LGALS3BP

galectin 3 binding protein, the group of Receptor ligands|Scavenger receptor cysteine rich domain containing|BTB domain containing

Basic information

Region (hg38): 17:78971238-78979947

Links

ENSG00000108679 ∙ NCBI:3959 ∙ OMIM:600626 ∙ HGNC:6564 ∙ Uniprot:Q08380 ∙ 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 LGALS3BP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LGALS3BP 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	4	5
missense			29	3	1	33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	4	5

Variants in LGALS3BP

This is a list of pathogenic ClinVar variants found in the LGALS3BP region.

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

Position	Type	Phenotype	Significance	ClinVar
17-78971587-C-A		not specified	Uncertain significance (May 31, 2023)
17-78971646-G-A		not specified	Uncertain significance (Jun 06, 2023)
17-78971688-T-G		not specified	Uncertain significance (May 27, 2022)
17-78971706-G-T		not specified	Uncertain significance (May 26, 2024)
17-78971723-G-A			Benign (Jul 13, 2018)
17-78971728-C-T		not specified	Uncertain significance (Mar 04, 2024)
17-78971734-C-T		not specified	Uncertain significance (Aug 13, 2021)
17-78971793-C-T		not specified	Uncertain significance (Nov 09, 2022)
17-78971796-T-G		not specified	Uncertain significance (Feb 13, 2024)
17-78971920-G-T		not specified	Uncertain significance (Oct 04, 2022)
17-78971986-G-T		not specified	Uncertain significance (Jun 10, 2024)
17-78972027-C-G			Benign (Apr 06, 2018)
17-78972060-G-A		not specified	Uncertain significance (Jun 06, 2023)
17-78972126-G-A		not specified	Uncertain significance (Jul 26, 2022)
17-78972156-C-T			Likely benign (May 15, 2018)
17-78972227-G-A			Benign (Jul 13, 2018)
17-78972229-G-A		not specified	Uncertain significance (Jan 02, 2024)
17-78972306-A-G		not specified	Uncertain significance (Apr 01, 2024)
17-78972335-A-G			Benign (Jul 13, 2018)
17-78972336-C-T		not specified	Uncertain significance (Aug 08, 2023)
17-78972337-G-A		not specified	Uncertain significance (Mar 01, 2023)
17-78972338-C-G		not specified	Uncertain significance (Jan 17, 2024)
17-78972382-C-T		not specified	Uncertain significance (Dec 21, 2023)
17-78972428-G-T		not specified	Uncertain significance (Mar 01, 2023)
17-78972465-A-G		not specified	Uncertain significance (May 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LGALS3BP	protein_coding	protein_coding	ENST00000262776	5	8872

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.68e-7	0.308	125583	0	140	125723	0.000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0771	341	345	0.988	0.0000203	3765
Missense in Polyphen		124	121.44	1.0211		1369
Synonymous	0.183	159	162	0.982	0.0000106	1210
Loss of Function	0.451	11	12.7	0.864	6.28e-7	133

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000612	0.000611
Ashkenazi Jewish	0.00179	0.00179
East Asian	0.00	0.00
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000631	0.000624
Middle Eastern	0.00	0.00
South Asian	0.000768	0.000752
Other	0.00131	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes integrin-mediated cell adhesion. May stimulate host defense against viruses and tumor cells. {ECO:0000269|PubMed:11146440, ECO:0000269|PubMed:8034587, ECO:0000269|PubMed:9501082}.
• Pathway: Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.208

Intolerance Scores

• loftool: 0.726
• rvis_EVS: -0.97
• rvis_percentile_EVS: 8.9

Haploinsufficiency Scores

• pHI: 0.445
• hipred: N
• hipred_score: 0.298
• ghis: 0.517

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.890

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lgals3bp
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype

Gene ontology

• Biological process: platelet degranulation;receptor-mediated endocytosis;cellular defense response;cell adhesion;signal transduction
• Cellular component: extracellular region;extracellular space;membrane;platelet dense granule lumen;collagen-containing extracellular matrix;extracellular exosome;blood microparticle
• Molecular function: scavenger receptor activity;protein binding