MGAT4D

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

Basic information

Region (hg38): 4:140442262-140498377

Links

ENSG00000205301

∙ NCBI:152586 ∙ OMIM:610310 ∙ HGNC:43619 ∙ Uniprot:A6NG13 ∙ 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 MGAT4D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MGAT4D 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MGAT4D	protein_coding	protein_coding	ENST00000503109	11	56116

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000408	0.622	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.995	90	121	0.745	0.00000573	2467
Missense in Polyphen		25	38.54	0.64868		881
Synonymous	1.89	28	44.0	0.637	0.00000212	635
Loss of Function	0.933	10	13.7	0.728	6.89e-7	288

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Function: FUNCTION: May play a role in male spermatogenesis. In vitro acts as inhibitor of MGAT1 activity causing cell surface proteins to carry mainly high mannose N-glycans. The function is mediated by its lumenal domain and occurs specifically in the Golgi. A catalytic glucosyltransferase activity is not detected. May be involved in regulation of Sertoli-germ cell interactions during specific stages of spermatogenesis. {ECO:0000250|UniProtKB:Q9D4R2}.;
Pathway: N-Glycan biosynthesis - Homo sapiens (human) (Consensus)

Mouse Genome Informatics

Gene name: Mgat4d
Phenotype: immune system phenotype; digestive/alimentary phenotype; hematopoietic system phenotype;

Gene ontology

Biological process: spermatogenesis;cell differentiation;negative regulation of protein glycosylation
Cellular component: Golgi membrane;endoplasmic reticulum membrane;endoplasmic reticulum-Golgi intermediate compartment;Golgi stack;integral component of membrane
Molecular function: transferase activity, transferring glycosyl groups