GALNT9

protein-coding

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

Gene summary

This gene encodes a member of the UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase (GalNAc-T) family of enzymes. GalNAc-Ts initiate mucin-type O-linked glycosylation in the Golgi apparatus by catalyzing the transfer of GalNAc to serine and threonine residues on target proteins. They are characterized by an N-terminal transmembrane domain, a stem region, a lumenal catalytic domain containing a GT1 motif and Gal/GalNAc transferase motif, and a C-terminal ricin/lectin-like domain. GalNAc-Ts have different, but overlapping, substrate specificities and patterns of expression. This gene is expressed specifically in the brain, with highest expression in the cerebellum. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001122636.2

Inheritance

—

ClinVar variants

U:13B:4

Top phenotype

GALNT9-related disorder

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr12:132,196,372-132,329,589

External References & Databases

Ensembl (ENSG00000182870)

Transcript & Mutation Effects

hg38 • Region Span ~133.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GALNT9 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 10

not providedTotal: 4

GALNT9-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001122636.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			11 clinvar	2 clinvar		13
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar	1 clinvar		2
Total	0	0	13	4	0	17

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001122636.2	RefSeq	NP_001116108.1	11	MANE Select
ENST00000328957.13	Ensembl	ENSP00000329846.8	11	MANE Select
NM_021808.3	RefSeq	NP_068580.2	5	Standard
ENST00000397325.6	Ensembl	ENSP00000380488.2	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

protein O-linked glycosylation
O-glycan processing

Molecular Function

polypeptide N-acetylgalactosaminyltransferase activity
carbohydrate binding
metal ion binding

Cellular Component

Golgi membrane
Golgi apparatus
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000397325
Coding exons: 5
Length: 225012
Individuals with no LoFs: 124828
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 124840
p: 0.0000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.326	156	168	0.929	0.0000117	1536
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000064	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000050	0.000046	rare
European (Non-Finnish)	0.000091	0.000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.370
RVIS EVS: -0.67
RVIS percentile EVS: 15.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0783

Gene Damage Prediction

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