GALNT15

protein-coding

polypeptide N-acetylgalactosaminyltransferase 15, the group of Polypeptide N-acetylgalactosaminyltransferases

Gene summary

Predicted to enable polypeptide N-acetylgalactosaminyltransferase activity. Predicted to be involved in protein O-linked glycosylation. Located in transport vesicle. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

GALNTL2

MANE transcript

NM_054110.5

Inheritance

—

ClinVar variants

U:112B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.93

Max pathogenic AF

—

Genomic locus

chr3:16,174,680-16,231,992

External References & Databases

Ensembl (ENSG00000131386)

Transcript & Mutation Effects

hg38 • Region Span ~57.3 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 GALNT15 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 114

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_054110.5. 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 clinvar		2
missense			109 clinvar	5 clinvar		114
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	112	6	0	118

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_054110.5	RefSeq	NP_473451.3	10	MANE Select
ENST00000339732.10	Ensembl	ENSP00000344260.5	10	MANE Select
NM_001319051.2	RefSeq	NP_001305980.1	10	Standard
NM_001319052.2	RefSeq	NP_001305981.1	4	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-Glycan biosynthesis

Biological Process

O-glycan processing

Molecular Function

polypeptide N-acetylgalactosaminyltransferase activity
carbohydrate binding
metal ion binding

Cellular Component

Golgi membrane
Golgi apparatus
integral component of membrane
transport vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000339732
Coding exons: 10
Length: 57344
Individuals with no LoFs: 125560
Homozygous LoFs: 0
Heterozygous LoFs: 188
Defined: 125748
p: 0.000748

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.226	381	369	1.03	0.0000207	4200
Missense (PolyPhen)		111	119.2	0.93122		1444
Synonymous	0.305	139	144	0.968	0.00000758	1251
Loss of Function	0.342	28	30.0	0.933	0.00000154	311

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00051	0.00049	rare
Latino/Admixed American	0.0019	0.0019	notable
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.0021	0.0021	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00057	0.00055	rare
South Asian	0.00033	0.00033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D- galactosamine residue to a serine or threonine residue on the protein receptor. Although it displays a much weaker activity toward all substrates tested compared to GALNT2, it is able to transfer up to seven GalNAc residues to the Muc5AC peptide, suggesting that it can fill vicinal Thr/Ser residues in cooperation with other GALNT proteins. Prefers Muc1a as substrate.;

Recessive Scores

pRec: 0.0970

Intolerance Scores

RVIS EVS: -0.66
RVIS percentile EVS: 16.02

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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