GLB1L3

galactosidase beta 1 like 3, the group of Galactosidases beta

Basic information

Region (hg38): 11:134274245-134319564

Links

ENSG00000166105 ∙ NCBI:112937 ∙ ∙ HGNC:25147 ∙ Uniprot:Q8NCI6 ∙ 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 GLB1L3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLB1L3 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			35	5		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	5	0

Variants in GLB1L3

This is a list of pathogenic ClinVar variants found in the GLB1L3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-134277351-G-T		not specified	Uncertain significance (Sep 27, 2024)
11-134277402-A-G		not specified	Uncertain significance (Jun 10, 2024)
11-134277408-G-A		not specified	Likely benign (Nov 29, 2023)
11-134277415-A-G		not specified	Likely benign (Nov 26, 2024)
11-134277723-C-T		not specified	Uncertain significance (Jun 07, 2024)
11-134277741-G-C		not specified	Uncertain significance (Oct 20, 2023)
11-134277787-C-A		not specified	Uncertain significance (Oct 19, 2024)
11-134277811-C-G		not specified	Uncertain significance (Oct 30, 2023)
11-134277890-T-C		not specified	Uncertain significance (Aug 10, 2024)
11-134281385-C-T		not specified	Uncertain significance (Sep 22, 2023)
11-134281397-A-G		not specified	Uncertain significance (Oct 05, 2023)
11-134282032-G-A		not specified	Uncertain significance (Jun 21, 2023)
11-134282053-G-A		not specified	Uncertain significance (Jun 19, 2024)
11-134282054-G-T		not specified	Uncertain significance (Oct 29, 2024)
11-134282071-C-T		not specified	Uncertain significance (Jun 17, 2024)
11-134282072-G-A		not specified	Uncertain significance (Dec 02, 2022)
11-134282092-A-G		not specified	Uncertain significance (May 03, 2023)
11-134283750-G-C		not specified	Uncertain significance (Sep 22, 2023)
11-134283771-A-G		not specified	Uncertain significance (Sep 13, 2023)
11-134283772-C-A		not specified	Uncertain significance (Jun 02, 2023)
11-134283790-T-C		not specified	Likely benign (May 14, 2024)
11-134283799-T-C		not specified	Uncertain significance (Oct 14, 2021)
11-134292201-C-T		not specified	Uncertain significance (Feb 16, 2023)
11-134293160-A-G		not specified	Uncertain significance (Dec 12, 2022)
11-134293164-G-T		not specified	Uncertain significance (Sep 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLB1L3	protein_coding	protein_coding	ENST00000431683	20	45320

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.73e-23	0.00302	125533	0	214	125747	0.000851

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0424	359	357	1.01	0.0000192	4243
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00219	0.00215
Ashkenazi Jewish	0.00479	0.00477
East Asian	0.00107	0.000979
Finnish	0.000373	0.000370
European (Non-Finnish)	0.000524	0.000501
Middle Eastern	0.00107	0.000979
South Asian	0.000563	0.000555
Other	0.00199	0.00196

dbNSFP

Source: dbNSFP

• Pathway: lactose degradation III (Consensus)

Intolerance Scores

• loftool: 0.305
• rvis_EVS: -0.86
• rvis_percentile_EVS: 10.89

Haploinsufficiency Scores

• pHI: 0.0581
• hipred: N
• hipred_score: 0.139
• ghis: 0.568

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0382

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Glb1l3

Gene ontology

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