GALNT13

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

Basic information

Region (hg38): 2:153871922-154453979

Links

ENSG00000144278 ∙ NCBI:114805 ∙ OMIM:608369 ∙ HGNC:23242 ∙ Uniprot:Q8IUC8 ∙ 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 GALNT13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALNT13 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in GALNT13

This is a list of pathogenic ClinVar variants found in the GALNT13 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-153944520-A-G		not specified	Uncertain significance (Mar 08, 2024)
2-153944525-G-A		not specified	Uncertain significance (Feb 23, 2023)
2-154140349-G-A		not specified	Uncertain significance (Feb 28, 2023)
2-154140366-G-A		not specified	Uncertain significance (Nov 21, 2023)
2-154242037-A-G		not specified	Uncertain significance (Aug 19, 2023)
2-154242076-G-A		not specified	Uncertain significance (May 05, 2023)
2-154242091-A-G		not specified	Uncertain significance (Feb 28, 2024)
2-154242107-C-T		not specified	Uncertain significance (Jul 12, 2023)
2-154242727-G-A		not specified	Uncertain significance (May 31, 2023)
2-154242787-C-T		not specified	Uncertain significance (May 05, 2023)
2-154242843-T-G		not specified	Uncertain significance (Jul 14, 2022)
2-154245966-A-G		not specified	Uncertain significance (Jun 12, 2023)
2-154245967-G-T		not specified	Uncertain significance (Jun 12, 2023)
2-154259082-A-T		not specified	Uncertain significance (Mar 30, 2024)
2-154301419-G-A		not specified	Uncertain significance (Jan 03, 2024)
2-154301475-G-T		not specified	Uncertain significance (Jun 10, 2024)
2-154301503-C-G		not specified	Uncertain significance (Jun 29, 2023)
2-154301538-G-A		not specified	Uncertain significance (Dec 15, 2023)
2-154396104-C-A		not specified	Uncertain significance (Aug 08, 2022)
2-154409041-A-G		not specified	Uncertain significance (Feb 05, 2024)
2-154409051-T-A		not specified	Uncertain significance (Dec 14, 2023)
2-154409057-A-T		not specified	Uncertain significance (Apr 10, 2023)
2-154438661-G-C		not specified	Uncertain significance (Mar 06, 2023)
2-154438691-A-G		not specified	Uncertain significance (Jan 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GALNT13	protein_coding	protein_coding	ENST00000392825	11	581936

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.991	0.00934	125732	0	15	125747	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.27	236	298	0.793	0.0000149	3675
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000176	0.000176
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000531	0.0000527
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
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 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.
• 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: 0.0791

Intolerance Scores

• loftool: 0.432
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.16

Haploinsufficiency Scores

• pHI: 0.318
• hipred: Y
• hipred_score: 0.738
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0878

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Galnt13
• Phenotype: normal phenotype

Gene ontology

• Biological process: O-glycan processing;protein O-linked glycosylation via serine;protein O-linked glycosylation via threonine
• Cellular component: Golgi membrane;Golgi apparatus;integral component of membrane
• Molecular function: polypeptide N-acetylgalactosaminyltransferase activity;carbohydrate binding;metal ion binding