GLT6D1

Summary

GLT6D1 (glycosyltransferase 6 domain containing 1, HGNC:23671) is a protein-coding gene on chromosome 9q34.3, encoding Putative glycosyltransferase 6 domain-containing protein 1 (Q7Z4J2).

The GT6 glycosyltransferases gene family, which includes the ABO blood group (ABO; MIM 110300) and GLT6D1, shows a complex evolution pattern, with multiple events of gain and loss in different mammal species. In humans, the ABO gene is considered the sole functional member, although the O allele is null and is fixed in certain populations (summary by Casals et al. (2009) [PubMed 19218399]).

Source: NCBI Gene 360203 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 65 total
• MANE Select transcript: NM_182974

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23671
Approved symbol	GLT6D1
Name	glycosyltransferase 6 domain containing 1
Location	9q34.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000204007
Ensembl biotype	protein_coding
OMIM	613699
Entrez	360203

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000371763, ENST00000851048, ENST00000851049

RefSeq mRNA: 1 — MANE Select: NM_182974 NM_182974

CCDS: CCDS43900

Canonical transcript exons

ENST00000371763 — 5 exons

Exon	Start	End
ENSE00001456045	135623648	135624670
ENSE00001456046	135626069	135626206
ENSE00001456047	135631431	135631478
ENSE00001456049	135639117	135639193
ENSE00001456050	135639293	135639540

Expression profiles

Bgee: expression breadth broad, 11 present calls, max score 53.48.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	53.48	gold quality
testis	UBERON:0000473	52.42	gold quality
right testis	UBERON:0004534	47.69	gold quality
granulocyte	CL:0000094	40.24	gold quality
bone marrow cell	CL:0002092	38.31	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
superior frontal gyrus	UBERON:0002661	36.18	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
mucosa of stomach	UBERON:0001199	34.67	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
bone marrow	UBERON:0002371	32.84	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
leukocyte	CL:0000738	31.29	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
monocyte	CL:0000576	30.91	gold quality
Ammon’s horn	UBERON:0001954	30.43	gold quality
primary visual cortex	UBERON:0002436	30.43	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
liver	UBERON:0002107	28.82	gold quality
cerebral cortex	UBERON:0000956	28.61	gold quality
duodenum	UBERON:0002114	28.14	gold quality
left ovary	UBERON:0002119	28.07	gold quality
ovary	UBERON:0000992	27.99	gold quality
lymph node	UBERON:0000029	27.57	gold quality
skin of abdomen	UBERON:0001416	27.26	gold quality
temporal lobe	UBERON:0001871	27.15	silver quality
tonsil	UBERON:0002372	27.05	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.14

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

45 targeting GLT6D1, 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-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-3059-5P	99.70	69.93	2491
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-3618	99.69	68.57	1012
HSA-MIR-5197-5P	99.64	69.08	1494
HSA-MIR-892A	99.54	68.16	1141
HSA-MIR-543	99.52	69.03	2595
HSA-MIR-136-5P	99.50	67.26	1153
HSA-MIR-297	99.40	69.58	1418
HSA-MIR-4999-5P	99.35	69.15	926
HSA-MIR-520F-5P	99.34	70.40	1632
HSA-MIR-223-5P	99.24	68.82	1206
HSA-MIR-664A-3P	99.22	71.08	2696
HSA-MIR-593-3P	99.22	67.28	1327
HSA-MIR-4784	99.15	67.41	1733
HSA-MIR-3150B-3P	98.81	67.21	1728
HSA-MIR-6895-3P	98.79	65.69	996

Literature-anchored findings (GeneRIF, showing 3)

• GLT6D1 is a susceptibility locus for periodontitis. (PMID:19897590)
• study independently replicated finding that rs1537415, variant in glycosyl transferase gene GLT6D1, is associated with AgP and provided 1st report of genetic associations with AgP Sudanese population. (PMID:25682733)
• Analysis of GLT6D1 and CDKN2BAS gene polymorphisms in Brazilian patients with advanced periodontitis. (PMID:35703703)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Glt6d1	ENSMUSG00000036401
rattus_norvegicus	Glt6d1	ENSRNOG00000027900

Paralogs (3): GBGT1 (ENSG00000148288), ABO (ENSG00000175164), A3GALT2 (ENSG00000184389)

Protein

Protein identifiers

Putative glycosyltransferase 6 domain-containing protein 1 — Q7Z4J2 (reviewed: Q7Z4J2)

Alternative names: Galactosyltransferase family 6 domain-containing 1

All UniProt accessions (1): Q7Z4J2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Tissue specificity. Expressed in both healthy and inflamed gingival tissue samples at similar levels, with higher expression in the gingival connective tissue compared to gingival epithelium. Strongest expression in testis, followed by leukocytes.

