GALNT1

polypeptide N-acetylgalactosaminyltransferase 1, the group of MicroRNA protein coding host genes|Polypeptide N-acetylgalactosaminyltransferases

Basic information

Region (hg38): 18:35581117-35711834

Links

ENSG00000141429

∙ NCBI:2589 ∙ OMIM:602273 ∙ HGNC:4123 ∙ Uniprot:Q10472 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GALNT1 gene.

not_specified (21 variants)
not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALNT1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020474.4. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			21 clinvar			21
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	21	0	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GALNT1	protein_coding	protein_coding	ENST00000269195	11	130718

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00191	0.998	125727	1	14	125742	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.52	174	296	0.588	0.0000146	3701
Missense in Polyphen		29	96.374	0.30091		1191
Synonymous	1.15	84	98.5	0.852	0.00000475	1026
Loss of Function	3.26	10	28.9	0.346	0.00000156	347

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000304	0.0000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000895	0.0000879
Middle Eastern	0.0000545	0.0000544
South Asian	0.000172	0.0000980
Other	0.00	0.00

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. Has a broad spectrum of substrates for peptides such as EA2, Muc5AC, Muc1a, Muc1b and Muc7. {ECO:0000269|PubMed:9295285}.;
Pathway: Mucin type O-glycan biosynthesis - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Metabolism of Spingolipids in ER and Golgi apparatus;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;mucin core 1 and core 2 <i>O</i>-glycosylation;O-Glycan biosynthesis;COPI-independent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;O-linked glycosylation of mucins;O-linked glycosylation;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

pRec: 0.118

Intolerance Scores

loftool: 0.408
rvis_EVS: -0.41
rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

pHI: 0.454
hipred: Y
hipred_score: 0.792
ghis: 0.662

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.333

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Galnt1
Phenotype: cellular phenotype; homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; hematopoietic system phenotype; immune system phenotype;

Gene ontology

Biological process: protein O-linked glycosylation;O-glycan processing;protein O-linked glycosylation via serine;protein O-linked glycosylation via threonine
Cellular component: Golgi membrane;extracellular region;endoplasmic reticulum membrane;Golgi apparatus;membrane;integral component of membrane;Golgi cisterna membrane;perinuclear region of cytoplasm
Molecular function: polypeptide N-acetylgalactosaminyltransferase activity;manganese ion binding;carbohydrate binding