GCNT7

Summary

GCNT7 (glucosaminyl (N-acetyl) transferase family member 7, HGNC:16099) is a protein-coding gene on chromosome 20q13.31, encoding Probable beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 7 (Q6ZNI0). Probable glycosyltransferase.

Predicted to enable acetylglucosaminyltransferase activity. Predicted to be involved in protein glycosylation. Predicted to be located in Golgi membrane.

Source: NCBI Gene 140687 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 107 total

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16099
Approved symbol	GCNT7
Name	glucosaminyl (N-acetyl) transferase family member 7
Location	20q13.31
Locus type	gene with protein product
Status	Approved
Aliases	dJ1153D9.2
Ensembl gene	ENSG00000124091
Ensembl biotype	protein_coding
Entrez	140687

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000243913

RefSeq mRNA: 1 — MANE Select: None NM_080615

Canonical transcript exons

ENST00000243913 — 7 exons

Exon	Start	End
ENSE00000845709	56491492	56491783
ENSE00000845710	56495202	56495297
ENSE00000845711	56496639	56497668
ENSE00001417637	56514085	56514305
ENSE00001420444	56513796	56513837
ENSE00001421125	56525783	56525925
ENSE00001430162	56504055	56504294

Expression profiles

Bgee: expression breadth ubiquitous, 126 present calls, max score 72.88.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	72.88	silver quality
bone marrow cell	CL:0002092	71.27	silver quality
blood	UBERON:0000178	58.51	gold quality
monocyte	CL:0000576	58.42	gold quality
leukocyte	CL:0000738	58.19	gold quality
bone marrow	UBERON:0002371	55.80	gold quality
granulocyte	CL:0000094	55.40	gold quality
tibialis anterior	UBERON:0001385	55.12	silver quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
adrenal tissue	UBERON:0018303	54.22	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
epithelial cell of pancreas	CL:0000083	53.75	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
pancreatic ductal cell	CL:0002079	52.61	silver quality
ileal mucosa	UBERON:0000331	52.16	silver quality
calcaneal tendon	UBERON:0003701	51.74	silver quality
vermiform appendix	UBERON:0001154	51.71	gold quality
lower esophagus mucosa	UBERON:0035834	51.56	gold quality
tonsil	UBERON:0002372	51.14	gold quality
sural nerve	UBERON:0015488	50.62	silver quality
gall bladder	UBERON:0002110	50.51	gold quality
deltoid	UBERON:0001476	50.30	gold quality
myocardium	UBERON:0002349	50.25	gold quality
mucosa of stomach	UBERON:0001199	50.20	gold quality
left ovary	UBERON:0002119	50.08	gold quality
right ovary	UBERON:0002118	49.41	gold quality
caecum	UBERON:0001153	49.09	gold quality
buccal mucosa cell	CL:0002336	49.04	gold quality
quadriceps femoris	UBERON:0001377	48.91	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.26

Regulation

Is transcription factor: no

Cross-species orthologs

22 orthologs

Organism	Symbol	Gene ID
danio_rerio	gcnt7	ENSDARG00000040608
mus_musculus	Gcnt7	ENSMUSG00000074569
rattus_norvegicus	Gcnt7	ENSRNOG00000084373
drosophila_melanogaster	oxt	FBGN0015360
drosophila_melanogaster	CG9164	FBGN0030634
caenorhabditis_elegans	gly-15	WBGENE00001640
caenorhabditis_elegans	gly-16	WBGENE00001641
caenorhabditis_elegans	gly-17	WBGENE00001642
caenorhabditis_elegans	gly-18	WBGENE00001643
caenorhabditis_elegans	gly-19	WBGENE00001644
caenorhabditis_elegans		WBGENE00005024
caenorhabditis_elegans		WBGENE00009148
caenorhabditis_elegans	F30A10.4	WBGENE00009263
caenorhabditis_elegans		WBGENE00011090
caenorhabditis_elegans	T09E11.6	WBGENE00011655
caenorhabditis_elegans	T09E11.9	WBGENE00011658
caenorhabditis_elegans	T27F6.1	WBGENE00012102
caenorhabditis_elegans		WBGENE00012135
caenorhabditis_elegans		WBGENE00013119
caenorhabditis_elegans	ZK1225.2	WBGENE00014236
caenorhabditis_elegans		WBGENE00019270
caenorhabditis_elegans		WBGENE00019919