Cofactor. Binds 1 Mn(2+) ion per subunit.

Polymorphism. The stop codon in position 277 is polymorphic and is replaced, though at very low frequency, by a Lys codon allowing the translation of a longer protein. It is not clear if the common, shorter variant shown here is functional or not.

Similarity. Belongs to the glycosyltransferase 6 family.

RefSeq proteins (1): NP_892019* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005076	Glyco_trans_6	Family
IPR029044	Nucleotide-diphossugar_trans	Homologous_superfamily

Pfam: PF03414

UniProt features (12 total): sequence variant 3, binding site 3, topological domain 2, chain 1, transmembrane region 1, active site 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7Z4J2-F1	91.00	0.76

Functional residue map

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

Catalytic / active sites (1): 263 (nucleophile)

Ligand- & substrate-binding residues (3): 82–87; 173–175; 195–198

Glycosylation sites (1): 74

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 35 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_UP, AATGGAG_MIR136, GOBP_CARBOHYDRATE_METABOLIC_PROCESS, GOMF_HEXOSYLTRANSFERASE_ACTIVITY, GOMF_GLYCOSYLTRANSFERASE_ACTIVITY, chr9q34, MIR5696, MIR4729, MIR3143, MIR664A_3P, MIR5196_5P, MIR4747_5P, MIR765, MIR520F_5P, MIR11181_3P

GO Biological Process (1): carbohydrate metabolic process (GO:0005975)

GO Molecular Function (3): glycosyltransferase activity (GO:0016757), hexosyltransferase activity (GO:0016758), transferase activity (GO:0016740)

GO Cellular Component (3): Golgi apparatus (GO:0005794), membrane (GO:0016020), vesicle (GO:0031982)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
primary metabolic process	1
transferase activity	1
glycosyltransferase activity	1
catalytic activity	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1
membrane-bounded organelle	1

Protein interactions and networks

STRING

232 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GLT6D1	CTSC	P53634	753
GLT6D1	STPG3	Q8N7X2	671
GLT6D1	TEX36	Q5VZQ5	618
GLT6D1	GATA3	P23771	618
GLT6D1	SLFNL1	Q499Z3	617
GLT6D1	Q5T8A5	Q5T8A5	574
GLT6D1	SIGLEC5	O15389	550
GLT6D1	DSPP	Q9NZW4	548
GLT6D1	SPPL2C	Q8IUH8	499
GLT6D1	FAM180A	Q6UWF9	479
GLT6D1	CDKN2B	P42772	449
GLT6D1	SH2D4A	Q9H788	433
GLT6D1	PRSS58	Q8IYP2	425
GLT6D1	ADGRE1	Q14246	378
GLT6D1	B3GALT1	Q9Y5Z6	376

IntAct

2 interactions, top by confidence:

A	B	Type	Score
GLT6D1	CANX	psi-mi:“MI:0914”(association)	0.350

BioGRID (7): GLB1L2 (Affinity Capture-MS), RMND1 (Affinity Capture-MS), DNAJB9 (Affinity Capture-MS), CANX (Affinity Capture-MS), FAM213A (Affinity Capture-MS), ALG9 (Affinity Capture-MS), GLT6D1 (Negative Genetic)

ESM2 similar proteins: A0A4Z3, A1Y9I9, A4FUH1, B6CZ46, B6CZ56, B6CZ62, D3ZNQ3, G3V9Q9, O43505, O60512, O60909, O94766, P14616, P14617, P58158, Q09326, Q10469, Q2NKH9, Q2YDM8, Q3V1N9, Q3V5L5, Q4R5T7, Q5EA01, Q5EB73, Q5JU69, Q5M936, Q5NVN3, Q5R4S2, Q5R868, Q5YB40, Q5ZLK4, Q64716, Q6AYR4, Q765H6, Q7Z4J2, Q8BGT9, Q8BWP8, Q8IXK2, Q8NCL4, Q8R1J9

Diamond homologs: A0A4Z3, A1YGR5, A1YGR6, A2AUQ7, D3ZNQ3, G3V9Q9, P14769, P16442, P23336, P38649, P50127, Q2NKH9, Q2YDM8, Q3L7M0, Q3V1N9, Q4R5T7, Q5ZLK4, Q7Z4J2, Q8CFC4, Q8HY56, Q8HYB2, Q8N5D6, Q8SPR2, Q8SQ20, Q8VI38, Q95158, Q9ET32, U3KPV4, Q4G0N0, Q5JBG6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	58
Likely benign	6
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1040 predictions. Top by Δscore:

