GLB1L2

galactosidase beta 1 like 2, the group of Galactosidases beta

Basic information

Region (hg38): 11:134331873-134378341

Links

ENSG00000149328 ∙ NCBI:89944 ∙ ∙ HGNC:25129 ∙ Uniprot:Q8IW92 ∙ 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 GLB1L2 gene.

• Inborn genetic diseases (33 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLB1L2 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			31	2	1	34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	31	2	1

Variants in GLB1L2

This is a list of pathogenic ClinVar variants found in the GLB1L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-134332083-C-T		not specified	Uncertain significance (Jun 06, 2022)
11-134332098-A-G			Benign (Oct 09, 2017)
11-134332111-T-A		not specified	Uncertain significance (Oct 25, 2023)
11-134342782-C-T		not specified	Likely benign (Feb 28, 2023)
11-134342794-C-G		not specified	Uncertain significance (Feb 22, 2023)
11-134342818-G-T		not specified	Uncertain significance (Dec 27, 2022)
11-134342843-C-G		not specified	Uncertain significance (Mar 07, 2024)
11-134342853-G-C		not specified	Uncertain significance (Dec 27, 2022)
11-134342926-G-A		not specified	Uncertain significance (Jun 09, 2022)
11-134342941-A-T		not specified	Uncertain significance (Jun 24, 2022)
11-134344408-T-A		not specified	Uncertain significance (Oct 06, 2023)
11-134345068-T-C		not specified	Uncertain significance (May 01, 2022)
11-134345113-C-T		not specified	Uncertain significance (Mar 01, 2023)
11-134345116-G-A		not specified	Uncertain significance (Nov 09, 2023)
11-134345120-G-A		not specified	Uncertain significance (Jul 06, 2021)
11-134356308-G-T		not specified	Uncertain significance (Oct 24, 2023)
11-134356324-T-G		not specified	Uncertain significance (Aug 30, 2021)
11-134356338-A-C		not specified	Uncertain significance (Dec 27, 2023)
11-134356378-G-T		not specified	Uncertain significance (Dec 02, 2022)
11-134356379-C-T		not specified	Uncertain significance (Dec 02, 2022)
11-134359063-C-A		not specified	Uncertain significance (Jul 13, 2022)
11-134359106-A-G		not specified	Uncertain significance (Oct 26, 2021)
11-134359132-G-T		not specified	Uncertain significance (Jun 27, 2022)
11-134364332-G-C		not specified	Uncertain significance (Dec 03, 2021)
11-134364334-C-T		not specified	Uncertain significance (Jun 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLB1L2	protein_coding	protein_coding	ENST00000535456	19	46468

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.50e-19	0.0389	125127	3	618	125748	0.00247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.170	379	370	1.02	0.0000211	4131
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00311	0.00311
Ashkenazi Jewish	0.00486	0.00487
East Asian	0.0158	0.0158
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000538	0.000536
Middle Eastern	0.0158	0.0158
South Asian	0.00386	0.00376
Other	0.00195	0.00196

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.88
• rvis_percentile_EVS: 10.5

Haploinsufficiency Scores

• pHI: 0.210
• hipred: N
• hipred_score: 0.162
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.123

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Glb1l2
• Phenotype: hematopoietic system phenotype; immune system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: carbohydrate metabolic process
• Cellular component: extracellular region;vacuole
• Molecular function: beta-galactosidase activity