GLT1D1

Summary

GLT1D1 (glycosyltransferase 1 domain containing 1, HGNC:26483) is a protein-coding gene on chromosome 12q24.33, encoding Glycosyltransferase 1 domain-containing protein 1 (Q96MS3).

Predicted to enable glycosyltransferase activity. Located in cytosol.

Source: NCBI Gene 144423 — RefSeq curated summary.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 62 total
• MANE Select transcript: NM_001366886

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26483
Approved symbol	GLT1D1
Name	glycosyltransferase 1 domain containing 1
Location	12q24.33
Locus type	gene with protein product
Status	Approved
Aliases	FLJ31978
Ensembl gene	ENSG00000151948
Ensembl biotype	protein_coding
Entrez	144423

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 9 protein_coding, 3 nonsense_mediated_decay

ENST00000281703, ENST00000413816, ENST00000441390, ENST00000442111, ENST00000537468, ENST00000539044, ENST00000905389, ENST00000905390, ENST00000905391, ENST00000915217, ENST00000958634, ENST00000958635

RefSeq mRNA: 5 — MANE Select: NM_001366886 NM_001366886, NM_001366887, NM_001366888, NM_001366889, NM_144669

CCDS: CCDS91773, CCDS9265

Canonical transcript exons

ENST00000442111 — 12 exons

Exon	Start	End
ENSE00001099222	128899236	128899287
ENSE00002245589	128853478	128853649
ENSE00002246443	128982929	128984968
ENSE00003483544	128927105	128927154
ENSE00003505450	128947338	128947458
ENSE00003510470	128875914	128876062
ENSE00003518281	128926359	128926454
ENSE00003542887	128957545	128957643
ENSE00003567975	128888639	128888744
ENSE00003592930	128945326	128945369
ENSE00003598863	128912424	128912460
ENSE00003607684	128914933	128914989

Expression profiles

Bgee: expression breadth ubiquitous, 197 present calls, max score 97.61.

FANTOM5 (CAGE): breadth broad, TPM avg 3.7320 / max 773.4901, expressed in 394 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
128708	3.6163	387
206955	0.0971	46
128707	0.0187	7

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	97.61	gold quality
blood	UBERON:0000178	95.44	gold quality
monocyte	CL:0000576	94.45	gold quality
secondary oocyte	CL:0000655	94.36	gold quality
leukocyte	CL:0000738	94.16	gold quality
Brodmann (1909) area 23	UBERON:0013554	92.30	gold quality
middle temporal gyrus	UBERON:0002771	92.14	gold quality
granulocyte	CL:0000094	88.47	gold quality
bone marrow	UBERON:0002371	87.89	gold quality
primary visual cortex	UBERON:0002436	87.71	gold quality
prefrontal cortex	UBERON:0000451	87.63	gold quality
right lobe of liver	UBERON:0001114	87.06	gold quality
oocyte	CL:0000023	86.67	gold quality
liver	UBERON:0002107	86.57	gold quality
bone marrow cell	CL:0002092	86.26	gold quality
endothelial cell	CL:0000115	86.12	silver quality
frontal cortex	UBERON:0001870	85.86	gold quality
trabecular bone tissue	UBERON:0002483	85.83	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	85.12	gold quality
superior frontal gyrus	UBERON:0002661	85.10	gold quality
neocortex	UBERON:0001950	85.09	gold quality
entorhinal cortex	UBERON:0002728	84.56	gold quality
right frontal lobe	UBERON:0002810	84.19	gold quality
occipital lobe	UBERON:0002021	84.15	gold quality
anterior cingulate cortex	UBERON:0009835	83.74	gold quality
Brodmann (1909) area 9	UBERON:0013540	83.67	gold quality
Brodmann (1909) area 46	UBERON:0006483	83.63	gold quality
cerebral cortex	UBERON:0000956	83.55	gold quality
nucleus accumbens	UBERON:0001882	82.29	gold quality
postcentral gyrus	UBERON:0002581	81.86	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.65

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

65 targeting GLT1D1, 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-188-3P	100.00	68.76	1240
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-4650-5P	99.98	64.69	999
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-6744-5P	99.93	66.82	748
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-1299	99.77	71.24	2389
HSA-MIR-4255	99.72	67.70	1541
HSA-MIR-6801-5P	99.72	66.50	981
HSA-MIR-10393-3P	99.72	66.56	961
HSA-MIR-3714	99.71	70.74	2671

Literature-anchored findings (GeneRIF, showing 2)

• GLT1D1 single nucleotide polymorphism rs7300146 is associated with childhood-onset systemic lupus erythematosus. (PMID:29967481)
• Overexpression of GLT1D1 induces immunosuppression through glycosylation of PD-L1 and predicts poor prognosis in B-cell lymphoma. (PMID:32157792)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	glt1d1	ENSDARG00000091241
mus_musculus	Glt1d1	ENSMUSG00000049971
rattus_norvegicus	Glt1d1	ENSRNOG00000000961

Paralogs (3): ALG2 (ENSG00000119523), PIGA (ENSG00000165195), ALG11 (ENSG00000253710)

Protein

Protein identifiers

Glycosyltransferase 1 domain-containing protein 1 — Q96MS3 (reviewed: Q96MS3)

All UniProt accessions (3): Q96MS3, F5H088, H0Y5M0

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Similarity. Belongs to the glycosyltransferase group 1 family. Glycosyltransferase 4 subfamily.

