GLT6D1

protein-coding

glycosyltransferase 6 domain containing 1, the group of Glycosyltransferase family 6

Gene summary

The GT6 glycosyltransferases gene family, which includes the ABO blood group (ABO; MIM 110300) and GLT6D1, shows a complex evolution pattern, with multiple events of gain and loss in different mammal species. In humans, the ABO gene is considered the sole functional member, although the O allele is null and is fixed in certain populations (summary by Casals et al. (2009) [PubMed 19218399]).[supplied by OMIM, Jan 2011]

Previous symbols:

GLTDC1

MANE transcript

NM_182974.3

Inheritance

—

ClinVar variants

U:58B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.38

Max pathogenic AF

—

Genomic locus

chr9:135,623,648-135,639,540

External References & Databases

Ensembl (ENSG00000204007)

Transcript & Mutation Effects

hg38 • Region Span ~15.9 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 GLT6D1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 64

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182974.3. 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			58 clinvar	6 clinvar		64
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	58	6	1	65

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182974.3	RefSeq	NP_892019.2	4	MANE Select
ENST00000371763.6	Ensembl	ENSP00000360829.1	4	MANE Select
ENST00000851048.1	Ensembl	ENSP00000521117.1	4	Standard
ENST00000851049.1	Ensembl	ENSP00000521118.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

carbohydrate metabolic process
lipid glycosylation

Molecular Function

transferase activity, transferring glycosyl groups
transferase activity, transferring hexosyl groups

Cellular Component

Golgi apparatus
integral component of membrane
vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371763
Coding exons: 4
Length: 15885
Individuals with no LoFs: 124783
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 124787
p: 0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.907	195	162	1.20	0.00000932	1825
Missense (PolyPhen)		58	50.946	1.1385		588
Synonymous	0.153	64	65.6	0.976	0.00000425	510
Loss of Function	1.34	2	5.33	0.375	2.26e-7	65

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000030	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0889

Intolerance Scores

LoFtool: 0.666
RVIS EVS: 1.33
RVIS percentile EVS: 94.17

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.204

Gene Damage Prediction

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