796:T:A	donor_gain	1.0000
1:156291380:CATA:C	acceptor_loss	0.9900
1:156291381:ATAG:A	acceptor_gain	0.9900
1:156291382:T:G	acceptor_gain	0.9900
1:156291382:TA:T	acceptor_loss	0.9900
1:156291383:AG:A	acceptor_gain	0.9900
1:156291383:AGG:A	acceptor_loss	0.9900
1:156291384:G:A	acceptor_gain	0.9900
1:156291384:G:GA	acceptor_loss	0.9900
1:156291384:GGC:G	acceptor_gain	0.9900
1:156293205:TCGAC:T	acceptor_gain	0.9900
1:156293206:CGAC:C	acceptor_gain	0.9900
1:156293206:CGACC:C	acceptor_gain	0.9900
1:156293210:C:CC	acceptor_gain	0.9900
1:156294014:TGACC:T	donor_loss	0.9900
1:156294015:GAC:G	donor_loss	0.9900

AlphaMissense

2597 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:156294021:G:C	F265L	0.988
1:156294021:G:T	F265L	0.988
1:156294023:A:G	F265L	0.988
1:156293531:A:G	W282R	0.985
1:156293531:A:T	W282R	0.985
1:156293538:A:C	F279L	0.985
1:156293538:A:T	F279L	0.985
1:156293540:A:G	F279L	0.985
1:156294923:A:G	W72R	0.983
1:156294923:A:T	W72R	0.983
1:156293321:A:G	W352R	0.981
1:156293321:A:T	W352R	0.981
1:156294022:A:C	F265C	0.974
1:156294867:G:C	S90R	0.972
1:156294867:G:T	S90R	0.972
1:156294869:T:G	S90R	0.972
1:156294475:A:G	W157R	0.970
1:156294475:A:T	W157R	0.970
1:156293529:C:A	W282C	0.967
1:156293529:C:G	W282C	0.967
1:156294918:G:C	S73R	0.962
1:156294918:G:T	S73R	0.962
1:156294920:T:G	S73R	0.962
1:156294225:A:C	F197L	0.959
1:156294225:A:T	F197L	0.959
1:156294227:A:G	F197L	0.959
1:156294473:C:A	W157C	0.959
1:156294473:C:G	W157C	0.959
1:156294956:C:G	A61P	0.955
1:156294114:A:C	F234L	0.953

dbSNP variants (sampled 300 via entrez): RS1001191777 (1:156296921 G>A), RS1001550071 (1:156292248 G>A), RS1002147218 (1:156292524 C>T), RS1003205872 (1:156293445 T>C,G), RS1003646472 (1:156293705 C>G,T), RS1005691983 (1:156297670 A>G,T), RS1006728352 (1:156296250 G>A), RS1007772965 (1:156296936 C>G), RS1008158380 (1:156292708 C>A), RS1008412149 (1:156292703 T>A,C), RS1010112137 (1:156296890 T>C), RS1011010746 (1:156294737 G>T), RS1011117186 (1:156295091 AG>A,AGG), RS1011457592 (1:156295014 C>T), RS1013864130 (1:156297547 G>A,T)

Disease associations

OMIM: gene MIM:619958 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST000582_7	Mean corpuscular hemoglobin concentration	3.000000e-09
GCST002390_1	Glycated hemoglobin levels	1.000000e-23

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004509	hemoglobin measurement
EFO:0004528	mean corpuscular hemoglobin concentration
EFO:0004541	HbA1c measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

39 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, increases expression	4
methylmercuric chloride	decreases expression	2
bisphenol A	increases expression	2
Cadmium	decreases expression, increases abundance, increases expression	2
Cadmium Chloride	decreases expression, increases abundance	2
aristolochic acid I	decreases expression	1
triphenyl phosphate	affects expression	1
sodium arsenite	increases expression	1
hydroquinone	decreases expression	1
isobutyl alcohol	affects cotreatment, decreases expression, increases abundance	1
perfluorooctane sulfonic acid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine	increases expression, increases response to substance	1
jinfukang	affects cotreatment, increases expression	1
incobotulinumtoxinA	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	decreases expression	1
Acetaminophen	decreases expression	1
Atrazine	decreases expression	1
Cisplatin	affects cotreatment, increases expression	1
Coumestrol	affects cotreatment, decreases expression	1
Estradiol	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Gasoline	increases abundance, affects cotreatment, decreases expression	1
Methyl Methanesulfonate	increases expression	1
Polycyclic Aromatic Hydrocarbons	affects cotreatment, decreases expression, increases abundance	1

Cellosaurus cell lines

2 cell lines: 1 transformed cell line, 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_D9FI	Ubigene HEK293 GLMP KO	Transformed cell line	Female
CVCL_E0DU	Ubigene HeLa GLMP KO	Cancer cell line	Female

Clinical trials (associated diseases)

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