GALNT14

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

Basic information

Region (hg38): 2:30910467-31155202

Links

ENSG00000158089NCBI:79623OMIM:608225HGNC:22946Uniprot:Q96FL9AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GALNT14 gene.

  • not_specified (88 variants)
  • not_provided (5 variants)
  • GALNT14-related_disorder (3 variants)
  • Non-immune_hydrops_fetalis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALNT14 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024572.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
2
clinvar
3
missense
87
clinvar
3
clinvar
1
clinvar
91
nonsense
1
clinvar
1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 1 0 87 4 3

Highest pathogenic variant AF is 0.0000824024

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
GALNT14protein_codingprotein_codingENST00000324589 16244736
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
7.06e-170.1041256600881257480.000350
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4353123340.9330.00001983652
Missense in Polyphen130148.10.877791581
Synonymous0.2181301330.9760.000008131055
Loss of Function1.092936.00.8050.00000195371

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0007880.000788
Ashkenazi Jewish0.00009990.0000992
East Asian0.0007620.000761
Finnish0.000.00
European (Non-Finnish)0.0004330.000431
Middle Eastern0.0007620.000761
South Asian0.00009810.0000980
Other0.0001630.000163

dbNSFP

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.;
Pathway
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;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

pRec
0.0913

Intolerance Scores

loftool
0.864
rvis_EVS
-0.22
rvis_percentile_EVS
37.66

Haploinsufficiency Scores

pHI
0.0665
hipred
N
hipred_score
0.306
ghis
0.466

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.871

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Galnt14
Phenotype
behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process
O-glycan processing
Cellular component
Golgi membrane;Golgi apparatus;integral component of membrane
Molecular function
polypeptide N-acetylgalactosaminyltransferase activity;carbohydrate binding;metal ion binding