GCNT1

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

Basic information

Region (hg38): 9:76419849-76651203

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.

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	1	2
missense			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	1

Variants in GCNT1

This is a list of pathogenic ClinVar variants found in the GCNT1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-76502401-G-A		not specified	Uncertain significance (Nov 09, 2021)
9-76502424-A-C		not specified	Uncertain significance (Jun 18, 2021)
9-76502472-G-A		not specified	Uncertain significance (Jul 13, 2022)
9-76502508-G-T		not specified	Uncertain significance (Feb 16, 2023)
9-76502545-G-A		not specified	Uncertain significance (Feb 28, 2024)
9-76502565-G-A		not specified	Likely benign (Dec 18, 2023)
9-76502700-C-T		not specified	Uncertain significance (Mar 24, 2023)
9-76502742-T-C		not specified	Uncertain significance (Jan 10, 2023)
9-76502760-A-C		not specified	Uncertain significance (May 17, 2023)
9-76502769-C-A		not specified	Uncertain significance (Jun 04, 2024)
9-76502866-A-G		not specified	Uncertain significance (Apr 09, 2024)
9-76502919-A-C		not specified	Uncertain significance (Jun 09, 2022)
9-76502935-T-C		not specified	Uncertain significance (Jun 10, 2022)
9-76502955-C-T		not specified	Uncertain significance (Jun 02, 2023)
9-76503048-A-G		not specified	Uncertain significance (Dec 28, 2023)
9-76503084-T-C			Benign (Mar 30, 2018)
9-76503176-G-A			Likely benign (Jul 01, 2022)
9-76503406-A-G		not specified	Uncertain significance (Feb 27, 2024)
9-76503468-G-A		not specified	Uncertain significance (Mar 29, 2024)
9-76503496-G-A		not specified	Uncertain significance (May 31, 2022)
9-76503540-G-A		not specified	Uncertain significance (Oct 20, 2023)
9-76503549-T-C		not specified	Uncertain significance (Feb 22, 2023)
9-76503594-G-T		not specified	Uncertain significance (May 24, 2023)
9-76503630-C-T		not specified	Uncertain significance (Jan 16, 2024)
9-76619356-A-T		not specified	Uncertain significance (Feb 21, 2024)

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