GLT6D1

glycosyltransferase 6 domain containing 1, the group of Glycosyltransferase family 6

Basic information

Region (hg38): 9:135623648-135639540

Previous symbols: [ "GLTDC1" ]

Links

ENSG00000204007 ∙ NCBI:360203 ∙ OMIM:613699 ∙ HGNC:23671 ∙ Uniprot:Q7Z4J2 ∙ 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 GLT6D1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLT6D1 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			22	3		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	3	1

Variants in GLT6D1

This is a list of pathogenic ClinVar variants found in the GLT6D1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-135624146-G-C		not specified	Uncertain significance (Dec 12, 2022)
9-135624182-C-G		not specified	Uncertain significance (Jan 08, 2024)
9-135624201-T-C		not specified	Uncertain significance (Sep 30, 2024)
9-135624218-T-C		not specified	Likely benign (Jun 11, 2024)
9-135624236-A-G		not specified	Uncertain significance (Jan 24, 2024)
9-135624293-G-A		not specified	Uncertain significance (Dec 07, 2023)
9-135624356-A-C		not specified	Uncertain significance (Aug 28, 2024)
9-135624362-G-A		not specified	Uncertain significance (Aug 08, 2024)
9-135624362-G-C		not specified	Uncertain significance (Nov 10, 2022)
9-135624373-C-G		not specified	Uncertain significance (May 17, 2023)
9-135624381-C-T		not specified	Uncertain significance (Mar 15, 2024)
9-135624443-A-G		not specified	Uncertain significance (Oct 12, 2024)
9-135624455-A-G		not specified	Uncertain significance (Jun 30, 2024)
9-135624469-G-C		not specified	Uncertain significance (Mar 20, 2023)
9-135624474-T-C		not specified	Uncertain significance (Feb 14, 2023)
9-135624493-A-T		not specified	Uncertain significance (Apr 17, 2024)
9-135624512-G-A		not specified	Uncertain significance (Sep 14, 2021)
9-135624534-A-C		not specified	Uncertain significance (Jun 11, 2021)
9-135624539-C-T		not specified	Uncertain significance (Oct 06, 2021)
9-135624553-C-G		not specified	Uncertain significance (Mar 28, 2024)
9-135624555-C-G		not specified	Likely benign (Sep 15, 2021)
9-135624647-G-A		not specified	Likely benign (Nov 13, 2024)
9-135624653-A-G		not specified	Uncertain significance (Sep 14, 2021)
9-135626076-T-C		not specified	Uncertain significance (Feb 02, 2022)
9-135626079-C-T		not specified	Uncertain significance (Sep 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLT6D1	protein_coding	protein_coding	ENST00000371763	4	15885

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.120	0.788	124783	0	4	124787	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.907	195	162	1.20	0.00000932	1825
Missense in Polyphen		58	50.946	1.1385		588
Synonymous	0.153	64	65.6	0.976	0.00000425	510
Loss of Function	1.34	2	5.33	0.375	2.26e-7	65

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000298	0.0000298
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0889

Intolerance Scores

• loftool: 0.666
• rvis_EVS: 1.33
• rvis_percentile_EVS: 94.17

Haploinsufficiency Scores

• pHI: 0.0480
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.204

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Glt6d1

Gene ontology

• Biological process: carbohydrate metabolic process;lipid glycosylation
• Cellular component: Golgi apparatus;integral component of membrane;vesicle
• Molecular function: transferase activity, transferring glycosyl groups;transferase activity, transferring hexosyl groups