GALNT10

protein-coding

polypeptide N-acetylgalactosaminyltransferase 10, the group of Polypeptide N-acetylgalactosaminyltransferases|MicroRNA protein coding host genes

Gene summary

This gene encodes a member of the GalNAc polypeptide N-acetylgalactosaminyltransferases. These enzymes catalyze the first step in the synthesis of mucin-type oligosaccharides. These proteins transfer GalNAc from UDP-GalNAc to either serine or threonine residues of polypeptide acceptors. The protein encoded by this locus may have increased catalytic activity toward glycosylated peptides compared to activity toward non-glycosylated peptides.[provided by RefSeq, Apr 2010]

MANE transcript

NM_198321.4

Inheritance

—

ClinVar variants

U:101B:4

Top phenotype

GALNT10-related disorder

gnomAD constraint

pLI —, LoF o/e 0.41

Max pathogenic AF

—

Genomic locus

chr5:154,190,730-154,420,984

External References & Databases

Ensembl (ENSG00000164574)

Transcript & Mutation Effects

hg38 • Region Span ~230.3 kb

Loading mutation effect viewer...

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 GALNT10 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 95

not providedTotal: 4

GALNT10-related disorderTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198321.4. 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			2 clinvar	1 clinvar	1 clinvar	4
missense			96 clinvar	2 clinvar		98
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	101	3	1	105

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198321.4	RefSeq	NP_938080.1	12	MANE Select
ENST00000297107.11	Ensembl	ENSP00000297107.6	12	MANE Select
ENST00000377661.2	Ensembl	ENSP00000366889.2	11	Standard
ENST00000377661.3	Ensembl	ENSP00000366889.2	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

protein O-linked glycosylation
O-glycan processing

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: ENST00000297107
Coding exons: 12
Length: 230255
Individuals with no LoFs: 125720
Homozygous LoFs: 0
Heterozygous LoFs: 28
Defined: 125748
p: 0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.53	292	375	0.778	0.0000238	3944
Missense (PolyPhen)		130	178.44	0.72853		1880
Synonymous	0.110	144	146	0.988	0.00000922	1170
Loss of Function	3.22	14	34.3	0.408	0.00000201	340

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.00016	0.00016	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. Has activity toward Muc5Ac and EA2 peptide substrates.;

Recessive Scores

pRec: 0.112

Intolerance Scores

LoFtool: 0.651
RVIS EVS: -1.2
RVIS percentile EVS: 5.79

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.560

Gene Damage Prediction

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