Paralogs (8): XYLT2 (ENSG00000015532), WSCD2 (ENSG00000075035), XYLT1 (ENSG00000103489), GCNT2 (ENSG00000111846), GCNT3 (ENSG00000140297), GCNT4 (ENSG00000176928), WSCD1 (ENSG00000179314), GCNT1 (ENSG00000187210)

Protein

Protein identifiers

Probable beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 7 — Q6ZNI0 (reviewed: Q6ZNI0)

All UniProt accessions (1): Q6ZNI0

UniProt curated annotations — full annotation on UniProt →

Function. Probable glycosyltransferase.

Subcellular location. Golgi apparatus membrane.

Pathway. Protein modification; protein glycosylation.

Similarity. Belongs to the glycosyltransferase 14 family.

RefSeq proteins (1): NP_542182 (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003406	Glyco_trans_14	Family

Pfam: PF02485

UniProt features (12 total): disulfide bond 4, topological domain 2, sequence variant 2, glycosylation site 2, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZNI0-F1	84.71	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.

Disulfide bonds (4): 53–205, 139–354, 160–187, 363–395

Glycosylation sites (2): 87, 272

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-913709	O-linked glycosylation of mucins

MSigDB gene sets: 25 (showing top): ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOMF_HEXOSYLTRANSFERASE_ACTIVITY, GOMF_GLYCOSYLTRANSFERASE_ACTIVITY, GOMF_UDP_GLYCOSYLTRANSFERASE_ACTIVITY, GOMF_ACETYLGLUCOSAMINYLTRANSFERASE_ACTIVITY, REACTOME_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, REACTOME_O_LINKED_GLYCOSYLATION, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_IFNG_KO_DN, GSE13485_DAY1_VS_DAY21_YF17D_VACCINE_PBMC_UP, DESCARTES_MAIN_FETAL_SLC26A4_PAEP_POSITIVE_CELLS, NAKAYA_PBMC_FLUMIST_AGE_18_50YO_3DY_DN, GSE17974_IL4_AND_ANTI_IL12_VS_UNTREATED_2H_ACT_CD4_TCELL_DN, GSE18148_CBFB_KO_VS_WT_TREG_DN, REACTOME_O_LINKED_GLYCOSYLATION_OF_MUCINS, GSE7460_CTRL_VS_TGFB_TREATED_ACT_FOXP3_HET_TCONV_UP

GO Biological Process (2): obsolete protein glycosylation (GO:0006486), glycoprotein biosynthetic process (GO:0009101)

GO Molecular Function (4): acetylglucosaminyltransferase activity (GO:0008375), UDP-glycosyltransferase activity (GO:0008194), transferase activity (GO:0016740), glycosyltransferase activity (GO:0016757)

GO Cellular Component (3): Golgi membrane (GO:0000139), Golgi apparatus (GO:0005794), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
O-linked glycosylation	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
macromolecule biosynthetic process	1
glycoprotein metabolic process	1
carbohydrate derivative biosynthetic process	1
UDP-glycosyltransferase activity	1
hexosyltransferase activity	1
glycosyltransferase activity	1
catalytic activity	1
transferase activity	1
Golgi apparatus	1
bounding membrane of organelle	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

400 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GCNT7	TMCO5A	Q8N6Q1	490
GCNT7	CFAP58	Q5T655	455
GCNT7	LHFPL7	Q6ICI0	434
GCNT7	GRAMD1C	Q8IYS0	412
GCNT7	MSLNL	Q96KJ4	404
GCNT7	ST6GALNAC4	Q9H4F1	371
GCNT7	SVOPL	Q8N434	369
GCNT7	FUT1	P19526	367
GCNT7	B4GALNT3	Q6L9W6	356
GCNT7	GPKOW	Q92917	350
GCNT7	HAO1	Q9UJM8	348
GCNT7	B3GNT2	Q9NY97	345
GCNT7	TFAP2D	Q7Z6R9	341
GCNT7	UMODL1	Q5DID0	339
GCNT7	PCDHB1	Q9Y5F3	338

IntAct

2 interactions, top by confidence:

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

BioGRID (3): GCNT7 (Negative Genetic), NISCH (Cross-Linking-MS (XL-MS)), GCNT7 (Protein-peptide)

