GCNT4

protein-coding

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

Gene summary

Predicted to enable acetylglucosaminyltransferase activity. Predicted to be involved in carbohydrate metabolic process and protein O-linked glycosylation via N-acetyl-galactosamine. Predicted to act upstream of or within several processes, including inter-male aggressive behavior; kidney morphogenesis; and thyroid hormone metabolic process. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

LINC01336

MANE transcript

NM_001366737.1

Inheritance

—

ClinVar variants

U:42B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.49

Max pathogenic AF

—

Genomic locus

chr5:75,025,346-75,052,558

External References & Databases

Ensembl (ENSG00000176928)

Transcript & Mutation Effects

hg38 • Region Span ~27.2 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 GCNT4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 44

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001366737.1. 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			42 clinvar	2 clinvar		44
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	42	3	0	45

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001366737.1	RefSeq	NP_001353666.1	1	MANE Select
ENST00000652361.2	Ensembl	ENSP00000498836.1	1	MANE Select
ENST00000322348.5	Ensembl	ENSP00000317027.4	1	Standard
ENST00000856429.1	Ensembl	ENSP00000526488.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

inter-male aggressive behavior
carbohydrate metabolic process
protein O-linked glycosylation
O-glycan processing
thyroid hormone metabolic process

Molecular Function

beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity
N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity

Cellular Component

Golgi membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000322348
Coding exons: 1
Length: 3436
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0268	231	230	1.00	0.0000111	2987
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Intolerance Scores

LoFtool: 0.661
RVIS EVS: 0.33
RVIS percentile EVS: 73.41

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0280

Gene Damage Prediction

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