GLT8D2

protein-coding

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

Gene summary

Predicted to enable UDP-glycosyltransferase activity. Predicted to be located in membrane. Predicted to be active in Golgi apparatus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001384711.1

Inheritance

—

ClinVar variants

U:44

Top phenotype

Marfanoid habitus and intellectual disability

gnomAD constraint

pLI —, LoF o/e 1.01

Max pathogenic AF

—

Genomic locus

chr12:103,988,987-104,064,183

External References & Databases

Ensembl (ENSG00000120820)

Transcript & Mutation Effects

hg38 • Region Span ~75.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GLT8D2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 40

Marfanoid habitus and intellectual disabilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001384711.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			43 clinvar			43
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	44	0	0	44

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 58 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001384711.1	RefSeq	NP_001371640.1	9	MANE Select
ENST00000360814.9	Ensembl	ENSP00000354053.4	9	MANE Select
NM_001316967.2	RefSeq	NP_001303896.1	9	Standard
NM_001384712.1	RefSeq	NP_001371641.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

transferase activity, transferring glycosyl groups

Cellular Component

Golgi apparatus
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000360814
Coding exons: 9
Length: 75200
Individuals with no LoFs: 125631
Homozygous LoFs: 0
Heterozygous LoFs: 117
Defined: 125748
p: 0.000465

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.457	178	196	0.908	0.0000102	2299
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0.0014	0.0014	notable
East Asian	0.00038	0.00038	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00039	0.00039	rare
South Asian	0.0012	0.0012	notable
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.918
RVIS EVS: -0.11
RVIS percentile EVS: 45.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.356

Gene Damage Prediction

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