CSGALNACT2

chondroitin sulfate N-acetylgalactosaminyltransferase 2, the group of Beta 4-glycosyltransferases

Basic information

Region (hg38): 10:43138444-43185302

Links

ENSG00000169826 ∙ NCBI:55454 ∙ OMIM:616616 ∙ HGNC:24292 ∙ Uniprot:Q8N6G5 ∙ 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 CSGALNACT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSGALNACT2 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			33	1		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	1	0

Variants in CSGALNACT2

This is a list of pathogenic ClinVar variants found in the CSGALNACT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-43155174-C-G		not specified	Uncertain significance (Dec 19, 2022)
10-43155181-G-A		not specified	Uncertain significance (Oct 12, 2022)
10-43155252-G-A		not specified	Uncertain significance (May 14, 2024)
10-43155289-T-G		not specified	Uncertain significance (Nov 09, 2023)
10-43155378-C-T		not specified	Uncertain significance (Feb 12, 2024)
10-43155430-G-A		not specified	Uncertain significance (Aug 14, 2023)
10-43155567-C-T		not specified	Uncertain significance (Oct 27, 2022)
10-43155643-G-A		not specified	Uncertain significance (Jun 16, 2024)
10-43155700-T-C		not specified	Uncertain significance (Jan 19, 2022)
10-43155701-T-G		not specified	Uncertain significance (Apr 29, 2024)
10-43155706-C-T		not specified	Uncertain significance (Nov 10, 2022)
10-43155718-T-A		not specified	Uncertain significance (Jul 31, 2023)
10-43155729-C-T		not specified	Uncertain significance (May 24, 2023)
10-43155756-G-C		not specified	Uncertain significance (Jun 13, 2022)
10-43155760-A-C		not specified	Uncertain significance (Nov 30, 2022)
10-43158733-G-A		not specified	Uncertain significance (Dec 16, 2023)
10-43158736-A-C		not specified	Uncertain significance (Dec 19, 2022)
10-43158737-T-G		not specified	Uncertain significance (Sep 16, 2021)
10-43158756-C-G		not specified	Uncertain significance (Oct 03, 2022)
10-43158806-C-G		not specified	Uncertain significance (Oct 29, 2021)
10-43158808-G-A		not specified	Uncertain significance (Oct 26, 2022)
10-43158844-T-G		not specified	Uncertain significance (Jan 29, 2024)
10-43158847-T-C		not specified	Uncertain significance (Nov 22, 2021)
10-43158864-A-G		not specified	Likely benign (Jul 14, 2023)
10-43160571-A-T		not specified	Uncertain significance (Mar 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSGALNACT2	protein_coding	protein_coding	ENST00000374466	7	46823

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.238	0.762	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	243	297	0.817	0.0000155	3590
Missense in Polyphen		92	118.06	0.77924		1511
Synonymous	0.120	101	103	0.985	0.00000504	998
Loss of Function	3.51	6	24.9	0.241	0.00000139	296

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000877	0.0000877
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000880	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000671	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transfers 1,4-N-acetylgalactosamine (GalNAc) from UDP- GalNAc to the non-reducing end of glucuronic acid (GlcUA). Required for addition of the first GalNAc to the core tetrasaccharide linker and for elongation of chondroitin chains. {ECO:0000269|PubMed:12433924, ECO:0000269|PubMed:12446672}.
• Pathway: Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate - Homo sapiens (human);Metabolism of carbohydrates;Chondroitin sulfate biosynthesis;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;chondroitin sulfate biosynthesis (late stages);Proteoglycan biosynthesis;chondroitin sulfate biosynthesis;dermatan sulfate biosynthesis;Metabolism;chondroitin and dermatan biosynthesis (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.703
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.71

Haploinsufficiency Scores

• pHI: 0.330
• hipred: Y
• hipred_score: 0.543
• ghis: 0.575

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.289

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Csgalnact2
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; respiratory system phenotype; skeleton phenotype; limbs/digits/tail phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: proteoglycan biosynthetic process;chondroitin sulfate biosynthetic process;chondroitin sulfate proteoglycan biosynthetic process;dermatan sulfate proteoglycan biosynthetic process;dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process;chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process
• Cellular component: Golgi membrane;membrane;integral component of Golgi membrane;Golgi cisterna membrane
• Molecular function: protein binding;acetylgalactosaminyltransferase activity;metal ion binding;glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity;glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity