GALNTL6

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

Basic information

Region (hg38): 4:171812254-173041559

Links

ENSG00000174473 ∙ NCBI:442117 ∙ OMIM:615138 ∙ HGNC:33844 ∙ Uniprot:Q49A17 ∙ 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 GALNTL6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALNTL6 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			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	0

Variants in GALNTL6

This is a list of pathogenic ClinVar variants found in the GALNTL6 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-172229729-A-T		not specified	Uncertain significance (Aug 02, 2021)
4-172311659-A-G		not specified	Uncertain significance (Jun 22, 2021)
4-172311664-G-A		not specified	Uncertain significance (Apr 12, 2024)
4-172311742-C-T		not specified	Uncertain significance (May 25, 2022)
4-172348530-C-T		not specified	Uncertain significance (Nov 08, 2022)
4-172348587-G-C		not specified	Uncertain significance (Feb 12, 2024)
4-172809397-G-A		not specified	Uncertain significance (Nov 06, 2023)
4-172809448-G-A		not specified	Uncertain significance (Jan 03, 2024)
4-172809454-G-A		not specified	Uncertain significance (Dec 07, 2023)
4-172813600-A-G		not specified	Uncertain significance (Jan 31, 2022)
4-172813644-G-A		not specified	Uncertain significance (Jan 25, 2023)
4-172813701-G-A		not specified	Uncertain significance (Aug 21, 2023)
4-172882828-G-A		not specified	Uncertain significance (Dec 20, 2021)
4-172882830-A-G		not specified	Uncertain significance (Jan 23, 2023)
4-172931230-G-A		not specified	Uncertain significance (Dec 05, 2022)
4-172952171-G-T		not specified	Uncertain significance (Oct 26, 2022)
4-172952220-T-C		not specified	Uncertain significance (Nov 08, 2022)
4-172952229-G-A		not specified	Uncertain significance (Jan 23, 2024)
4-172952239-C-T		not specified	Uncertain significance (Jun 22, 2023)
4-173009229-G-A		not specified	Uncertain significance (Nov 09, 2021)
4-173009256-G-A		not specified	Uncertain significance (Jul 09, 2021)
4-173009277-A-T		not specified	Uncertain significance (Apr 04, 2024)
4-173021507-G-A		not specified	Uncertain significance (Mar 28, 2023)
4-173021569-G-A		not specified	Uncertain significance (Jun 28, 2022)
4-173039979-A-G		not specified	Uncertain significance (Jul 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GALNTL6	protein_coding	protein_coding	ENST00000506823	12	1229306

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.32e-9	0.988	125705	0	43	125748	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.14	234	346	0.676	0.0000188	3978
Missense in Polyphen		84	153.79	0.5462		1727
Synonymous	-0.330	130	125	1.04	0.00000700	1101
Loss of Function	2.37	19	33.9	0.561	0.00000181	375

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000559	0.000559
Ashkenazi Jewish	0.000399	0.000397
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.000164	0.000163
South Asian	0.0000654	0.0000653
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. {ECO:0000250}.
• 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-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.575
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.68

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.525
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.252

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Galntl6

Gene ontology

• Biological process: 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