LGALS4

galectin 4, the group of Galectins

Basic information

Region (hg38): 19:38801671-38812945

Links

ENSG00000171747 ∙ NCBI:3960 ∙ OMIM:602518 ∙ HGNC:6565 ∙ Uniprot:P56470 ∙ 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 LGALS4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LGALS4 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			11	1	1	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	2	1

Variants in LGALS4

This is a list of pathogenic ClinVar variants found in the LGALS4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-38801871-C-T		not specified	Uncertain significance (Jan 23, 2024)
19-38801885-C-T		not specified	Uncertain significance (Aug 13, 2021)
19-38801998-G-T		not specified	Uncertain significance (Jan 18, 2023)
19-38802026-G-T		not specified	Uncertain significance (Aug 26, 2022)
19-38802087-C-T		not specified	Uncertain significance (Jun 22, 2023)
19-38802098-C-T		not specified	Uncertain significance (Jul 09, 2021)
19-38802106-A-C		not specified	Uncertain significance (Jun 11, 2024)
19-38808768-G-C		not specified	Uncertain significance (Jan 17, 2024)
19-38808805-A-G		not specified	Uncertain significance (May 13, 2024)
19-38808817-C-T		not specified	Likely benign (Apr 11, 2023)
19-38808850-G-A		not specified	Uncertain significance (Dec 22, 2023)
19-38808862-A-G		not specified	Uncertain significance (Jan 24, 2024)
19-38808916-G-A		not specified	Uncertain significance (Feb 10, 2022)
19-38808941-C-T		not specified	Uncertain significance (Jan 22, 2024)
19-38812510-A-C		not specified	Uncertain significance (May 30, 2024)
19-38812518-G-A			Benign (Jan 30, 2018)
19-38812881-G-A			Likely benign (Jun 20, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LGALS4	protein_coding	protein_coding	ENST00000307751	10	11694

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.75e-7	0.757	125689	0	59	125748	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.637	185	211	0.877	0.0000131	2116
Missense in Polyphen		64	87.356	0.73264		860
Synonymous	0.164	85	86.9	0.978	0.00000620	625
Loss of Function	1.32	13	19.2	0.676	9.85e-7	200

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000740	0.000738
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000185	0.000185
Middle Eastern	0.000218	0.000217
South Asian	0.000327	0.000327
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Galectin that binds lactose and a related range of sugars. May be involved in the assembly of adherens junctions.

Recessive Scores

• pRec: 0.716

Intolerance Scores

• loftool: 0.707
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.54

Haploinsufficiency Scores

• pHI: 0.100
• hipred: N
• hipred_score: 0.170
• ghis: 0.453

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.776

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lgals4

Gene ontology

• Biological process: cell adhesion
• Cellular component: extracellular space;cytosol;plasma membrane
• Molecular function: galactoside binding;carbohydrate binding