A4GNT

protein-coding

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

Gene summary

This gene encodes a protein from the glycosyltransferase 32 family. The enzyme catalyzes the transfer of N-acetylglucosamine (GlcNAc) to core 2 branched O-glycans. It forms a unique glycan, GlcNAcalpha1-->4Galbeta-->R and is largely associated with the Golgi apparatus membrane. [provided by RefSeq, Jul 2008]

MANE transcript

NM_016161.3

Inheritance

—

ClinVar variants

U:54B:5

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 0.29

Max pathogenic AF

—

Genomic locus

chr3:138,123,713-138,132,390

External References & Databases

Ensembl (ENSG00000118017)

Transcript & Mutation Effects

hg38 • Region Span ~8.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to A4GNT variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 54

not providedTotal: 3

Inborn genetic diseasesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016161.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			53 clinvar	4 clinvar		57
nonsense				1 clinvar		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	54	5	0	59

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016161.3	RefSeq	NP_057245.1	2	MANE Select
ENST00000236709.4	Ensembl	ENSP00000236709.3	2	MANE Select
ENST00000858667.1	Ensembl	ENSP00000528726.1	2	Standard
ENST00000858667.2	Ensembl	ENSP00000528726.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational protein modification
Metabolism of proteins
heparan sulfate biosynthesis (late stages)
heparan sulfate biosynthesis
O-linked glycosylation of mucins

Biological Process

carbohydrate metabolic process
protein O-linked glycosylation
glycoprotein biosynthetic process
O-glycan processing
negative regulation of epithelial cell proliferation

Molecular Function

acetylglucosaminyltransferase activity

Cellular Component

Golgi membrane
membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000236709
Coding exons: 2
Length: 8670
Individuals with no LoFs: 125110
Homozygous LoFs: 3
Heterozygous LoFs: 635
Defined: 125748
p: 0.00254

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.235	179	188	0.952	0.0000101	2239
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00068	0.00068	rare
Latino/Admixed American	0.0013	0.0013	notable
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0.0094	0.0094	notable
European (Non-Finnish)	0.0032	0.0032	notable
South Asian	0.00013	0.00013	rare
Other	0.0018	0.0018	notable

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0885

Intolerance Scores

LoFtool: 0.260
RVIS EVS: 1.11
RVIS percentile EVS: 92.04

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.148

Gene Damage Prediction

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