ESM2 similar proteins: A2AJQ3, A2AUQ7, A5GFW8, A6NG13, A7RX69, D3ZNQ3, E1BPQ3, E9PU17, E9PX95, E9Q649, G3V9Q9, O15466, P0DN25, P23336, P27473, P38566, P38567, P48794, P61646, P97402, Q02742, Q09324, Q21389, Q2NKH9, Q2YDM8, Q3L7M0, Q3SX46, Q499P3, Q4R5T7, Q4V8F8, Q53G44, Q5U258, Q5ZLK4, Q6ZNI0, Q6ZXC8, Q71SG7, Q7Z388, Q7Z4J2, Q812F3, Q8BV66

Diamond homologs: A5GFW8, E9Q649, O95395, P97402, Q02742, Q09324, Q1M0V6, Q3V3K7, Q5JCT0, Q5U258, Q6ZNI0, Q71SG7, Q7YQE1, Q805R1, Q80RC7, Q866Z4, Q866Z5, Q866Z6, Q8CH87, Q8N0V5, Q92180, Q99CW3, Q9IZK2, Q9P109, Q5QQ53, Q7KVA1, Q5QQ54, Q5QQ55

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	100
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

932 predictions. Top by Δscore:

Variant	Effect	Δscore
20:56491784:C:CC	acceptor_gain	1.0000
20:56495197:TTTAC:T	donor_loss	1.0000
20:56495199:TA:T	donor_loss	1.0000
20:56495200:AC:A	donor_loss	1.0000
20:56495201:C:CT	donor_loss	1.0000
20:56495201:CCT:C	donor_gain	1.0000
20:56495228:T:TA	donor_gain	1.0000
20:56495294:GCAT:G	acceptor_gain	1.0000
20:56495295:CAT:C	acceptor_gain	1.0000
20:56495295:CATC:C	acceptor_gain	1.0000
20:56495298:C:CC	acceptor_gain	1.0000
20:56513303:T:TA	acceptor_gain	1.0000
20:56513313:AGTGT:A	acceptor_gain	1.0000
20:56513314:GT:G	acceptor_gain	1.0000
20:56513314:GTGT:G	acceptor_gain	1.0000
20:56513314:GTGTG:G	acceptor_gain	1.0000
20:56513428:GGT:G	donor_loss	1.0000
20:56517102:A:AG	acceptor_gain	1.0000
20:56517102:ACAG:A	acceptor_loss	1.0000
20:56517103:C:G	acceptor_gain	1.0000
20:56517104:A:AG	acceptor_gain	1.0000
20:56517104:A:T	acceptor_loss	1.0000
20:56517105:G:A	acceptor_loss	1.0000
20:56517105:G:GC	acceptor_gain	1.0000
20:56517105:GA:G	acceptor_gain	1.0000
20:56517105:GAA:G	acceptor_gain	1.0000
20:56517105:GAAGC:G	acceptor_gain	1.0000
20:56517202:GTG:G	donor_loss	1.0000
20:56517203:T:A	donor_loss	1.0000
20:56518085:A:AG	acceptor_gain	1.0000

AlphaMissense

2052 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000002174 (20:56527567 C>T), RS1000143480 (20:56492244 A>G), RS1000161665 (20:56526733 G>A), RS1000280797 (20:56522496 C>T), RS1000319060 (20:56512968 A>G), RS1000326944 (20:56491566 C>G), RS1000529142 (20:56519154 G>A,C), RS1000562973 (20:56524050 C>T), RS1000583032 (20:56508374 T>C), RS1000766975 (20:56513743 C>T), RS1000800917 (20:56508430 T>A), RS1000828762 (20:56498129 A>G), RS1000848436 (20:56508670 C>A,T), RS1000892213 (20:56527619 G>A), RS1000942819 (20:56497856 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

2 associations (top):

Study	Trait	p-value
GCST002579_14	Heschl’s gyrus morphology	8.000000e-06
GCST002685_17	Refractive astigmatism	2.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases methylation	2
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation	1
benzo(e)pyrene	increases methylation	1
di-n-butylphosphoric acid	affects expression	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
Acetaminophen	decreases expression	1
Catechin	affects cotreatment, decreases expression	1
Methapyrilene	increases methylation	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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