GALNT15

polypeptide N-acetylgalactosaminyltransferase 15, the group of Polypeptide N-acetylgalactosaminyltransferases

Basic information

Region (hg38): 3:16174680-16231992

Previous symbols: [ "GALNTL2" ]

Links

ENSG00000131386 ∙ NCBI:117248 ∙ OMIM:615131 ∙ HGNC:21531 ∙ Uniprot:Q8N3T1 ∙ 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 GALNT15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALNT15 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			58	2		60
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	58	2	0

Variants in GALNT15

This is a list of pathogenic ClinVar variants found in the GALNT15 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-16175189-G-C		not specified	Uncertain significance (Feb 23, 2023)
3-16175298-C-A		not specified	Uncertain significance (Jan 23, 2024)
3-16175324-G-A		not specified	Uncertain significance (May 24, 2023)
3-16175338-G-A		not specified	Uncertain significance (Nov 15, 2024)
3-16175422-C-T		not specified	Uncertain significance (May 21, 2024)
3-16175423-G-A		not specified	Uncertain significance (Feb 16, 2023)
3-16175452-T-G		not specified	Uncertain significance (Aug 12, 2021)
3-16175455-C-T		not specified	Uncertain significance (Aug 26, 2022)
3-16175465-G-A		not specified	Uncertain significance (Nov 19, 2022)
3-16175482-G-A		not specified	Uncertain significance (Aug 08, 2022)
3-16175504-G-A		not specified	Uncertain significance (Nov 14, 2023)
3-16175506-C-T		not specified	Uncertain significance (Mar 30, 2024)
3-16175528-A-G		not specified	Likely benign (Jun 28, 2023)
3-16175560-G-A		not specified	Uncertain significance (Feb 28, 2023)
3-16175572-G-A		not specified	Uncertain significance (Apr 07, 2022)
3-16175600-C-A		not specified	Uncertain significance (Jul 06, 2024)
3-16175600-C-T		not specified	Uncertain significance (Feb 21, 2024)
3-16175652-C-G		not specified	Uncertain significance (Aug 02, 2023)
3-16175681-G-A		not specified	Uncertain significance (Aug 12, 2022)
3-16195760-G-A		not specified	Likely benign (Dec 15, 2023)
3-16195782-G-A		not specified	Uncertain significance (Jun 29, 2022)
3-16195803-G-A		not specified	Uncertain significance (Mar 14, 2023)
3-16195836-A-G		not specified	Uncertain significance (Apr 13, 2023)
3-16195845-C-T		not specified	Uncertain significance (Feb 06, 2024)
3-16195846-G-A		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GALNT15	protein_coding	protein_coding	ENST00000339732	10	57344

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.65e-18	0.00980	125560	0	188	125748	0.000748

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.226	381	369	1.03	0.0000207	4200
Missense in Polyphen		111	119.2	0.93122		1444
Synonymous	0.305	139	144	0.968	0.00000758	1251
Loss of Function	0.342	28	30.0	0.933	0.00000154	311

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00242	0.00240
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00207	0.00207
Finnish	0.00	0.00
European (Non-Finnish)	0.000574	0.000554
Middle Eastern	0.00207	0.00207
South Asian	0.000327	0.000327
Other	0.000164	0.000163

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. Although it displays a much weaker activity toward all substrates tested compared to GALNT2, it is able to transfer up to seven GalNAc residues to the Muc5AC peptide, suggesting that it can fill vicinal Thr/Ser residues in cooperation with other GALNT proteins. Prefers Muc1a as substrate.
• 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: 0.0970

Intolerance Scores

• rvis_EVS: -0.66
• rvis_percentile_EVS: 16.02

Haploinsufficiency Scores

• pHI: 0.303
• hipred: N
• hipred_score: 0.306
• ghis: 0.523

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Galnt15

Gene ontology

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