GALNT4

polypeptide N-acetylgalactosaminyltransferase 4, the group of Polypeptide N-acetylgalactosaminyltransferases

Basic information

Region (hg38): 12:89519412-89524796

Links

ENSG00000257594 ∙ NCBI:8693 ∙ OMIM:603565 ∙ HGNC:4126 ∙ Uniprot:Q8N4A0 ∙ 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 GALNT4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALNT4 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		2
missense			37	1	1	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	37	2	1

Variants in GALNT4

This is a list of pathogenic ClinVar variants found in the GALNT4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-89522853-T-C		not specified	Uncertain significance (Aug 12, 2021)
12-89522878-G-A		not specified	Uncertain significance (Dec 08, 2023)
12-89522880-C-T		not specified	Uncertain significance (Dec 13, 2022)
12-89522895-C-T		not specified	Uncertain significance (Aug 08, 2022)
12-89522907-A-G		not specified	Uncertain significance (Apr 11, 2023)
12-89523004-G-T			Benign/Likely benign (Oct 01, 2023)
12-89523118-G-A		not specified	Uncertain significance (Jun 16, 2023)
12-89523201-C-A		not specified	Uncertain significance (Aug 02, 2023)
12-89523202-T-C		not specified	Uncertain significance (Sep 22, 2023)
12-89523206-A-C		not specified	Uncertain significance (Jul 26, 2022)
12-89523218-C-A		not specified	Uncertain significance (Jan 05, 2022)
12-89523250-T-C		not specified	Uncertain significance (Sep 22, 2022)
12-89523297-C-T		not specified	Uncertain significance (Aug 27, 2024)
12-89523356-G-A		Childhood-onset schizophrenia	Likely pathogenic (Jan 01, 2014)
12-89523366-T-C		not specified	Uncertain significance (May 24, 2023)
12-89523450-C-T		not specified	Uncertain significance (Mar 06, 2023)
12-89523453-T-C		not specified	Uncertain significance (Jun 30, 2022)
12-89523565-T-C		not specified	Uncertain significance (May 11, 2022)
12-89523572-C-T			Likely benign (Dec 01, 2022)
12-89523726-A-G		not specified	Uncertain significance (Feb 23, 2023)
12-89523764-A-T			Benign (Jun 23, 2018)
12-89523783-A-G		not specified	Uncertain significance (Jun 06, 2023)
12-89523832-G-C		not specified	Uncertain significance (May 23, 2023)
12-89523886-C-T		not specified	Uncertain significance (Oct 03, 2022)
12-89523925-T-C		not specified	Uncertain significance (Dec 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GALNT4	protein_coding	protein_coding	ENST00000529983	1	6855

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.267	0.733	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00975	322	322	1.00	0.0000166	3778
Missense in Polyphen		145	161.76	0.89638		1834
Synonymous	-0.372	124	119	1.04	0.00000601	1127
Loss of Function	3.22	5	20.9	0.239	0.00000120	244

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
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. Has a highest activity toward Muc7, EA2 and Muc2, with a lowest activity than GALNT2. Glycosylates 'Thr-57' of SELPLG.
• 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)

Intolerance Scores

• loftool: 0.688
• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.23

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.273
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Galnt4
• Phenotype: normal phenotype

Gene ontology

• Biological process: O-glycan processing;protein O-linked glycosylation via serine;protein O-linked glycosylation via threonine
• Cellular component: Golgi membrane;Golgi apparatus;integral component of membrane;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: polypeptide N-acetylgalactosaminyltransferase activity;manganese ion binding;carbohydrate binding