GLB1L2

protein-coding

galactosidase beta 1 like 2, 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, Jun 2026]

MANE transcript

NM_001370461.1

Inheritance

—

ClinVar variants

U:120B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.83

Max pathogenic AF

—

Genomic locus

chr11:134,331,988-134,378,341

External References & Databases

Ensembl (ENSG00000149328)

Transcript & Mutation Effects

hg38 • Region Span ~46.4 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 GLB1L2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 113

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001370461.1. 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						0
missense			114 clinvar	5 clinvar	1 clinvar	120
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	120	5	1	126

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001370461.1	RefSeq	NP_001357390.1	19	MANE Select
ENST00000535456.7	Ensembl	ENSP00000444628.1	19	MANE Select
NM_001370460.1	RefSeq	NP_001357389.1	20	Standard
NM_001370462.1	RefSeq	NP_001357391.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

carbohydrate metabolic process

Molecular Function

beta-galactosidase activity

Cellular Component

extracellular region
vacuole

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000535456
Coding exons: 19
Length: 46468
Individuals with no LoFs: 125127
Homozygous LoFs: 3
Heterozygous LoFs: 618
Defined: 125748
p: 0.00247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.170	379	370	1.02	0.0000211	4131
Missense (PolyPhen)		113	115.31	0.97997		1274
Synonymous	0.587	145	154	0.940	0.00000975	1230
Loss of Function	0.954	32	38.4	0.834	0.00000194	426

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00068	0.00068	rare
Latino/Admixed American	0.0024	0.0024	notable
Ashkenazi Jewish	0.0049	0.0049	notable
East Asian	0.016	0.016	notable
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00054	0.00054	rare
South Asian	0.0039	0.0038	notable
Other	0.0020	0.0020	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: -0.88
RVIS percentile EVS: 10.5

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.123

Gene Damage Prediction

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