LGALSL

galectin like

Basic information

Region (hg38): 2:64453968-64461381

Links

ENSG00000119862 ∙ NCBI:29094 ∙ OMIM:617902 ∙ HGNC:25012 ∙ Uniprot:Q3ZCW2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• amyotrophic lateral sclerosis (Limited), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LGALSL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LGALSL 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					1	1
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	1

Variants in LGALSL

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

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

Position	Type	Phenotype	Significance	ClinVar
2-64454559-T-C		not specified	Uncertain significance (Apr 17, 2023)
2-64454579-G-A		not specified	Uncertain significance (Dec 14, 2023)
2-64455350-G-A		not specified	Uncertain significance (Jun 24, 2022)
2-64455393-C-T		not specified	Uncertain significance (Mar 18, 2024)
2-64455602-G-A		not specified	Uncertain significance (Sep 13, 2023)
2-64455610-A-G		not specified	Uncertain significance (Dec 14, 2021)
2-64456364-A-G		not specified	Uncertain significance (Dec 20, 2023)
2-64456416-A-T		not specified	Uncertain significance (May 31, 2022)
2-64458296-T-C			Benign (Mar 29, 2018)
2-64458352-A-G		not specified	Uncertain significance (Mar 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LGALSL	protein_coding	protein_coding	ENST00000238875	5	7413

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0184	0.904	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.989	70	97.5	0.718	0.00000524	1122
Missense in Polyphen		12	27.016	0.44418		340
Synonymous	0.148	35	36.1	0.969	0.00000204	331
Loss of Function	1.49	4	8.77	0.456	5.29e-7	97

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Does not bind lactose, and may not bind carbohydrates. {ECO:0000269|PubMed:18320588, ECO:0000269|PubMed:18433051}.

Recessive Scores

• pRec: 0.123

Intolerance Scores

• rvis_EVS: 0.13
• rvis_percentile_EVS: 62.74

Haploinsufficiency Scores

• pHI: 0.150
• hipred: Y
• hipred_score: 0.592
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lgalsl

Gene ontology

• Molecular function: protein binding;carbohydrate binding