GALNT18

polypeptide N-acetylgalactosaminyltransferase 18, the group of Polypeptide N-acetylgalactosaminyltransferases

Basic information

Region (hg38): 11:11270876-11622005

Previous symbols: [ "GALNTL4" ]

Links

ENSG00000110328 ∙ NCBI:374378 ∙ OMIM:615136 ∙ HGNC:30488 ∙ Uniprot:Q6P9A2 ∙ 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 GALNT18 gene.

• Inborn genetic diseases (26 variants)
• Okur-Chung neurodevelopmental syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALNT18 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			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding		1				1
Total	0	1	26	0	0

Variants in GALNT18

This is a list of pathogenic ClinVar variants found in the GALNT18 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-11271151-G-A		not specified	Uncertain significance (Jan 17, 2023)
11-11271152-C-T		not specified	Uncertain significance (Apr 27, 2022)
11-11271169-T-C		not specified	Uncertain significance (Jun 24, 2022)
11-11271172-G-C		not specified	Uncertain significance (Apr 04, 2023)
11-11271202-T-C		not specified	Uncertain significance (Oct 06, 2023)
11-11271221-C-T		not specified	Uncertain significance (Jun 24, 2022)
11-11271233-C-T		not specified	Uncertain significance (Nov 21, 2022)
11-11271276-C-G		not specified	Uncertain significance (May 27, 2022)
11-11271277-T-A		not specified	Uncertain significance (Jan 06, 2023)
11-11293038-C-A		not specified	Uncertain significance (May 11, 2022)
11-11293097-G-A		not specified	Uncertain significance (Dec 15, 2022)
11-11293106-C-T		not specified	Uncertain significance (Aug 08, 2022)
11-11293120-C-T		not specified	Uncertain significance (Jan 26, 2023)
11-11293129-T-C		not specified	Uncertain significance (Jun 09, 2022)
11-11327174-T-C		not specified	Uncertain significance (Mar 07, 2023)
11-11332714-C-T		not specified	Uncertain significance (Aug 02, 2022)
11-11332758-C-T		not specified	Uncertain significance (Nov 10, 2022)
11-11332822-T-C		not specified	Uncertain significance (Jan 30, 2024)
11-11340901-C-T		not specified	Uncertain significance (Aug 09, 2021)
11-11340929-A-T		not specified	Uncertain significance (Nov 28, 2023)
11-11340955-G-T		not specified	Uncertain significance (Apr 04, 2023)
11-11340961-C-T		not specified	Uncertain significance (Mar 01, 2023)
11-11352540-A-G		Okur-Chung neurodevelopmental syndrome	Likely pathogenic (Feb 01, 2022)
11-11377338-C-T		not specified	Uncertain significance (Jul 21, 2022)
11-11377344-C-T		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GALNT18	protein_coding	protein_coding	ENST00000227756	11	351130

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000303	0.999	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.880	317	364	0.870	0.0000222	3982
Missense in Polyphen		98	144.7	0.67726		1537
Synonymous	-0.925	165	151	1.10	0.00000956	1161
Loss of Function	3.03	11	28.4	0.387	0.00000135	323

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000979	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000163	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. {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: 0.0995

Intolerance Scores

• rvis_EVS: -0.78
• rvis_percentile_EVS: 13.05

Haploinsufficiency Scores

• pHI: 0.205
• hipred: Y
• hipred_score: 0.614
• ghis: 0.539

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: Galnt18
• Phenotype: immune system phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype

Gene ontology

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