LGALS13

galectin 13, the group of Galectins

Basic information

Region (hg38): 19:39602524-39607474

Links

ENSG00000105198 ∙ NCBI:29124 ∙ OMIM:608717 ∙ HGNC:15449 ∙ Uniprot:Q9UHV8 ∙ 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 LGALS13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LGALS13 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			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in LGALS13

This is a list of pathogenic ClinVar variants found in the LGALS13 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-39602580-A-C		not specified	Uncertain significance (Jun 07, 2023)
19-39604615-T-G		not specified	Uncertain significance (Dec 19, 2022)
19-39604636-G-A		not specified	Uncertain significance (Mar 04, 2024)
19-39605267-A-G		not specified	Uncertain significance (Oct 12, 2024)
19-39605309-A-G		not specified	Uncertain significance (Dec 06, 2021)
19-39605329-C-T		not specified	Uncertain significance (Feb 22, 2023)
19-39605350-T-C		not specified	Uncertain significance (Aug 30, 2021)
19-39605368-G-A		not specified	Uncertain significance (Dec 22, 2023)
19-39607263-G-A			Likely benign (Apr 17, 2018)
19-39607274-T-C		not specified	Uncertain significance (Sep 27, 2024)
19-39607299-C-T		not specified	Uncertain significance (Dec 20, 2024)
19-39607308-T-A		not specified	Uncertain significance (Dec 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LGALS13	protein_coding	protein_coding	ENST00000221797	4	4953

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00113	0.634	125407	3	337	125747	0.00135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.208	85	79.8	1.07	0.00000467	912
Missense in Polyphen		34	23.739	1.4322		318
Synonymous	-1.17	39	30.7	1.27	0.00000190	258
Loss of Function	0.598	5	6.67	0.750	4.47e-7	61

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0189	0.0186
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds beta-galactoside and lactose. Strong inducer of T- cell apoptosis (PubMed:10527825, PubMed:19497882). Has hemagglutinating activity towards chicken erythrocytes (PubMed:29343868). {ECO:0000269|PubMed:10527825, ECO:0000269|PubMed:19497882, ECO:0000269|PubMed:29343868}.

Recessive Scores

• pRec: 0.158

Intolerance Scores

• loftool: 0.753
• rvis_EVS: 0.57
• rvis_percentile_EVS: 81.99

Haploinsufficiency Scores

• pHI: 0.229
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.486

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plac8
• Phenotype: immune system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: phospholipid metabolic process;apoptotic process;positive regulation of T cell apoptotic process
• Cellular component: cytoplasm;nuclear matrix
• Molecular function: lysophospholipase activity;protein binding;carbohydrate binding