Variant	Effect	Δscore
9:135624669:ACC:A	acceptor_loss	1.0000
9:135624671:C:CC	acceptor_gain	1.0000
9:135624672:T:C	acceptor_loss	1.0000
9:135626064:CCTA:C	donor_loss	1.0000
9:135626066:TAC:T	donor_loss	1.0000
9:135626067:A:AC	donor_gain	1.0000
9:135626068:C:CC	donor_gain	1.0000
9:135626068:C:T	donor_loss	1.0000
9:135626068:CCTG:C	donor_gain	1.0000
9:135626202:GTTTT:G	acceptor_gain	1.0000
9:135626204:TTT:T	acceptor_gain	1.0000
9:135626205:TT:T	acceptor_gain	1.0000
9:135626206:TC:T	acceptor_loss	1.0000
9:135626207:C:A	acceptor_loss	1.0000
9:135626207:C:CC	acceptor_gain	1.0000
9:135639288:CCAA:C	donor_loss	1.0000
9:135639289:CAA:C	donor_loss	1.0000
9:135639290:AAC:A	donor_loss	1.0000
9:135624666:CAAAC:C	acceptor_gain	0.9900
9:135624668:AAC:A	acceptor_gain	0.9900
9:135624669:AC:A	acceptor_gain	0.9900
9:135624670:CC:C	acceptor_gain	0.9900
9:135626067:ACCTG:A	donor_gain	0.9900
9:135626068:CCTGC:C	donor_gain	0.9900
9:135626203:TTTT:T	acceptor_gain	0.9900
9:135626209:G:C	acceptor_gain	0.9900
9:135626215:C:CT	acceptor_gain	0.9900
9:135638143:G:T	acceptor_gain	0.9900
9:135624667:AAAC:A	acceptor_gain	0.9800
9:135624671:C:T	acceptor_gain	0.9800

AlphaMissense

1837 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:135626143:G:C	F61L	0.968
9:135626143:G:T	F61L	0.968
9:135626145:A:G	F61L	0.968
9:135624424:G:C	F168L	0.967
9:135624424:G:T	F168L	0.967
9:135624426:A:G	F168L	0.967
9:135631439:A:C	F37L	0.966
9:135631439:A:T	F37L	0.966
9:135631441:A:G	F37L	0.966
9:135624619:G:C	F103L	0.961
9:135624619:G:T	F103L	0.961
9:135624621:A:G	F103L	0.961
9:135624253:G:C	F225L	0.954
9:135624253:G:T	F225L	0.954
9:135624255:A:G	F225L	0.954
9:135624394:G:C	F178L	0.946
9:135624394:G:T	F178L	0.946
9:135624396:A:G	F178L	0.946
9:135624418:G:C	F170L	0.945
9:135624418:G:T	F170L	0.945
9:135624420:A:G	F170L	0.945
9:135624620:A:G	F103S	0.934
9:135624106:T:A	K274N	0.933
9:135624106:T:G	K274N	0.933
9:135624395:A:G	F178S	0.927
9:135631444:A:G	W36R	0.925
9:135631444:A:T	W36R	0.925
9:135624419:A:G	F170S	0.923
9:135624633:C:G	A99P	0.923
9:135624643:G:C	F95L	0.923

dbSNP variants (sampled 300 via entrez): RS1000028881 (9:135641631 A>T), RS1000039498 (9:135640940 G>A,T), RS1000061518 (9:135641930 TTG>T), RS1000283029 (9:135623902 A>C), RS1000301784 (9:135625148 CG>C), RS1000452440 (9:135629840 C>A,T), RS1000710557 (9:135631720 T>C), RS1000800651 (9:135630073 A>T), RS1000835174 (9:135634355 T>C), RS1000877982 (9:135640375 C>A,T), RS1000887478 (9:135634127 G>A,T), RS1000992828 (9:135639900 G>T), RS1001334602 (9:135635967 T>C), RS1001445223 (9:135639512 A>G), RS1001939355 (9:135631312 C>A,T)

Disease associations

OMIM: gene MIM:613699 | 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
GCST000521_1	Periodontitis	6.000000e-09

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Resveratrol	affects cotreatment, decreases expression	1
Arsenic Trioxide	increases expression	1
Benzo(a)pyrene	affects methylation	1
Phthalic Acids	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_0237	Capan-1	Cancer cell line	Male
CVCL_0A59	Capan1M9	Cancer cell line	Male
CVCL_S022	Capan-1 SimpleCell O-GalNAc	Cancer cell line	Male

Clinical trials (associated diseases)

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