C1GALT1

protein-coding

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

Gene summary

The protein encoded by this gene generates the common core 1 O-glycan structure, Gal-beta-1-3GalNAc-R, by the transfer of Gal from UDP-Gal to GalNAc-alpha-1-R. Core 1 is a precursor for many extended mucin-type O-glycans on cell surface and secreted glycoproteins. Studies in mice suggest that this gene plays a key role in thrombopoiesis and kidney homeostasis.[provided by RefSeq, Sep 2010]

MANE transcript

NM_020156.5

Inheritance

—

ClinVar variants

U:47B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr7:7,156,934-7,248,616

External References & Databases

Ensembl (ENSG00000106392)

Transcript & Mutation Effects

hg38 • Region Span ~91.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to C1GALT1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 47

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020156.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			46 clinvar	2 clinvar	1 clinvar	49
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	47	4	1	52

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 128 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020156.5	RefSeq	NP_064541.1	3	MANE Select
ENST00000436587.7	Ensembl	ENSP00000389176.2	3	MANE Select
ENST00000223122.4	Ensembl	ENSP00000223122.2	3	Standard
ENST00000223122.5	Ensembl	ENSP00000223122.2	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

angiogenesis
kidney development
O-glycan processing, core 1
intestinal epithelial cell development

Molecular Function

protein binding
glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase activity
metal ion binding

Cellular Component

Golgi membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000436587
Coding exons: 3
Length: 91718
Individuals with no LoFs: 125728
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125735
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.118	184	189	0.976	0.00000913	2401
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000045	0.000044	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.188

Intolerance Scores

LoFtool: 0.185
RVIS EVS: 0.08
RVIS percentile EVS: 60.09

Essentials

Essential (CRISPR): N
Indispensability pred.: E
Indispensability score: 0.867

Gene Damage Prediction

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