GALNT16

polypeptide N-acetylgalactosaminyltransferase 16, the group of Polypeptide N-acetylgalactosaminyltransferases

Basic information

Region (hg38): 14:69259277-69357033

Previous symbols: [ "GALNTL1" ]

Links

ENSG00000100626 ∙ NCBI:57452 ∙ OMIM:615132 ∙ HGNC:23233 ∙ Uniprot:Q8N428 ∙ 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 GALNT16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALNT16 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			40	1		41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	1	0

Variants in GALNT16

This is a list of pathogenic ClinVar variants found in the GALNT16 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-69260390-T-A		not specified	Uncertain significance (Mar 15, 2024)
14-69260402-C-T		not specified	Uncertain significance (Jan 26, 2022)
14-69260403-G-A		not specified	Uncertain significance (Jan 06, 2023)
14-69260417-G-T		not specified	Uncertain significance (Dec 14, 2023)
14-69320718-G-A		not specified	Uncertain significance (Jan 31, 2024)
14-69320727-C-T		not specified	Uncertain significance (Apr 18, 2023)
14-69320740-T-A		not specified	Uncertain significance (Aug 19, 2023)
14-69320757-C-T		not specified	Uncertain significance (Dec 18, 2023)
14-69320817-A-C		not specified	Uncertain significance (Jun 10, 2022)
14-69320826-A-T		not specified	Uncertain significance (Oct 03, 2023)
14-69320840-C-T		not specified	Uncertain significance (Aug 23, 2021)
14-69320852-G-A		not specified	Uncertain significance (Nov 21, 2023)
14-69324754-A-G		not specified	Uncertain significance (Dec 27, 2022)
14-69324762-C-T		not specified	Uncertain significance (Oct 13, 2023)
14-69324786-A-G		not specified	Uncertain significance (Sep 07, 2022)
14-69325962-C-T		not specified	Uncertain significance (Aug 22, 2023)
14-69325996-G-C		not specified	Uncertain significance (Jun 16, 2024)
14-69326010-G-A		not specified	Uncertain significance (Dec 15, 2022)
14-69328536-G-A		not specified	Uncertain significance (Oct 06, 2021)
14-69328553-G-T		not specified	Uncertain significance (Jun 21, 2023)
14-69328561-G-A		not specified	Uncertain significance (Apr 29, 2024)
14-69331473-C-T		not specified	Uncertain significance (Aug 13, 2021)
14-69331492-T-C		not specified	Uncertain significance (Oct 06, 2022)
14-69333126-C-G		not specified	Uncertain significance (Jan 16, 2024)
14-69333144-C-T		not specified	Uncertain significance (Jun 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GALNT16	protein_coding	protein_coding	ENST00000337827	15	95190

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000139	1.00	125707	0	41	125748	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	273	341	0.801	0.0000204	3622
Missense in Polyphen		118	175.14	0.67376		1825
Synonymous	0.161	132	134	0.982	0.00000777	1094
Loss of Function	3.46	13	35.1	0.370	0.00000187	363

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000430	0.000427
Ashkenazi Jewish	0.000496	0.000496
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000151	0.000149
Middle Eastern	0.0000544	0.0000544
South Asian	0.000263	0.000261
Other	0.000328	0.000326

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. {ECO:0000269|PubMed:22186971}.
• 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: 0.109

Intolerance Scores

• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.73

Haploinsufficiency Scores

• pHI: 0.535
• hipred: Y
• hipred_score: 0.614
• ghis: 0.579

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	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Galnt16

Gene ontology

• Biological process: 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