GALNT9

polypeptide N-acetylgalactosaminyltransferase 9, the group of Polypeptide N-acetylgalactosaminyltransferases

Basic information

Region (hg38): 12:132196372-132329589

Links

ENSG00000182870 ∙ NCBI:50614 ∙ OMIM:606251 ∙ HGNC:4131 ∙ Uniprot:Q9HCQ5 ∙ 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 GALNT9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALNT9 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			7	1		8
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	8	2	0

Variants in GALNT9

This is a list of pathogenic ClinVar variants found in the GALNT9 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-132203548-TCATC-T			Uncertain significance (Jan 06, 2022)
12-132203624-T-A			Likely benign (Jul 01, 2022)
12-132240678-T-A			Likely benign (Jul 01, 2022)
12-132261045-G-A		not specified	Uncertain significance (Mar 08, 2024)
12-132262492-C-T		not specified	Uncertain significance (Sep 22, 2022)
12-132262607-GTAGCTCATCTGTCTGCACCTGCAGGAAACACGGTTTGGGGTGCGGTCAGGGCGCAGCATGAGGGACCCCGGAAGCCA-G		GALNT9-related disorder	Likely benign (Apr 20, 2022)
12-132286428-G-T		not specified	Uncertain significance (Dec 06, 2022)
12-132328993-C-G		not specified	Uncertain significance (Apr 07, 2022)
12-132329070-C-T		not specified	Uncertain significance (Jun 03, 2024)
12-132329089-G-A		not specified	Uncertain significance (Jan 09, 2025)
12-132329103-G-A		not specified	Uncertain significance (Feb 28, 2023)
12-132329124-T-G		not specified	Uncertain significance (Feb 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GALNT9	protein_coding	protein_coding	ENST00000397325	5	225012

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00524	0.900	124828	0	12	124840	0.0000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.326	156	168	0.929	0.0000117	1536
Missense in Polyphen		58	62.471	0.92843		536
Synonymous	-0.249	71	68.4	1.04	0.00000498	452
Loss of Function	1.43	5	9.84	0.508	4.17e-7	117

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000646	0.0000642
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000505	0.0000464
European (Non-Finnish)	0.0000912	0.0000883
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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. Does not glycosylate apomucin or SDC3. {ECO:0000269|PubMed:10978536, ECO:0000269|PubMed:12407114}.
• 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: 0.106

Intolerance Scores

• loftool: 0.370
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.76

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.440
• ghis: 0.692

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0783

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Galnt9

Gene ontology

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