LGALS1

galectin 1, the group of Galectins|Receptor ligands

Basic information

Region (hg38): 22:37675636-37679802

Links

ENSG00000100097

∙ NCBI:3956 ∙ OMIM:150570 ∙ HGNC:6561 ∙ Uniprot:P09382 ∙ 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 LGALS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LGALS1 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			7 clinvar	1 clinvar		8
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	1	0

Variants in LGALS1

This is a list of pathogenic ClinVar variants found in the LGALS1 region.

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

Position	Phenotype	Significance	ClinVar
22-37677049-G-T	not specified	Uncertain significance (Feb 15, 2023)	2484658
22-37677058-G-A	not specified	Uncertain significance (Oct 27, 2023)	3118433
22-37678487-G-A	not specified	Uncertain significance (Aug 02, 2022)	2387257
22-37678547-G-A	not specified	Uncertain significance (May 10, 2022)	2288489
22-37678566-C-G	not specified	Uncertain significance (Dec 15, 2022)	2406786
22-37678571-G-A	not specified	Uncertain significance (Nov 14, 2023)	3118430
22-37678586-G-A	not specified	Uncertain significance (Jan 30, 2024)	3118431
22-37679636-G-A	not specified	Likely benign (Oct 05, 2023)	3118432

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LGALS1	protein_coding	protein_coding	ENST00000215909	4	4199

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00449	0.690	125695	0	20	125715	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.454	73	84.8	0.861	0.00000498	886
Missense in Polyphen		17	21.1	0.80568		259
Synonymous	0.171	36	37.3	0.964	0.00000261	259
Loss of Function	0.667	4	5.72	0.699	2.46e-7	62

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000307	0.0000307
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000710	0.0000704
Middle Eastern	0.0000544	0.0000544
South Asian	0.000294	0.000294
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Lectin that binds beta-galactoside and a wide array of complex carbohydrates. Plays a role in regulating apoptosis, cell proliferation and cell differentiation. Inhibits CD45 protein phosphatase activity and therefore the dephosphorylation of Lyn kinase. Strong inducer of T-cell apoptosis. {ECO:0000269|PubMed:14617626, ECO:0000269|PubMed:18796645, ECO:0000269|PubMed:19497882, ECO:0000269|PubMed:24945728}.;
Pathway: Regulation of Ras family activation;Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);Validated targets of C-MYC transcriptional repression (Consensus)

Recessive Scores

pRec: 0.621

Intolerance Scores

loftool: 0.570
rvis_EVS: -0.03
rvis_percentile_EVS: 51.4

Haploinsufficiency Scores

pHI: 0.705
hipred: Y
hipred_score: 0.506
ghis: 0.515

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Lgals1
Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); taste/olfaction phenotype; muscle phenotype; craniofacial phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);

Gene ontology

Biological process: plasma cell differentiation;apoptotic process;negative regulation of cell-substrate adhesion;negative regulation of neuron projection development;T cell costimulation;positive regulation of erythrocyte aggregation;response to isolation stress;response to drug;regulation of apoptotic process;positive regulation of I-kappaB kinase/NF-kappaB signaling;post-translational protein modification;cellular protein metabolic process;myoblast differentiation;positive regulation of viral entry into host cell;response to axon injury;cellular response to glucose stimulus;cellular response to organic cyclic compound;positive regulation of dendritic cell differentiation
Cellular component: extracellular region;extracellular space;nucleus;cytoplasm;endoplasmic reticulum lumen;cytosol;cell surface;collagen-containing extracellular matrix;extracellular exosome
Molecular function: RNA binding;protein binding;lactose binding;protein homodimerization activity;laminin binding