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.

• not_specified (29 variants)
• not_provided (6 variants)
• Amyotrophic_lateral_sclerosis (2 variants)
• Frontotemporal_dementia (1 variants)
• GLT8D1-related_disorder (1 variants)

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. These statistics are base on transcript: NM_000018446.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			30	1	1	32
nonsense						0
start loss						0
frameshift		1				1
splice donor/acceptor (+/-2bp)						0
Total	0	1	30	2	1

Highest pathogenic variant AF is 0.000002055459

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