GALNT2

polypeptide N-acetylgalactosaminyltransferase 2, the group of Polypeptide N-acetylgalactosaminyltransferases

Basic information

Region (hg38): 1:230057989-230282122

Links

ENSG00000143641 ∙ NCBI:2590 ∙ OMIM:602274 ∙ HGNC:4124 ∙ Uniprot:Q10471 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital disorder of glycosylation, type iit (Strong), mode of inheritance: AR
• congenital disorder of glycosylation, type iit (Strong), mode of inheritance: AR
• congenital disorder of glycosylation, type iit (Strong), mode of inheritance: AR
• congenital disorder of glycosylation, type iit (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Congenital disorder of glycosylation, type IIt	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Endocrine; Musculoskeletal; Neurologic	27508872; 32293671

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GALNT2 gene.

• not provided (66 variants)
• Inborn genetic diseases (26 variants)
• Congenital disorder of glycosylation, type iit (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALNT2 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				16	8	24
missense		3	37	1	1	42
nonsense	2					2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			3	3	2	8
non coding			1	8	5	14
Total	2	3	38	25	14

Variants in GALNT2

This is a list of pathogenic ClinVar variants found in the GALNT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-230067320-C-T			Likely benign (Aug 19, 2023)
1-230067352-C-T			Likely benign (May 30, 2022)
1-230067353-T-G			Uncertain significance (Jun 23, 2021)
1-230067369-C-T			Uncertain significance (Nov 26, 2022)
1-230067374-G-T		Inborn genetic diseases	Likely benign (Mar 04, 2024)
1-230067377-G-A			Uncertain significance (Jun 01, 2023)
1-230067394-C-T			Likely benign (Aug 21, 2022)
1-230067398-G-C		Inborn genetic diseases	Uncertain significance (Jul 19, 2023)
1-230067418-G-A			Likely benign (Jul 28, 2023)
1-230067425-C-T			Likely benign (Nov 03, 2023)
1-230178240-C-G		Inborn genetic diseases	Uncertain significance (Sep 12, 2023)
1-230178254-G-T		Inborn genetic diseases	Uncertain significance (Feb 21, 2024)
1-230178256-C-T			Likely benign (Aug 15, 2022)
1-230178261-A-G		Inborn genetic diseases	Uncertain significance (Jun 23, 2023)
1-230178266-A-G		Inborn genetic diseases	Uncertain significance (Aug 08, 2023)
1-230178286-A-C			Likely benign (Jun 03, 2022)
1-230178306-C-T		Inborn genetic diseases	Uncertain significance (Oct 25, 2022)
1-230178322-G-A			Likely benign (May 06, 2023)
1-230203146-G-A		Inborn genetic diseases	Uncertain significance (Nov 14, 2022)
1-230203168-A-G			Likely benign (Apr 12, 2023)
1-230203201-G-A			Likely benign (Mar 03, 2023)
1-230203211-T-TA		Congenital disorder of glycosylation, type iit	Pathogenic (May 20, 2020)
1-230203227-T-C		Congenital disorder of glycosylation, type iit	Likely pathogenic (Dec 18, 2020)
1-230203300-C-G		GALNT2-related disorder	Benign/Likely benign (Jan 11, 2024)
1-230203301-C-A			Benign (Jan 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GALNT2	protein_coding	protein_coding	ENST00000366672	16	224335

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00842	0.992	125728	0	18	125746	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.00	243	348	0.698	0.0000216	3746
Missense in Polyphen		72	147.33	0.48871		1504
Synonymous	-0.243	139	135	1.03	0.00000879	1069
Loss of Function	3.99	11	37.3	0.295	0.00000218	385

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000235	0.000235
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000929	0.0000924
European (Non-Finnish)	0.0000707	0.0000703
Middle Eastern	0.000109	0.000109
South Asian	0.0000654	0.0000653
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 broad spectrum of substrates for peptides such as EA2, Muc5AC, Muc1a, Muc1b. Probably involved in O-linked glycosylation of the immunoglobulin A1 (IgA1) hinge region. {ECO:0000269|PubMed:12438318, ECO:0000269|PubMed:16434399, ECO:0000269|PubMed:7592619, ECO:0000269|PubMed:9295285}.
• Pathway: Mucin type O-glycan biosynthesis - Homo sapiens (human);Globo Sphingolipid Metabolism;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;mucin core 1 and core 2 <i>O</i>-glycosylation;O-Glycan biosynthesis;COPI-independent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;O-linked glycosylation of mucins;O-linked glycosylation;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.566
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.73

Haploinsufficiency Scores

• pHI: 0.227
• hipred: Y
• hipred_score: 0.705
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.492

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Galnt2

Gene ontology

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