GLB1L3

protein-coding

galactosidase beta 1 like 3, the group of Galactosidases beta

Gene summary

Predicted to enable beta-galactosidase activity. Predicted to be involved in galactose catabolic process. Predicted to be active in vacuole. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001080407.3

Inheritance

—

ClinVar variants

U:108B:13

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.92

Max pathogenic AF

—

Genomic locus

chr11:134,274,245-134,319,564

External References & Databases

Ensembl (ENSG00000166105)

Transcript & Mutation Effects

hg38 • Region Span ~45.3 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 GLB1L3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 114

not providedTotal: 2

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001080407.3. 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				2 clinvar		2
missense			104 clinvar	11 clinvar		115
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	108	13	0	121

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001080407.3	RefSeq	NP_001073876.2	20	MANE Select
ENST00000431683.7	Ensembl	ENSP00000396615.2	20	MANE Select
ENST00000389887.9	Ensembl	ENSP00000374537.5	10	Standard
ENST00000455971.6	Ensembl	ENSP00000397929.2	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

lactose degradation III

Biological Process

carbohydrate metabolic process

Molecular Function

beta-galactosidase activity

Cellular Component

vacuole

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000431683
Coding exons: 20
Length: 45320
Individuals with no LoFs: 125533
Homozygous LoFs: 0
Heterozygous LoFs: 214
Defined: 125747
p: 0.000851

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0424	359	357	1.01	0.0000192	4243
Missense (PolyPhen)		109	109.9	0.99183		1299
Synonymous	-0.997	159	144	1.11	0.00000853	1226
Loss of Function	0.487	36	39.3	0.916	0.00000211	451

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0011	0.0010	notable
Latino/Admixed American	0.0011	0.0011	notable
Ashkenazi Jewish	0.0048	0.0048	notable
East Asian	0.0011	0.00098	notable
Finnish	0.00037	0.00037	rare
European (Non-Finnish)	0.00052	0.00050	rare
South Asian	0.00056	0.00056	rare
Other	0.0020	0.0020	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.305
RVIS EVS: -0.86
RVIS percentile EVS: 10.89

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0382

Gene Damage Prediction

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