GALNT6

polypeptide N-acetylgalactosaminyltransferase 6, the group of Polypeptide N-acetylgalactosaminyltransferases

Basic information

Region (hg38): 12:51351247-51392867

Links

ENSG00000139629 ∙ NCBI:11226 ∙ OMIM:605148 ∙ HGNC:4128 ∙ Uniprot:Q8NCL4 ∙ 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 GALNT6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALNT6 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				1	1	2
missense			60	2	2	64
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	60	3	3

Variants in GALNT6

This is a list of pathogenic ClinVar variants found in the GALNT6 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-51354384-C-T		not specified	Likely benign (Oct 19, 2024)
12-51354398-T-G		not specified	Uncertain significance (Dec 02, 2022)
12-51354400-A-C		not specified	Uncertain significance (Feb 14, 2023)
12-51354490-A-T		not specified	Uncertain significance (Jan 26, 2025)
12-51355799-G-A			Benign (Jul 13, 2018)
12-51355826-C-T		not specified	Uncertain significance (May 15, 2024)
12-51355857-G-A			Likely benign (Mar 01, 2022)
12-51355867-C-T		not specified	Uncertain significance (Nov 09, 2024)
12-51355921-T-C		not specified	Uncertain significance (Feb 07, 2025)
12-51357357-C-T		not specified	Uncertain significance (Apr 12, 2022)
12-51357366-C-T		not specified	Uncertain significance (May 07, 2024)
12-51357402-G-A		not specified	Uncertain significance (Jul 13, 2022)
12-51357425-C-A		not specified	Uncertain significance (Feb 10, 2022)
12-51358137-T-C		not specified	Uncertain significance (Nov 26, 2024)
12-51358191-T-C		not specified	Uncertain significance (Oct 06, 2021)
12-51358204-T-C		not specified	Uncertain significance (Dec 21, 2022)
12-51358242-G-A		not specified	Uncertain significance (Oct 10, 2023)
12-51358252-C-T		not specified	Uncertain significance (Mar 07, 2025)
12-51358258-A-C		not specified	Uncertain significance (Feb 05, 2024)
12-51359159-A-T		not specified	Uncertain significance (Aug 21, 2023)
12-51359206-C-T		not specified	Uncertain significance (Oct 04, 2022)
12-51359208-A-G		not specified	Uncertain significance (Aug 20, 2024)
12-51359214-A-G		not specified	Uncertain significance (Oct 12, 2021)
12-51359219-A-T		not specified	Uncertain significance (Oct 29, 2021)
12-51359223-C-T		not specified	Uncertain significance (May 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GALNT6	protein_coding	protein_coding	ENST00000543196	10	41621

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.42e-9	0.945	125594	0	154	125748	0.000613

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.354	357	376	0.949	0.0000225	4095
Missense in Polyphen		146	165.59	0.88167		1756
Synonymous	-0.130	155	153	1.01	0.00000924	1224
Loss of Function	2.00	19	31.0	0.613	0.00000185	305

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00242	0.00242
Ashkenazi Jewish	0.000314	0.000298
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000317	0.000316
Middle Eastern	0.000272	0.000272
South Asian	0.000980	0.000980
Other	0.000326	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. May participate in synthesis of oncofetal fibronectin. Has activity toward Muc1a, Muc2, EA2 and fibronectin peptides.
• 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: 0.104

Intolerance Scores

• loftool: 0.839
• rvis_EVS: -0.55
• rvis_percentile_EVS: 19.93

Haploinsufficiency Scores

• pHI: 0.124
• hipred: N
• hipred_score: 0.322
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Galnt6

Gene ontology

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