GLB1L

galactosidase beta 1 like, the group of Galactosidases beta

Basic information

Region (hg38): 2:219236598-219245478

Links

ENSG00000163521 ∙ NCBI:79411 ∙ ∙ HGNC:28129 ∙ Uniprot:Q6UWU2 ∙ 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 GLB1L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLB1L 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			44	2	1	47
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	44	2	1

Variants in GLB1L

This is a list of pathogenic ClinVar variants found in the GLB1L region.

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

Position	Type	Phenotype	Significance	ClinVar
2-219237136-T-C			Benign (Jul 16, 2018)
2-219237170-T-C		not specified	Uncertain significance (Feb 23, 2023)
2-219237173-G-C		not specified	Uncertain significance (Sep 15, 2021)
2-219237206-G-C		not specified	Uncertain significance (Sep 16, 2021)
2-219237313-C-T		not specified	Uncertain significance (Aug 04, 2024)
2-219237549-A-G		not specified	Uncertain significance (Oct 01, 2024)
2-219237555-C-A		not specified	Uncertain significance (Jun 18, 2021)
2-219237627-T-C		not specified	Uncertain significance (Jul 05, 2023)
2-219237673-A-G		not specified	Uncertain significance (May 01, 2024)
2-219237703-C-T		not specified	Uncertain significance (Jan 18, 2022)
2-219237836-C-T		not specified	Uncertain significance (Jan 30, 2025)
2-219237870-T-C		not specified	Uncertain significance (Oct 23, 2024)
2-219237884-T-C		not specified	Uncertain significance (Jan 04, 2024)
2-219237929-A-T		not specified	Uncertain significance (Dec 25, 2024)
2-219237932-T-C		not specified	Uncertain significance (Sep 12, 2023)
2-219237935-C-T		not specified	Uncertain significance (Apr 04, 2023)
2-219237953-A-C		not specified	Uncertain significance (Nov 13, 2024)
2-219238261-T-C		not specified	Uncertain significance (Jan 20, 2023)
2-219238266-T-C		not specified	Uncertain significance (Dec 06, 2021)
2-219238544-C-T		not specified	Likely benign (May 04, 2022)
2-219238560-C-A		not specified	Uncertain significance (Feb 18, 2025)
2-219239111-A-G		not specified	Uncertain significance (Sep 27, 2024)
2-219239114-G-A		not specified	Uncertain significance (Aug 12, 2024)
2-219239116-A-T		not specified	Uncertain significance (Nov 21, 2024)
2-219239151-T-C		not specified	Uncertain significance (Dec 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLB1L	protein_coding	protein_coding	ENST00000295759	16	8873

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.69e-13	0.723	125661	0	87	125748	0.000346

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.201	381	370	1.03	0.0000204	4262
Missense in Polyphen		177	171.4	1.0327		1947
Synonymous	0.0347	142	143	0.996	0.00000765	1309
Loss of Function	1.71	25	36.1	0.692	0.00000187	398

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000597	0.000597
Ashkenazi Jewish	0.00	0.00
East Asian	0.000602	0.000598
Finnish	0.000416	0.000416
European (Non-Finnish)	0.000371	0.000369
Middle Eastern	0.000602	0.000598
South Asian	0.000296	0.000294
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable glycosyl hydrolase. {ECO:0000305}.
• Pathway: Metabolism of carbohydrates;Keratan sulfate degradation;Keratan sulfate/keratin metabolism;Metabolism of lipids;HS-GAG degradation;Heparan sulfate/heparin (HS-GAG) metabolism;Glycosaminoglycan metabolism;Glycosphingolipid biosynthesis - ganglioseries;Metabolism;Glycosphingolipid metabolism;Galactose metabolism;Glycerophospholipid metabolism;Glycosphingolipid metabolism;Sphingolipid metabolism (Consensus)

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.181
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.85

Haploinsufficiency Scores

• pHI: 0.298
• hipred: N
• hipred_score: 0.167
• ghis: 0.512

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.439

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Glb1l

Gene ontology

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