LGALS2

galectin 2, the group of Galectins

Basic information

Region (hg38): 22:37570248-37582616

Links

ENSG00000100079 ∙ NCBI:3957 ∙ OMIM:150571 ∙ HGNC:6562 ∙ Uniprot:P05162 ∙ 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 LGALS2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LGALS2 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		1	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	1

Variants in LGALS2

This is a list of pathogenic ClinVar variants found in the LGALS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-37570361-G-A		not specified	Uncertain significance (Dec 17, 2023)
22-37570402-G-A			Benign (Apr 24, 2018)
22-37570622-T-C		not specified	Uncertain significance (Dec 15, 2023)
22-37570628-C-G		not specified	Uncertain significance (Mar 11, 2024)
22-37570647-A-G		LGALS2-related disorder	Likely benign (Mar 03, 2020)
22-37570658-A-G		not specified	Uncertain significance (May 31, 2023)
22-37570662-T-C		not specified	Uncertain significance (Jul 08, 2022)
22-37570671-C-T		not specified	Uncertain significance (Mar 28, 2024)
22-37570680-G-A		not specified	Uncertain significance (Oct 26, 2022)
22-37570721-A-G		not specified	Uncertain significance (Aug 02, 2021)
22-37576621-G-A		Myocardial infarction, susceptibility to	risk factor (May 06, 2004)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LGALS2	protein_coding	protein_coding	ENST00000215886	4	12369

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0202	0.760	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.363	83	74.2	1.12	0.00000396	879
Missense in Polyphen		31	25.446	1.2183		331
Synonymous	-0.312	34	31.8	1.07	0.00000195	242
Loss of Function	0.856	3	5.08	0.590	2.17e-7	60

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000616	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This protein binds beta-galactoside. Its physiological function is not yet known.

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.742
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.49

Haploinsufficiency Scores

• pHI: 0.121
• hipred: N
• hipred_score: 0.146
• ghis: 0.392

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.414

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lgals2
• Phenotype: cellular phenotype; immune system phenotype; digestive/alimentary phenotype; hematopoietic system phenotype

Zebrafish Information Network

• Gene name: lgals2a
• Affected structure: muscle
• Phenotype tag: abnormal
• Phenotype quality: disorganized

Gene ontology

• Molecular function: protein binding;galactoside binding;carbohydrate binding