Isoforms (3)

UniProt ID	Names	Canonical?
Q96MS3-1	1	yes
Q96MS3-2	2
Q96MS3-3	3

RefSeq proteins (5): NP_001353815, NP_001353816, NP_001353817, NP_001353818, NP_653270 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001296	Glyco_trans_1	Domain
IPR052622	Glycosyltransferase_G1	Family

Pfam: PF00534

UniProt features (5 total): splice variant 3, signal peptide 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96MS3-F1	95.75	0.95

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 37 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_DN, chr12q24, GOMF_GLYCOSYLTRANSFERASE_ACTIVITY, MEISSNER_NPC_HCP_WITH_H3K4ME2, ZNF22_TARGET_GENES, MIR1299, MIR4255, GSE11057_CD4_EFF_MEM_VS_PBMC_DN, GSE11864_CSF1_VS_CSF1_IFNG_IN_MAC_DN, GSE11864_CSF1_IFNG_VS_CSF1_PAM3CYS_IN_MAC_UP, MIR3157_5P, MIR5187_5P, MIR7109_3P, MIR328_5P, MIR6885_5P

GO Biological Process (0):

GO Molecular Function (2): glycosyltransferase activity (GO:0016757), transferase activity (GO:0016740)

GO Cellular Component (2): extracellular region (GO:0005576), cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
transferase activity	1
catalytic activity	1
cytoplasm	1

Protein interactions and networks

STRING

393 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GLT1D1	PRORP	O15091	453
GLT1D1	SLC15A4	Q8N697	428
GLT1D1	TMEM132D	Q14C87	424
GLT1D1	FAM153B	P0C7A2	419
GLT1D1	MEGF11	A6BM72	418
GLT1D1	LRMDA	Q9H2I8	416
GLT1D1	EQTN	Q9NQ60	396
GLT1D1	ACOX3	O15254	395
GLT1D1	XKR6	Q5GH73	393
GLT1D1	CTTNBP2NL	Q9P2B4	388
GLT1D1	TMEM132C	Q8N3T6	377
GLT1D1	DCAF12L2	Q5VW00	372
GLT1D1	FAM91A1	Q658Y4	358
GLT1D1	RIMBP2	O15034	356
GLT1D1	ANKRD45	Q5TZF3	337

IntAct

3 interactions, top by confidence:

A	B	Type	Score
GLT1D1	HSP90B1	psi-mi:“MI:0915”(physical association)	0.400
GLT1D1	UBB	psi-mi:“MI:0914”(association)	0.350

BioGRID (8): UBB (Affinity Capture-MS), ASAH1 (Affinity Capture-MS), RUFY3 (Affinity Capture-MS), GLT1D1 (Proximity Label-MS), ASAH1 (Affinity Capture-MS), UBB (Affinity Capture-MS), RUFY3 (Affinity Capture-MS), GLT1D1 (Affinity Capture-RNA)

ESM2 similar proteins: A0A1P8AWH8, A2RU49, A4FUP9, A5PJU6, M4IRL9, O80574, O82730, P13255, P37287, Q14749, Q1PET6, Q29513, Q29555, Q2KIR8, Q58DC0, Q58DM7, Q5F480, Q5HZ68, Q5IH13, Q5IH14, Q5R7E8, Q5RAF1, Q5U3W0, Q64323, Q6DHV7, Q6DIQ1, Q6DJF8, Q6NYU2, Q6PBF6, Q6YXW6, Q71N41, Q7ZXG7, Q80SY6, Q8BFS6, Q8CCT7, Q8R164, Q90WG6, Q91W63, Q94AH8, Q94AS5

Diamond homologs: A4FUP9, Q5RAF1, Q6DIQ1, Q96MS3, A7TZT2, C7R101, D4GU62, O34413, P46915, Q59002

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	44
Likely benign	7
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

3122 predictions. Top by Δscore:

Variant	Effect	Δscore
12:128853645:GTTCG:G	donor_gain	1.0000
12:128853650:G:GG	donor_gain	1.0000
12:128853650:GTAG:G	donor_loss	1.0000
12:128875906:T:TA	acceptor_gain	1.0000
12:128875910:AAAG:A	acceptor_gain	1.0000
12:128888737:G:GT	donor_gain	1.0000
12:128927155:G:GG	donor_gain	1.0000
12:128945320:TTTCA:T	acceptor_loss	1.0000
12:128945324:A:AG	acceptor_gain	1.0000
12:128945324:A:AT	acceptor_loss	1.0000
12:128945325:G:A	acceptor_loss	1.0000
12:128945325:G:GA	acceptor_gain	1.0000
12:128945368:AGGTA:A	donor_loss	1.0000
12:128945369:GGTAA:G	donor_loss	1.0000
12:128945370:G:GA	donor_loss	1.0000
12:128945371:T:G	donor_loss	1.0000
12:128947333:TTCA:T	acceptor_loss	1.0000
12:128947335:CA:C	acceptor_loss	1.0000
12:128947336:A:AG	acceptor_gain	1.0000
12:128947337:G:GT	acceptor_gain	1.0000
12:128947337:GA:G	acceptor_gain	1.0000
12:128947337:GAGCC:G	acceptor_gain	1.0000
12:128947456:G:GT	donor_gain	1.0000
12:128947456:GAGGT:G	donor_loss	1.0000
12:128947457:AGGTA:A	donor_loss	1.0000
12:128947458:GGT:G	donor_loss	1.0000
12:128947459:G:GA	donor_loss	1.0000
12:128947460:T:A	donor_loss	1.0000
12:128957639:CTCAG:C	donor_loss	1.0000
12:128957640:TCAG:T	donor_loss	1.0000

