LGALS8

galectin 8, the group of Galectins

Basic information

Region (hg38): 1:236518000-236552981

Links

ENSG00000116977 ∙ NCBI:3964 ∙ OMIM:606099 ∙ HGNC:6569 ∙ Uniprot:O00214 ∙ 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 LGALS8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LGALS8 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	2
missense			15	3	1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2		2	4
Total	0	0	17	4	4

Variants in LGALS8

This is a list of pathogenic ClinVar variants found in the LGALS8 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-236538926-A-T		not specified	Uncertain significance (Dec 27, 2023)
1-236538950-G-T		not specified	Uncertain significance (Jul 20, 2022)
1-236538962-C-T		not specified	Uncertain significance (Jan 03, 2024)
1-236538963-C-T			Likely benign (Jun 01, 2022)
1-236539060-G-T		not specified	Uncertain significance (Oct 06, 2021)
1-236540567-G-A		not specified	Uncertain significance (May 13, 2024)
1-236540574-A-G		not specified	Uncertain significance (Sep 29, 2023)
1-236540577-G-T		not specified	Uncertain significance (May 27, 2022)
1-236540609-G-A		not specified	Likely benign (Jun 24, 2022)
1-236540671-T-G		not specified	Uncertain significance (Mar 06, 2023)
1-236542934-A-G			Benign (Dec 31, 2019)
1-236542948-G-A		not specified	Uncertain significance (Apr 11, 2023)
1-236542979-A-G		not specified	Likely benign (Aug 17, 2022)
1-236543030-A-G		not specified	Likely benign (Jun 16, 2024)
1-236543613-C-T			Benign (May 21, 2018)
1-236543617-G-A		not specified	Likely benign (Jul 28, 2021)
1-236543623-G-A		not specified	Uncertain significance (Jul 12, 2022)
1-236544907-T-C		not specified	Uncertain significance (Mar 06, 2023)
1-236548025-G-A		not specified	Uncertain significance (Jan 09, 2024)
1-236548054-A-G		not specified	Uncertain significance (Oct 18, 2021)
1-236548060-G-A		not specified	Uncertain significance (Jul 20, 2021)
1-236548072-G-C		not specified	Uncertain significance (Mar 01, 2024)
1-236548154-G-A		not specified	Uncertain significance (Jul 11, 2023)
1-236550909-T-C		not specified	Uncertain significance (Jul 20, 2021)
1-236550954-G-T		not specified	Uncertain significance (Jan 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LGALS8	protein_coding	protein_coding	ENST00000526589	10	34982

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000388	0.833	125627	0	121	125748	0.000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0281	197	196	1.01	0.0000106	2368
Missense in Polyphen		52	54.097	0.96124		717
Synonymous	-0.729	79	71.2	1.11	0.00000409	662
Loss of Function	1.39	11	17.2	0.639	8.90e-7	214

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00255	0.00254
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000118	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000378	0.000378
Middle Eastern	0.000118	0.000109
South Asian	0.000996	0.000850
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Beta-galactoside-binding lectin that acts as a sensor of membrane damage caused by infection and restricts the proliferation of infecting pathogens by targeting them for autophagy (PubMed:22246324, PubMed:28077878). Detects membrane rupture by binding beta-galactoside ligands located on the lumenal side of the endosome membrane; these ligands becoming exposed to the cytoplasm following rupture (PubMed:22246324, PubMed:28077878). Restricts infection by initiating autophagy via interaction with CALCOCO2/NDP52 (PubMed:22246324, PubMed:28077878). Required to restrict infection of bacterial invasion such as S.typhimurium (PubMed:22246324). Also required to restrict infection of Picornaviridae viruses (PubMed:28077878). Has a marked preference for 3'-O-sialylated and 3'-O-sulfated glycans (PubMed:21288902). {ECO:0000269|PubMed:21288902, ECO:0000269|PubMed:22246324, ECO:0000269|PubMed:28077878}.

Recessive Scores

• pRec: 0.170

Intolerance Scores

• loftool: 0.996
• rvis_EVS: 1.06
• rvis_percentile_EVS: 91.58

Haploinsufficiency Scores

• pHI: 0.481
• hipred: N
• hipred_score: 0.152
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.586

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Lgals8
• Phenotype: immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: cellular response to virus;xenophagy;lymphatic endothelial cell migration
• Cellular component: extracellular space;cytoplasm;cytosol;membrane;cytoplasmic vesicle
• Molecular function: integrin binding;protein binding;carbohydrate binding