GLT8D1

glycosyltransferase 8 domain containing 1, the group of Glycosyltransferase family 8

Basic information

Region (hg38): 3:52694486-52706032

Links

ENSG00000016864 ∙ NCBI:55830 ∙ OMIM:618399 ∙ HGNC:24870 ∙ Uniprot:Q68CQ7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• familial amyotrophic lateral sclerosis (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GLT8D1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLT8D1 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			10		1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					6	6
Total	0	0	10	1	7

Variants in GLT8D1

This is a list of pathogenic ClinVar variants found in the GLT8D1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-52694788-C-T			Benign (May 12, 2021)
3-52694853-T-C		Amyotrophic lateral sclerosis	Uncertain significance (Jan 01, 2022)
3-52694929-A-T		not specified	Uncertain significance (Sep 23, 2023)
3-52694933-G-A		not specified	Conflicting classifications of pathogenicity (Sep 01, 2023)
3-52694943-C-T		not specified	Uncertain significance (Aug 07, 2024)
3-52694988-T-C		not specified	Uncertain significance (Nov 21, 2024)
3-52694996-T-G		not specified	Uncertain significance (Aug 04, 2023)
3-52695040-C-A			Uncertain significance (Jul 01, 2024)
3-52695285-C-A		not specified	Uncertain significance (May 23, 2023)
3-52695427-T-C		not specified	Uncertain significance (Dec 08, 2023)
3-52695449-G-C		not specified	Uncertain significance (Sep 20, 2023)
3-52695550-C-A		not specified	Uncertain significance (Dec 21, 2023)
3-52695669-T-TTAAA			Benign (May 12, 2021)
3-52695944-C-T			Benign (May 04, 2021)
3-52696251-T-C		not specified	Uncertain significance (Nov 20, 2024)
3-52696595-GT-G		Frontotemporal dementia	Likely pathogenic (Feb 02, 2022)
3-52696610-T-C		not specified	Uncertain significance (Oct 12, 2024)
3-52696683-T-G			Benign (May 12, 2021)
3-52697536-TCTC-T			Benign (May 21, 2021)
3-52697582-T-C			Benign (May 12, 2021)
3-52697722-G-A		not specified	Uncertain significance (May 16, 2023)
3-52697725-G-A		not specified	Uncertain significance (Oct 05, 2023)
3-52697862-T-C		not specified	Uncertain significance (Mar 19, 2024)
3-52697884-G-T		GLT8D1-related disorder	Likely benign (Nov 01, 2023)
3-52700564-CT-C			Benign (May 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLT8D1	protein_coding	protein_coding	ENST00000407584	9	11544

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.13e-8	0.552	125692	0	56	125748	0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.621	179	204	0.878	0.0000104	2429
Missense in Polyphen		70	87.696	0.79822		1050
Synonymous	0.918	61	70.8	0.861	0.00000354	711
Loss of Function	1.10	15	20.4	0.737	0.00000115	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000420	0.000420
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.000323	0.000323
European (Non-Finnish)	0.000211	0.000211
Middle Eastern	0.0000544	0.0000544
South Asian	0.000294	0.000294
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.939
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.35

Haploinsufficiency Scores

• pHI: 0.0887
• hipred: N
• hipred_score: 0.426
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.577

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Glt8d1
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); normal phenotype

Gene ontology

• Cellular component: Golgi apparatus;membrane;integral component of membrane
• Molecular function: transferase activity, transferring glycosyl groups