A4GNT

alpha-1,4-N-acetylglucosaminyltransferase, the group of Alpha 1,4-glycosyltransferases

Basic information

Region (hg38): 3:138123713-138132390

Links

ENSG00000118017 ∙ NCBI:51146 ∙ OMIM:616709 ∙ HGNC:17968 ∙ Uniprot:Q9UNA3 ∙ 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 A4GNT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the A4GNT 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			17	3		20
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	17	4	0

Variants in A4GNT

This is a list of pathogenic ClinVar variants found in the A4GNT region.

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

Position	Type	Phenotype	Significance	ClinVar
3-138124394-C-T		not specified	Uncertain significance (Apr 15, 2024)
3-138124395-G-A		not specified	Uncertain significance (Jul 22, 2022)
3-138124397-C-T		not specified	Uncertain significance (Nov 08, 2022)
3-138124478-C-T		not specified	Uncertain significance (May 09, 2023)
3-138124491-G-A			Likely benign (Jun 05, 2018)
3-138124519-G-T		not specified	Uncertain significance (Sep 14, 2023)
3-138124591-C-A		not specified	Uncertain significance (Jan 06, 2023)
3-138124594-C-T		not specified	Uncertain significance (Sep 26, 2023)
3-138124630-A-C		not specified	Uncertain significance (Jan 16, 2024)
3-138124645-G-T			Likely benign (Nov 01, 2022)
3-138124682-G-A		not specified	Uncertain significance (Feb 21, 2024)
3-138124713-T-C		Inborn genetic diseases	Uncertain significance (Jan 10, 2018)
3-138124724-C-T		not specified	Likely benign (Aug 22, 2023)
3-138124725-G-A		not specified	Uncertain significance (Aug 05, 2023)
3-138124827-G-A		not specified	Uncertain significance (Jan 29, 2024)
3-138124866-C-G		not specified	Uncertain significance (Apr 15, 2022)
3-138130860-A-G		not specified	Uncertain significance (Feb 08, 2023)
3-138130872-G-C		not specified	Uncertain significance (Mar 15, 2024)
3-138130923-C-T		not specified	Uncertain significance (Jan 24, 2024)
3-138130952-T-A		not specified	Uncertain significance (Dec 03, 2021)
3-138130965-A-G		not specified	Likely benign (May 11, 2022)
3-138131146-C-A		not specified	Uncertain significance (May 09, 2023)
3-138131195-T-C		not specified	Uncertain significance (Dec 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
A4GNT	protein_coding	protein_coding	ENST00000236709	2	8670

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.165	0.822	125110	3	635	125748	0.00254

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.235	179	188	0.952	0.0000101	2239
Missense in Polyphen		50	57.242	0.87349		713
Synonymous	-0.234	77	74.4	1.03	0.00000402	659
Loss of Function	2.14	3	10.5	0.286	4.48e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00201	0.00201
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00943	0.00942
European (Non-Finnish)	0.00319	0.00318
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.00179	0.00179

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the transfer of N-acetylglucosamine (GlcNAc) to core 2 branched O-glycans (PubMed:10430883). Necessary for the synthesis of type III mucin which is specifically produced in the stomach, duodenum, and pancreatic duct (PubMed:10430883). May protect against inflammation-associated gastric adenocarcinomas (By similarity). {ECO:0000250|UniProtKB:Q14BT6, ECO:0000269|PubMed:10430883}.
• Pathway: Post-translational protein modification;Metabolism of proteins;heparan sulfate biosynthesis (late stages);heparan sulfate biosynthesis;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.0885

Intolerance Scores

• loftool: 0.260
• rvis_EVS: 1.11
• rvis_percentile_EVS: 92.04

Haploinsufficiency Scores

• pHI: 0.0807
• hipred: N
• hipred_score: 0.221

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.148

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: A4gnt
• Phenotype: cellular phenotype; neoplasm; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); digestive/alimentary phenotype; immune system phenotype

Gene ontology

• Biological process: carbohydrate metabolic process;protein O-linked glycosylation;glycoprotein biosynthetic process;O-glycan processing;negative regulation of epithelial cell proliferation
• Cellular component: Golgi membrane;membrane;integral component of membrane
• Molecular function: acetylglucosaminyltransferase activity