GALNT14

protein-coding

polypeptide N-acetylgalactosaminyltransferase 14, the group of Polypeptide N-acetylgalactosaminyltransferases

Gene summary

This gene encodes a Golgi protein which is a member of the polypeptide N-acetylgalactosaminyltransferase (ppGalNAc-Ts) protein family. These enzymes catalyze the transfer of N-acetyl-D-galactosamine (GalNAc) to the hydroxyl groups on serines and threonines in target peptides. The encoded protein has been shown to transfer GalNAc to large proteins like mucins. Alterations in this gene may play a role in cancer progression and response to chemotherapy. [provided by RefSeq, Jun 2016]

MANE transcript

NM_024572.4

Inheritance

—

ClinVar variants

P:1U:99B:9

Top phenotype

GALNT14-related disorder

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr2:30,910,467-31,155,202

External References & Databases

Ensembl (ENSG00000158089)

Transcript & Mutation Effects

hg38 • Region Span ~244.7 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 GALNT14 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 98

not providedTotal: 5

GALNT14-related disorderTotal: 4

Non-immune hydrops fetalisTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024572.4. 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 clinvar	2 clinvar	4
missense			97 clinvar	5 clinvar	1 clinvar	103
nonsense	1 clinvar					1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	1	0	99	6	3	109

Highest pathogenic variant AF is 0.00008240243

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024572.4	RefSeq	NP_078848.2	15	MANE Select
ENST00000349752.10	Ensembl	ENSP00000288988.6	15	MANE Select
NM_001253826.2	RefSeq	NP_001240755.1	16	Standard
NM_001253827.2	RefSeq	NP_001240756.1	15	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

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000324589
Coding exons: 16
Length: 244736
Individuals with no LoFs: 125660
Homozygous LoFs: 0
Heterozygous LoFs: 88
Defined: 125748
p: 0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.435	312	334	0.933	0.0000198	3652
Missense (PolyPhen)		130	148.1	0.87779		1581
Synonymous	0.218	130	133	0.976	0.00000813	1055
Loss of Function	1.09	29	36.0	0.805	0.00000195	371

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00042	0.00040	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00076	0.00076	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00043	0.00043	rare
South Asian	0.000098	0.000098	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. Displays activity toward mucin-derived peptide substrates such as Muc2, Muc5AC, Muc7, and Muc13 (-58). May be involved in O-glycosylation in kidney.;

Recessive Scores

pRec: 0.0913

Intolerance Scores

LoFtool: 0.864
RVIS EVS: -0.22
RVIS percentile EVS: 37.66

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.871

Gene Damage Prediction

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