C1GALT1

core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1, the group of Beta 3-glycosyltransferases

Basic information

Region (hg38): 7:7156933-7248616

Links

ENSG00000106392 ∙ NCBI:56913 ∙ OMIM:610555 ∙ HGNC:24337 ∙ Uniprot:Q9NS00 ∙ 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 C1GALT1 gene.

• Inborn genetic diseases (17 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1GALT1 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
missense			16	1	1	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	2	1

Variants in C1GALT1

This is a list of pathogenic ClinVar variants found in the C1GALT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-7234372-T-C		not specified	Uncertain significance (Feb 15, 2023)
7-7234380-C-A		not specified	Uncertain significance (Jul 14, 2022)
7-7234423-T-G			Benign (Apr 10, 2018)
7-7234438-A-G		not specified	Uncertain significance (Jun 10, 2022)
7-7238347-A-C		not specified	Uncertain significance (Sep 06, 2023)
7-7238362-A-G		not specified	Uncertain significance (Jul 15, 2021)
7-7238375-G-A		not specified	Uncertain significance (Sep 22, 2023)
7-7238375-G-T		not specified	Uncertain significance (May 18, 2022)
7-7238385-A-C		not specified	Uncertain significance (Sep 22, 2022)
7-7238431-G-A		not specified	Uncertain significance (Jan 19, 2022)
7-7238441-C-G		not specified	Uncertain significance (Dec 27, 2023)
7-7238500-G-C		not specified	Uncertain significance (Jan 29, 2024)
7-7238549-C-T		not specified	Uncertain significance (Oct 26, 2021)
7-7238561-T-C		not specified	Uncertain significance (Apr 18, 2023)
7-7238738-G-A		not specified	Uncertain significance (Nov 21, 2023)
7-7238747-T-C		not specified	Uncertain significance (Aug 22, 2023)
7-7238761-C-T			Likely benign (Apr 10, 2018)
7-7238785-A-G		not specified	Uncertain significance (Oct 25, 2023)
7-7238816-T-C		not specified	Likely benign (Oct 18, 2021)
7-7238853-C-G		not specified	Uncertain significance (Jul 26, 2022)
7-7238875-C-T		not specified	Uncertain significance (Apr 10, 2023)
7-7243653-C-G		not specified	Uncertain significance (Jun 06, 2023)
7-7243660-G-A		not specified	Uncertain significance (Nov 17, 2022)
7-7243704-A-G		not specified	Uncertain significance (Jul 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1GALT1	protein_coding	protein_coding	ENST00000436587	3	91718

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.763	0.237	125728	0	7	125735	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.118	184	189	0.976	0.00000913	2401
Missense in Polyphen		15	49.712	0.30174		685
Synonymous	-1.16	79	66.9	1.18	0.00000343	652
Loss of Function	2.90	2	13.5	0.148	5.66e-7	196

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000448	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Glycosyltransferase that generates the core 1 O-glycan Gal-beta1-3GalNAc-alpha1-Ser/Thr (T antigen), which is a precursor for many extended O-glycans in glycoproteins. Plays a central role in many processes, such as angiogenesis, thrombopoiesis and kidney homeostasis development.
• Pathway: Mucin type O-glycan biosynthesis - Homo sapiens (human);Ectoderm Differentiation;Post-translational protein modification;Metabolism of proteins;mucin core 1 and core 2 <i>O</i>-glycosylation;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.188

Intolerance Scores

• loftool: 0.185
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.177
• hipred: N
• hipred_score: 0.452
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.867

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: C1galt1
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; renal/urinary system phenotype; reproductive 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); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); neoplasm; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; immune system phenotype

Gene ontology

• Biological process: angiogenesis;kidney development;O-glycan processing, core 1;intestinal epithelial cell development
• Cellular component: Golgi membrane;integral component of membrane
• Molecular function: protein binding;glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase activity;metal ion binding