GALNT8

polypeptide N-acetylgalactosaminyltransferase 8, the group of Polypeptide N-acetylgalactosaminyltransferases

Basic information

Region (hg38): 12:4720399-4851927

Links

ENSG00000130035 ∙ NCBI:26290 ∙ OMIM:606250 ∙ HGNC:4130 ∙ Uniprot:Q9NY28 ∙ 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 GALNT8 gene.

• Inborn genetic diseases (24 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALNT8 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
missense			22	3	3	28
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	22	3	4

Variants in GALNT8

This is a list of pathogenic ClinVar variants found in the GALNT8 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-4720735-G-A		not specified	Likely benign (Oct 20, 2021)
12-4720742-A-G		not specified	Uncertain significance (May 03, 2023)
12-4720814-C-G		not specified	Uncertain significance (Dec 16, 2023)
12-4726532-A-G		not specified	Uncertain significance (May 27, 2022)
12-4726550-C-G		not specified	Uncertain significance (Jan 23, 2024)
12-4726730-A-G		not specified	Uncertain significance (Jul 21, 2021)
12-4726747-C-G		not specified	Uncertain significance (Jan 19, 2024)
12-4726753-C-T		not specified	Uncertain significance (Jun 21, 2022)
12-4739217-A-G		not specified	Uncertain significance (Aug 13, 2021)
12-4739249-G-A		not specified	Uncertain significance (Nov 06, 2023)
12-4739255-T-A		not specified	Uncertain significance (Dec 22, 2023)
12-4739278-C-T		not specified	Uncertain significance (Nov 02, 2023)
12-4739284-C-G		not specified	Uncertain significance (Mar 07, 2024)
12-4744540-G-A			Benign (Jun 11, 2018)
12-4744566-G-C		not specified	Uncertain significance (Jan 05, 2022)
12-4744580-T-C		not specified	Uncertain significance (Jan 19, 2024)
12-4744621-G-T		not specified	Uncertain significance (Dec 01, 2022)
12-4744625-G-A		not specified	Uncertain significance (Jan 23, 2023)
12-4745542-A-G		not specified	Uncertain significance (Aug 22, 2023)
12-4745542-A-T		not specified	Uncertain significance (Dec 31, 2023)
12-4745556-G-A		not specified	Uncertain significance (Oct 12, 2022)
12-4746220-C-T		not specified	Uncertain significance (Mar 14, 2023)
12-4746227-A-G			Likely benign (Jun 11, 2018)
12-4746227-A-T		not specified	Uncertain significance (Apr 12, 2022)
12-4746241-G-A		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GALNT8	protein_coding	protein_coding	ENST00000252318	11	130771

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.07e-20	0.00200	125500	3	243	125746	0.000979

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0227	369	368	1.00	0.0000210	4169
Missense in Polyphen		105	111.92	0.9382		1387
Synonymous	0.404	136	142	0.957	0.00000825	1240
Loss of Function	-0.0895	29	28.5	1.02	0.00000144	335

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00223	0.00223
Ashkenazi Jewish	0.00198	0.00199
East Asian	0.00337	0.00338
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000679	0.000668
Middle Eastern	0.00337	0.00338
South Asian	0.000821	0.000817
Other	0.00179	0.00179

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably 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;Neuronal System;O-Glycan biosynthesis;Voltage gated Potassium channels;Potassium Channels;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.0727

Intolerance Scores

• loftool: 0.957
• rvis_EVS: 1.63
• rvis_percentile_EVS: 96.04

Haploinsufficiency Scores

• pHI: 0.0505
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0177

Gene Damage Prediction

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

Gene ontology

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