GCNT3

glucosaminyl (N-acetyl) transferase 3, mucin type, the group of Glucosaminyl (N-acetyl) transferases/xylosyltransferases

Basic information

Region (hg38): 15:59594875-59640239

Links

ENSG00000140297 ∙ NCBI:9245 ∙ OMIM:606836 ∙ HGNC:4205 ∙ Uniprot:O95395 ∙ 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 GCNT3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GCNT3 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						0
missense			49	1		50
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	49	1	1

Variants in GCNT3

This is a list of pathogenic ClinVar variants found in the GCNT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-59618291-G-A		not specified	Uncertain significance (Oct 06, 2021)
15-59618292-C-G		not specified	Uncertain significance (Jan 25, 2023)
15-59618327-C-T		not specified	Uncertain significance (Jan 27, 2022)
15-59618350-G-C		not specified	Uncertain significance (Apr 29, 2024)
15-59618352-C-G		not specified	Uncertain significance (Sep 02, 2024)
15-59618353-C-G		not specified	Uncertain significance (Aug 02, 2022)
15-59618367-G-T		not specified	Uncertain significance (Mar 20, 2024)
15-59618415-C-G		not specified	Uncertain significance (Jun 26, 2024)
15-59618444-A-G		not specified	Uncertain significance (Jan 04, 2022)
15-59618455-G-C		not specified	Uncertain significance (May 09, 2022)
15-59618473-G-A		not specified	Uncertain significance (Mar 20, 2023)
15-59618488-G-A		not specified	Uncertain significance (Jul 13, 2022)
15-59618495-T-G		not specified	Uncertain significance (Sep 14, 2022)
15-59618542-C-T		not specified	Uncertain significance (Dec 06, 2022)
15-59618620-G-A		not specified	Uncertain significance (Dec 30, 2023)
15-59618623-G-A		not specified	Uncertain significance (Feb 07, 2023)
15-59618629-T-C		not specified	Uncertain significance (Jan 26, 2023)
15-59618654-T-C		not specified	Uncertain significance (Nov 25, 2024)
15-59618658-T-A		not specified	Uncertain significance (Mar 25, 2024)
15-59618658-T-G		not specified	Uncertain significance (Mar 29, 2022)
15-59618689-C-T			Benign (Jul 16, 2018)
15-59618818-C-T		not specified	Uncertain significance (Dec 19, 2022)
15-59618819-G-A		not specified	Uncertain significance (Dec 19, 2022)
15-59618819-G-T		not specified	Uncertain significance (Jun 30, 2024)
15-59618845-G-A		not specified	Uncertain significance (Sep 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GCNT3	protein_coding	protein_coding	ENST00000396065	1	45365

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.12e-8	0.188	124852	2	892	125746	0.00356

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.65	300	230	1.31	0.0000123	2904
Missense in Polyphen		106	92.782	1.1425		1186
Synonymous	-4.10	137	88.1	1.56	0.00000466	831
Loss of Function	0.339	13	14.4	0.904	8.94e-7	170

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00511	0.00511
Ashkenazi Jewish	0.000596	0.000595
East Asian	0.000219	0.000217
Finnish	0.0104	0.0104
European (Non-Finnish)	0.00406	0.00404
Middle Eastern	0.000219	0.000217
South Asian	0.00190	0.00190
Other	0.00424	0.00408

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Glycosyltransferase that can synthesize all known mucin beta 6 N-acetylglucosaminides. Mediates core 2 and core 4 O-glycan branching, 2 important steps in mucin-type biosynthesis. Has also I-branching enzyme activity by converting linear into branched poly-N-acetyllactosaminoglycans, leading to introduce the blood group I antigen during embryonic development. {ECO:0000269|PubMed:9915862}.
• Pathway: Mucin type O-glycan biosynthesis - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;mucin core 1 and core 2 <i>O</i>-glycosylation;terminal <i>O</i>-glycans residues modification;O-Glycan biosynthesis;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.0979

Intolerance Scores

• loftool: 0.881
• rvis_EVS: 0.45
• rvis_percentile_EVS: 77.98

Haploinsufficiency Scores

• pHI: 0.112
• hipred: N
• hipred_score: 0.197

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.258

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gcnt3
• Phenotype: renal/urinary system phenotype; immune system phenotype; hematopoietic system phenotype; normal phenotype; digestive/alimentary phenotype

Gene ontology

• Biological process: immunoglobulin production in mucosal tissue;carbohydrate metabolic process;protein O-linked glycosylation;O-glycan processing;tissue morphogenesis;intestinal absorption;kidney morphogenesis
• Cellular component: Golgi membrane;membrane;integral component of membrane;extracellular exosome
• Molecular function: beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity;N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity;acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity