GLT8D2

glycosyltransferase 8 domain containing 2, the group of Glycosyltransferase family 8

Basic information

Region (hg38): 12:103988986-104064183

Links

ENSG00000120820 ∙ NCBI:83468 ∙ ∙ HGNC:24890 ∙ Uniprot:Q9H1C3 ∙ 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 GLT8D2 gene.

• Inborn genetic diseases (13 variants)
• Marfanoid habitus and intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLT8D2 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			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	0

Variants in GLT8D2

This is a list of pathogenic ClinVar variants found in the GLT8D2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-103989553-G-A		not specified	Uncertain significance (May 16, 2022)
12-103993415-G-C		not specified	Uncertain significance (Jun 07, 2023)
12-103993487-C-G		Marfanoid habitus and intellectual disability	Uncertain significance (-)
12-103993504-C-G		not specified	Uncertain significance (Jul 20, 2021)
12-103994350-A-G		not specified	Uncertain significance (Aug 04, 2023)
12-103994360-C-T		not specified	Uncertain significance (Nov 13, 2023)
12-103994469-C-G		not specified	Uncertain significance (Dec 01, 2022)
12-103994470-T-C		not specified	Uncertain significance (Jun 21, 2021)
12-103994471-T-C		not specified	Uncertain significance (Dec 14, 2021)
12-103994474-G-A		not specified	Uncertain significance (Nov 14, 2023)
12-103994497-G-A		not specified	Uncertain significance (Nov 22, 2023)
12-103996823-G-T		not specified	Uncertain significance (Mar 22, 2023)
12-103997458-A-C		not specified	Uncertain significance (Dec 06, 2021)
12-103997501-A-G		not specified	Uncertain significance (Sep 01, 2021)
12-103999400-C-G		not specified	Uncertain significance (Mar 29, 2022)
12-104003156-C-T		not specified	Uncertain significance (Jan 31, 2024)
12-104003225-G-C		not specified	Uncertain significance (May 26, 2022)
12-104003261-A-G		not specified	Uncertain significance (Feb 28, 2023)
12-104015060-A-G		not specified	Uncertain significance (Feb 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLT8D2	protein_coding	protein_coding	ENST00000360814	9	75200

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.73e-14	0.0145	125631	0	117	125748	0.000465

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.457	178	196	0.908	0.0000102	2299
Missense in Polyphen		66	72.968	0.90451		868
Synonymous	1.55	59	76.2	0.775	0.00000448	645
Loss of Function	-0.0552	21	20.7	1.01	0.00000120	224

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000456	0.000456
Ashkenazi Jewish	0.00139	0.00139
East Asian	0.000381	0.000381
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000389	0.000387
Middle Eastern	0.000381	0.000381
South Asian	0.00124	0.00124
Other	0.000661	0.000652

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.918
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.26

Haploinsufficiency Scores

• pHI: 0.121
• hipred: N
• hipred_score: 0.350
• ghis: 0.620

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.356

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Glt8d2
• Phenotype: immune system phenotype; skeleton phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

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