CSGALNACT1

chondroitin sulfate N-acetylgalactosaminyltransferase 1, the group of Beta 4-glycosyltransferases

Basic information

Region (hg38): 8:19404160-19758029

Links

ENSG00000147408 ∙ NCBI:55790 ∙ OMIM:616615 ∙ HGNC:24290 ∙ Uniprot:Q8TDX6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• skeletal dysplasia, mild, with joint laxity and advanced bone age (Moderate), mode of inheritance: AR
• skeletal dysplasia, mild, with joint laxity and advanced bone age (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Skeletal dysplasia, mild, with joint laxity and advanced bone age	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	Musculoskeletal	27599773; 31325655; 31705726

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CSGALNACT1 gene.

• not provided (203 variants)
• Inborn genetic diseases (28 variants)
• Skeletal dysplasia, mild, with joint laxity and advanced bone age (13 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSGALNACT1 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				35	7	42
missense		2	103	13	5	123
nonsense	2		1			3
start loss						0
frameshift	4		1	1		6
inframe indel		1	1			2
splice donor/acceptor (+/-2bp)						0
splice region			4	5		9
non coding			2	17	18	37
Total	6	3	108	66	30

Highest pathogenic variant AF is 0.000125

Variants in CSGALNACT1

This is a list of pathogenic ClinVar variants found in the CSGALNACT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-19405492-G-A			Benign (Nov 11, 2018)
8-19405772-C-A		CSGALNACT1-related disorder	Likely benign (Feb 19, 2019)
8-19405784-GTT-G			Uncertain significance (Feb 10, 2022)
8-19405802-TTC-T			Likely benign (Jan 24, 2024)
8-19405805-T-A		Inborn genetic diseases	Uncertain significance (Jan 05, 2024)
8-19405817-C-G		CSGALNACT1-related disorder	Benign/Likely benign (Jan 31, 2024)
8-19405821-G-T			Uncertain significance (May 12, 2022)
8-19405828-C-G			Uncertain significance (Nov 08, 2022)
8-19405831-T-C		Inborn genetic diseases	Uncertain significance (Jul 12, 2023)
8-19405832-A-G		Inborn genetic diseases	Uncertain significance (Dec 27, 2023)
8-19405853-A-C			Uncertain significance (Jan 29, 2024)
8-19405861-C-A		Inborn genetic diseases	Uncertain significance (Aug 01, 2022)
8-19405861-C-T			Likely benign (Feb 06, 2023)
8-19405866-C-T			Uncertain significance (Jan 05, 2024)
8-19405867-G-A			Likely benign (Sep 26, 2023)
8-19405868-T-C		Inborn genetic diseases	Uncertain significance (May 31, 2022)
8-19405879-G-A			Likely benign (Jan 24, 2024)
8-19405906-C-G		Inborn genetic diseases	Uncertain significance (Feb 05, 2024)
8-19405914-G-T			Uncertain significance (Oct 05, 2022)
8-19405917-C-T		Inborn genetic diseases	Uncertain significance (Aug 01, 2022)
8-19405918-G-A		CSGALNACT1-related disorder	Likely benign (Jun 07, 2023)
8-19405920-G-C		Inborn genetic diseases	Uncertain significance (Mar 02, 2023)
8-19405930-G-A			Benign (Jan 31, 2024)
8-19405931-T-C			Uncertain significance (Nov 08, 2022)
8-19405934-A-T			Uncertain significance (Aug 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSGALNACT1	protein_coding	protein_coding	ENST00000454498	7	353869

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.27e-14	0.0387	125687	1	60	125748	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.63	425	297	1.43	0.0000184	3527
Missense in Polyphen		180	136.35	1.3202		1632
Synonymous	-4.14	173	116	1.49	0.00000739	1001
Loss of Function	0.312	21	22.6	0.929	0.00000123	257

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000243	0.000242
Ashkenazi Jewish	0.00	0.00
East Asian	0.000707	0.000707
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000255	0.000255
Middle Eastern	0.000707	0.000707
South Asian	0.000359	0.000327
Other	0.000163	0.000163

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. Important role in chondroitin chain biosynthesis in cartilage formation and subsequent endochondral ossification (PubMed:11788602, PubMed:12163485, PubMed:12446672, PubMed:17145758). Moreover, is involved in the metabolism of aggrecan (By similarity). {ECO:0000250|UniProtKB:Q8BJQ9, ECO:0000269|PubMed:11788602, ECO:0000269|PubMed:12163485, ECO:0000269|PubMed:12446672, ECO:0000269|PubMed:17145758, ECO:0000269|PubMed:21160489, ECO:0000269|PubMed:27599773}.
• 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: 0.115

Intolerance Scores

• loftool: 0.799
• rvis_EVS: -0.1
• rvis_percentile_EVS: 45.65

Haploinsufficiency Scores

• pHI: 0.497
• hipred: N
• hipred_score: 0.441
• ghis: 0.482

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.425

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Csgalnact1
• Phenotype: limbs/digits/tail phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system 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); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: endochondral ossification;nervous system development;cell recognition;cell population proliferation;anatomical structure morphogenesis;heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process;UDP-N-acetylgalactosamine metabolic process;proteoglycan biosynthetic process;extracellular matrix organization;chondroitin sulfate biosynthetic process;heparin biosynthetic process;UDP-glucuronate metabolic process;chondroitin sulfate proteoglycan biosynthetic process;dermatan sulfate proteoglycan biosynthetic process;chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process;cartilage development
• Cellular component: Golgi membrane;integral component of Golgi membrane;Golgi cisterna membrane
• Molecular function: acetylgalactosaminyltransferase activity;peptidoglycan glycosyltransferase activity;glucuronosyltransferase activity;metal ion binding;glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity;glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity