GCNT4

glucosaminyl (N-acetyl) transferase 4, the group of Glucosaminyl (N-acetyl) transferases/xylosyltransferases

Basic information

Region (hg38): 5:75025346-75052558

Previous symbols: [ "LINC01336" ]

Links

ENSG00000176928 ∙ NCBI:51301 ∙ OMIM:616782 ∙ HGNC:17973 ∙ Uniprot:Q9P109 ∙ 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 GCNT4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GCNT4 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
missense			33	1		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	2	0

Variants in GCNT4

This is a list of pathogenic ClinVar variants found in the GCNT4 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-75028693-G-A		not specified	Uncertain significance (Apr 07, 2022)
5-75028707-A-C		not specified	Uncertain significance (Feb 15, 2023)
5-75028739-T-G		not specified	Uncertain significance (Nov 06, 2023)
5-75028783-T-C		not specified	Likely benign (Feb 26, 2025)
5-75028824-C-T		not specified	Uncertain significance (Nov 26, 2024)
5-75028896-C-A		not specified	Uncertain significance (Apr 07, 2022)
5-75028939-G-A		not specified	Uncertain significance (Apr 01, 2024)
5-75028982-A-C		not specified	Uncertain significance (Dec 01, 2022)
5-75029020-C-T		not specified	Uncertain significance (Nov 26, 2024)
5-75029031-T-C		not specified	Uncertain significance (Mar 10, 2025)
5-75029038-G-A		not specified	Uncertain significance (Nov 22, 2024)
5-75029074-G-C		not specified	Uncertain significance (Jan 10, 2023)
5-75029079-A-G		not specified	Uncertain significance (Sep 27, 2021)
5-75029158-G-T		not specified	Uncertain significance (Nov 15, 2024)
5-75029170-C-T		not specified	Uncertain significance (Aug 16, 2021)
5-75029172-T-C		not specified	Uncertain significance (Jan 04, 2022)
5-75029184-G-A		not specified	Uncertain significance (Feb 23, 2023)
5-75029220-C-T		not specified	Likely benign (Mar 01, 2024)
5-75029248-T-C		not specified	Uncertain significance (Oct 04, 2022)
5-75029256-T-G		not specified	Uncertain significance (Nov 26, 2024)
5-75029275-C-T		not specified	Uncertain significance (May 28, 2024)
5-75029286-A-G		not specified	Uncertain significance (May 26, 2023)
5-75029406-G-A		not specified	Uncertain significance (Dec 23, 2024)
5-75029466-T-C		not specified	Uncertain significance (Aug 29, 2024)
5-75029473-C-A		not specified	Uncertain significance (Nov 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GCNT4	protein_coding	protein_coding	ENST00000322348	1	3436

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00115	0.959	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0268	231	230	1.00	0.0000111	2987
Missense in Polyphen		70	94.248	0.74272		1220
Synonymous	2.05	63	87.4	0.721	0.00000438	836
Loss of Function	1.81	7	14.4	0.485	7.76e-7	204

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Glycosyltransferase that mediates core 2 O-glycan branching, an important step in mucin-type biosynthesis. Does not have core 4 O-glycan or I-branching enzyme activity. {ECO:0000269|PubMed:10753916}.
• 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;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Intolerance Scores

• loftool: 0.661
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.41

Haploinsufficiency Scores

• pHI: 0.185
• hipred: N
• hipred_score: 0.231

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0280

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gcnt4
• Phenotype: digestive/alimentary phenotype; immune system phenotype; renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; normal phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: inter-male aggressive behavior;carbohydrate metabolic process;protein O-linked glycosylation;O-glycan processing;thyroid hormone metabolic process;tissue morphogenesis;homeostasis of number of cells;kidney morphogenesis
• Cellular component: Golgi membrane;integral component of membrane
• Molecular function: beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity;N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity