MGAT4C

MGAT4 family member C, the group of Mannosyl-glycoprotein N-acetylglucosaminyltransferases

Basic information

Region (hg38): 12:85955666-86838904

Links

ENSG00000182050 ∙ NCBI:25834 ∙ OMIM:607385 ∙ HGNC:30871 ∙ Uniprot:Q9UBM8 ∙ 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 MGAT4C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MGAT4C 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		17
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	1	1

Variants in MGAT4C

This is a list of pathogenic ClinVar variants found in the MGAT4C region.

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

Position	Type	Phenotype	Significance	ClinVar
12-85979381-T-C		not specified	Conflicting classifications of pathogenicity (Oct 26, 2022)
12-85979395-C-T		not specified	Likely benign (May 27, 2022)
12-85979455-C-T		not specified	Uncertain significance (Feb 13, 2023)
12-85979474-T-C		not specified	Uncertain significance (Dec 21, 2023)
12-85979478-G-A			Benign (May 03, 2018)
12-85979490-A-T		not specified	Uncertain significance (Mar 29, 2022)
12-85979497-G-T		not specified	Uncertain significance (Aug 02, 2021)
12-85979525-G-A		not specified	Uncertain significance (May 23, 2023)
12-85980001-G-A		not specified	Uncertain significance (Mar 01, 2023)
12-85980130-C-A		not specified	Uncertain significance (Feb 10, 2023)
12-85980212-T-A		not specified	Uncertain significance (Oct 26, 2022)
12-85980280-C-T		not specified	Uncertain significance (Jan 26, 2023)
12-85980289-G-T		not specified	Uncertain significance (Apr 20, 2023)
12-85983615-C-A		not specified	Uncertain significance (Jan 02, 2024)
12-85983615-C-T		not specified	Uncertain significance (Jun 07, 2024)
12-85983664-C-T		not specified	Uncertain significance (Nov 20, 2023)
12-85989419-A-G		not specified	Uncertain significance (Jul 14, 2021)
12-85989450-C-A		not specified	Uncertain significance (Oct 26, 2022)
12-85989480-G-A		not specified	Uncertain significance (Sep 17, 2021)
12-85989538-T-G		not specified	Uncertain significance (Dec 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MGAT4C	protein_coding	protein_coding	ENST00000604798	3	860166

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000662	0.981	125683	0	25	125708	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.13	198	248	0.798	0.0000124	3163
Missense in Polyphen		60	91.775	0.65377		1165
Synonymous	1.33	67	82.3	0.814	0.00000372	874
Loss of Function	2.07	8	17.3	0.462	9.48e-7	242

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000593	0.0000593
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.0000551	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000163	0.000158
Middle Eastern	0.0000551	0.0000544
South Asian	0.0000328	0.0000327
Other	0.000169	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Glycosyltransferase that participates in the transfer of N-acetylglucosamine (GlcNAc) to the core mannose residues of N- linked glycans. Catalyzes the formation of the GlcNAcbeta1-4 branch on the GlcNAcbeta1-2Manalpha1-3 arm of the core structure of N-linked glycans. Essential for the production of tri- and tetra-antennary N-linked sugar chains (By similarity). Does not catalyze the transfer of GlcNAc to the Manalpha1-6 arm to form GlcNAcBeta1-4Manalpha1-6 linkage ('GnT-VI' activity). {ECO:0000250, ECO:0000269|PubMed:10962001}.
• Pathway: N-Glycan biosynthesis - Homo sapiens (human);Post-translational protein modification;N-Glycan antennae elongation;N-glycan antennae elongation in the medial/trans-Golgi;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;N-Glycan biosynthesis (Consensus)

Recessive Scores

• pRec: 0.373

Intolerance Scores

• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.82

Haploinsufficiency Scores

• pHI: 0.382
• hipred: N
• hipred_score: 0.458
• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.427

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mgat4c

Gene ontology

• Biological process: protein glycosylation
• Cellular component: Golgi membrane;integral component of membrane
• Molecular function: alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity;metal ion binding