GLT1D1

glycosyltransferase 1 domain containing 1, the group of Glycosyl transferases group 1 domain containing

Basic information

Region (hg38): 12:128853426-128984968

Links

ENSG00000151948 ∙ NCBI:144423 ∙ ∙ HGNC:26483 ∙ Uniprot:Q96MS3 ∙ 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 GLT1D1 gene.

• Inborn genetic diseases (14 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLT1D1 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	1

Variants in GLT1D1

This is a list of pathogenic ClinVar variants found in the GLT1D1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-128875933-G-T		not specified	Uncertain significance (Oct 12, 2021)
12-128875944-C-G		not specified	Uncertain significance (Aug 02, 2021)
12-128875945-G-A		not specified	Likely benign (Apr 07, 2022)
12-128875952-A-T		not specified	Uncertain significance (Dec 19, 2022)
12-128876053-C-T		not specified	Uncertain significance (Jan 17, 2023)
12-128888645-G-A		not specified	Uncertain significance (Jul 12, 2023)
12-128888743-A-G		not specified	Uncertain significance (Jan 10, 2023)
12-128899280-C-T		not specified	Uncertain significance (Sep 29, 2022)
12-128945327-T-C		not specified	Uncertain significance (Mar 01, 2023)
12-128947390-G-A		not specified	Uncertain significance (Jul 14, 2021)
12-128947436-G-T		not specified	Uncertain significance (Aug 21, 2023)
12-128957564-C-T		not specified	Uncertain significance (Dec 20, 2023)
12-128957569-T-A		not specified	Uncertain significance (May 25, 2022)
12-128957599-G-A		not specified	Uncertain significance (Aug 04, 2023)
12-128957599-G-C		not specified	Uncertain significance (Nov 13, 2023)
12-128957618-C-A		not specified	Uncertain significance (Jan 03, 2024)
12-128982985-C-T			Benign (Aug 11, 2017)
12-128982986-G-A		not specified	Uncertain significance (Oct 27, 2022)
12-128983040-G-C		not specified	Uncertain significance (Sep 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLT1D1	protein_coding	protein_coding	ENST00000281703	8	131538

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.14e-8	0.257	125674	0	74	125748	0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.000935	144	144	1.00	0.00000776	1717
Missense in Polyphen		15	10.447	1.4358		93
Synonymous	-0.435	61	56.8	1.07	0.00000360	513
Loss of Function	0.425	12	13.7	0.876	8.45e-7	143

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000693	0.000692
Ashkenazi Jewish	0.00198	0.00199
East Asian	0.000435	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000221	0.000220
Middle Eastern	0.000435	0.000435
South Asian	0.0000653	0.0000653
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.547
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.61

Haploinsufficiency Scores

• pHI: 0.144
• hipred: N
• hipred_score: 0.247
• ghis: 0.505

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.173

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Glt1d1

Gene ontology

• Cellular component: extracellular region;cytosol
• Molecular function: transferase activity, transferring glycosyl groups