GCNT1

glucosaminyl (N-acetyl) transferase 1, the group of Glucosaminyl (N-acetyl) transferases/xylosyltransferases

Basic information

Region (hg38): 9:76419850-76651203

Previous symbols: [ "NACGT2" ]

Links

ENSG00000187210

∙ NCBI:2650 ∙ OMIM:600391 ∙ HGNC:4203 ∙ Uniprot:Q02742 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GCNT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GCNT1 gene is commonly pathogenic or not. These statistics are base on transcript: . Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1 clinvar	1 clinvar	2
missense			24 clinvar	1 clinvar		25
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	24	2	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GCNT1	protein_coding	protein_coding	ENST00000442371	1	87581

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00333	0.955	125693	0	54	125747	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.791	201	235	0.855	0.0000131	2857
Missense in Polyphen		73	96.931	0.75311		1212
Synonymous	-0.189	91	88.7	1.03	0.00000523	800
Loss of Function	1.78	6	12.9	0.466	7.20e-7	165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000213
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000405	0.000404
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Glycosyltransferase that catalyzes the transfer of an N- acetylglucosamine moiety onto mucin-type core 1 O-glycan to form the branched mucin-type core 2 O-glycan. Mucin-type core 2 O- glycans play an important role in leukocyte extravasation as they serve as scaffolds for the display of the selectin ligand sialyl Lewis X by leukocytes. {ECO:0000269|PubMed:23027862}.;
Pathway: Mucin type O-glycan biosynthesis - Homo sapiens (human);Globo Sphingolipid Metabolism;Post-translational protein modification;Metabolism of proteins;mucin core 1 and core 2 <i>O</i>-glycosylation;O-Glycan biosynthesis;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

pRec: 0.159

Intolerance Scores

loftool: 0.658
rvis_EVS: 0.37
rvis_percentile_EVS: 75.43

Haploinsufficiency Scores

pHI: 0.0924
hipred: Y
hipred_score: 0.507
ghis: 0.405

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.294

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Gcnt1
Phenotype: normal phenotype; hematopoietic system phenotype; digestive/alimentary phenotype; immune system phenotype; renal/urinary system phenotype; cellular phenotype;

Gene ontology

Biological process: glycoprotein biosynthetic process;O-glycan processing;response to insulin;tissue morphogenesis;leukocyte tethering or rolling;cell adhesion molecule production;kidney morphogenesis
Cellular component: Golgi membrane;extracellular space;trans-Golgi network;integral component of membrane;Golgi cisterna
Molecular function: beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity;protein binding