GCNT7

glucosaminyl (N-acetyl) transferase family member 7, the group of Glucosaminyl (N-acetyl) transferases/xylosyltransferases

Basic information

Region (hg38): 20:56491492-56525925

Previous symbols: [ "C20orf105" ]

Links

ENSG00000124091 ∙ NCBI:140687 ∙ ∙ HGNC:16099 ∙ Uniprot:Q6ZNI0 ∙ 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 GCNT7 gene.

• Inborn genetic diseases (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GCNT7 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			4			4
Total	0	0	4	0	0

Variants in GCNT7

This is a list of pathogenic ClinVar variants found in the GCNT7 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-56513339-G-A		not specified	Uncertain significance (Jun 28, 2022)
20-56513355-A-G		not specified	Uncertain significance (Sep 15, 2021)
20-56513378-G-A		not specified	Uncertain significance (Jan 04, 2022)
20-56513390-A-G		not specified	Uncertain significance (May 13, 2024)
20-56516948-C-T		not specified	Uncertain significance (Aug 17, 2021)
20-56516977-G-T		not specified	Uncertain significance (Jan 04, 2024)
20-56516985-T-A		not specified	Uncertain significance (Mar 29, 2022)
20-56517133-C-T		not specified	Uncertain significance (Aug 17, 2022)
20-56517185-G-C		not specified	Uncertain significance (Jun 16, 2024)
20-56518145-G-T		not specified	Uncertain significance (Apr 25, 2022)
20-56518152-G-A		not specified	Uncertain significance (Jun 18, 2021)
20-56518158-A-G		not specified	Uncertain significance (Aug 08, 2023)
20-56518228-C-T		not specified	Uncertain significance (Apr 09, 2024)
20-56518233-C-T		not specified	Uncertain significance (Mar 15, 2024)
20-56524816-C-T		not specified	Uncertain significance (Jun 24, 2022)
20-56524828-C-T		not specified	Likely benign (Dec 08, 2023)
20-56524906-A-G		not specified	Uncertain significance (Feb 27, 2023)
20-56524941-C-T		not specified	Uncertain significance (Jan 04, 2022)
20-56525873-C-T		not specified	Uncertain significance (Jul 13, 2021)
20-56525894-A-G		not specified	Uncertain significance (Mar 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GCNT7	protein_coding	protein_coding	ENST00000243913	3	34434

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0873	0.875	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.703	141	167	0.847	0.00000908	2031
Missense in Polyphen		48	55.377	0.86679		750
Synonymous	0.940	52	61.4	0.847	0.00000373	572
Loss of Function	1.77	3	8.62	0.348	4.83e-7	107

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: Glycosyltransferase. {ECO:0000250}.
• Pathway: 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)

Haploinsufficiency Scores

• pHI: 0.0328
• ghis: 0.404

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0806

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gcnt7

Gene ontology

• Biological process: protein glycosylation
• Cellular component: Golgi membrane;integral component of membrane
• Molecular function: acetylglucosaminyltransferase activity