GALNT13

protein-coding

polypeptide N-acetylgalactosaminyltransferase 13, the group of Polypeptide N-acetylgalactosaminyltransferases

Gene summary

The GALNT13 protein is a member of the UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase (GalNAcT; EC 2.4.1.41) family, which initiate O-linked glycosylation of mucins (see MUC3A, MIM 158371) by the initial transfer of N-acetylgalactosamine (GalNAc) with an alpha-linkage to a serine or threonine residue.[supplied by OMIM, Apr 2004]

MANE transcript

NM_052917.4

Inheritance

—

ClinVar variants

U:57

Top phenotype

Zimmermann-Laband syndrome 3

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr2:153,871,922-154,453,979

External References & Databases

Ensembl (ENSG00000144278)

Transcript & Mutation Effects

hg38 • Region Span ~582.1 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 GALNT13 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 51

not providedTotal: 2

Zimmermann-Laband syndrome 3Total: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052917.4. 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			54 clinvar			54
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	57	0	0	57

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 57 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_052917.4	RefSeq	NP_443149.2	11	MANE Select
ENST00000392825.8	Ensembl	ENSP00000376570.3	11	MANE Select
NM_001301627.2	RefSeq	NP_001288556.1	11	Standard
NM_001376392.1	RefSeq	NP_001363321.1	11	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
protein O-linked glycosylation via serine
protein O-linked glycosylation via threonine

Molecular Function

polypeptide N-acetylgalactosaminyltransferase activity
carbohydrate binding
metal ion binding

Cellular Component

Golgi membrane
Golgi apparatus
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000392825
Coding exons: 11
Length: 581936
Individuals with no LoFs: 125732
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 125747
p: 0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.27	236	298	0.793	0.0000149	3675
Missense (PolyPhen)		55	96.213	0.57165		1137
Synonymous	0.696	94	103	0.913	0.00000524	1014
Loss of Function	4.30	3	27.3	0.110	0.00000130	358

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000053	0.000053	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

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. Has a much stronger activity than GALNT1 to transfer GalNAc to mucin peptides, such as Muc5Ac and Muc7. Able to glycosylate SDC3. May be responsible for the synthesis of Tn antigen in neuronal cells.;

Recessive Scores

pRec: 0.0791

Intolerance Scores

LoFtool: 0.432
RVIS EVS: -0.18
RVIS percentile EVS: 40.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0878

Gene Damage Prediction

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