AlphaMissense

2265 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:128947420:A:C	S248R	0.997
12:128947422:C:A	S248R	0.997
12:128947422:C:G	S248R	0.997
12:128926423:G:C	K178N	0.993
12:128926423:G:T	K178N	0.993
12:128926422:A:T	K178M	0.992
12:128957573:C:A	A270D	0.990
12:128853622:G:A	G14D	0.989
12:128947433:A:T	E252V	0.989
12:128853621:G:C	G14R	0.988
12:128957592:T:A	N276K	0.988
12:128957592:T:G	N276K	0.988
12:128853621:G:T	G14C	0.987
12:128926421:A:C	K178Q	0.986
12:128926422:A:C	K178T	0.986
12:128947419:T:A	N247K	0.986
12:128947419:T:G	N247K	0.986
12:128853626:C:A	N15K	0.985
12:128853626:C:G	N15K	0.985
12:128888657:G:A	G79E	0.985
12:128899244:T:A	V111D	0.985
12:128927147:G:A	G203D	0.985
12:128926421:A:G	K178E	0.984
12:128853622:G:T	G14V	0.983
12:128888677:G:C	D86H	0.983
12:128899249:T:C	F113L	0.983
12:128899251:C:A	F113L	0.983
12:128899251:C:G	F113L	0.983
12:128947434:A:C	E252D	0.983
12:128947434:A:T	E252D	0.983

dbSNP variants (sampled 300 via entrez): RS1000037063 (12:128963663 GT>G,GTT), RS1000044412 (12:128927592 A>C,G), RS1000050327 (12:128893919 T>C), RS1000092564 (12:128926855 T>C), RS1000161111 (12:128883314 G>A), RS1000163188 (12:128925422 G>A,T), RS1000183036 (12:128969687 A>G), RS1000237289 (12:128984848 C>T), RS1000249344 (12:128911131 T>C), RS1000250107 (12:128894955 G>A), RS1000251514 (12:128894039 T>A,C), RS1000254361 (12:128960779 A>G), RS1000261830 (12:128876846 G>A), RS1000266838 (12:128921202 T>G), RS1000302678 (12:128943375 A>G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

8 associations (top):

Study	Trait	p-value
GCST001304_3	Renal sinus fat	1.000000e-06
GCST002812_3	Schizophrenia (inflammation and infection response interaction)	8.000000e-06
GCST002951_15	Response to zileuton treatment in asthma (FEV1 change interaction)	7.000000e-07
GCST005212_2	Asthma	5.000000e-06
GCST009391_1078	Metabolite levels	4.000000e-06
GCST009391_1311	Metabolite levels	9.000000e-08
GCST009391_2113	Metabolite levels	4.000000e-06
GCST011743_53	HDL cholesterol levels in HIV infection	1.000000e-05

EFO canonical traits (8, from GWAS)

EFO ID	Trait name
EFO:0004864	renal sinus adipose tissue measurement
EFO:0007050	HSV1 seropositivity
EFO:0005921	FEV change measurement
EFO:0010529	ribose-5-phosphate measurement
EFO:0010530	ribulose-5-phosphate measurement
EFO:0010519	pantothenic acid measurement
EFO:0010381	phosphatidylcholine 36:3 measurement
EFO:0004612	high density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
trichostatin A	decreases expression, affects cotreatment	3
Valproic Acid	affects cotreatment, decreases expression, affects expression	3
Benzo(a)pyrene	affects methylation, decreases expression, decreases methylation	2
Tobacco Smoke Pollution	increases expression, increases methylation	2
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation	1
terbufos	increases methylation	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	affects methylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
theaflavin-3,3’-digallate	affects expression	1
Resveratrol	affects cotreatment, increases expression	1
Vorinostat	decreases expression	1
Norethindrone Acetate	affects cotreatment, increases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	affects expression, increases abundance	1
Air Pollutants, Occupational	decreases expression	1
Atrazine	increases expression	1
Fonofos	increases methylation	1
Estradiol	increases expression, affects cotreatment	1
Lipopolysaccharides	affects response to substance, increases expression	1
Methapyrilene	increases methylation	1
Nickel	decreases expression	1
Ozone	affects expression, increases abundance	1
Parathion	increases methylation	1
Phenobarbital	increases expression	1

Clinical trials (associated diseases)

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