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.

• not_specified (79 variants)
• not_provided (3 variants)

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. These statistics are base on transcript: NM_001286423.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			76	3	1	80
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	76	4	1

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