LGALS12

galectin 12, the group of Galectins

Basic information

Region (hg38): 11:63506051-63516774

Links

ENSG00000133317 ∙ NCBI:85329 ∙ OMIM:606096 ∙ HGNC:15788 ∙ Uniprot:Q96DT0 ∙ 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 LGALS12 gene.

• Inborn genetic diseases (18 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LGALS12 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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	17	1	0

Variants in LGALS12

This is a list of pathogenic ClinVar variants found in the LGALS12 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-63506408-G-T		not specified	Uncertain significance (Sep 06, 2022)
11-63506429-A-G		not specified	Uncertain significance (Apr 27, 2023)
11-63506492-G-A		not specified	Uncertain significance (Oct 12, 2021)
11-63506526-C-T		not specified	Uncertain significance (Oct 25, 2023)
11-63508566-T-C		not specified	Uncertain significance (Dec 21, 2021)
11-63508849-G-A		not specified	Uncertain significance (Nov 17, 2023)
11-63508851-T-C		not specified	Uncertain significance (Mar 11, 2022)
11-63508866-C-T		not specified	Uncertain significance (Apr 08, 2022)
11-63508899-C-T		not specified	Uncertain significance (Mar 29, 2022)
11-63508911-G-A		not specified	Uncertain significance (Mar 07, 2023)
11-63508923-C-G		not specified	Uncertain significance (Jan 16, 2024)
11-63508974-G-A		not specified	Uncertain significance (Apr 24, 2023)
11-63509812-G-A		not specified	Uncertain significance (Jun 29, 2023)
11-63509863-T-C		not specified	Uncertain significance (Dec 27, 2023)
11-63510475-G-C		not specified	Uncertain significance (Jan 17, 2024)
11-63510499-C-T		not specified	Uncertain significance (Aug 20, 2023)
11-63511755-G-A		not specified	Uncertain significance (Jul 25, 2023)
11-63511764-T-C		not specified	Uncertain significance (Jan 24, 2024)
11-63511839-C-G		not specified	Likely benign (Dec 12, 2023)
11-63515597-G-A		not specified	Uncertain significance (Dec 02, 2022)
11-63515598-C-T		not specified	Likely benign (May 31, 2023)
11-63515651-C-T		not specified	Uncertain significance (Jan 04, 2024)
11-63515678-G-A		not specified	Uncertain significance (Mar 06, 2023)
11-63516281-T-C		not specified	Uncertain significance (May 27, 2022)
11-63516290-A-G		not specified	Uncertain significance (Jun 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LGALS12	protein_coding	protein_coding	ENST00000340246	9	10691

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.52e-13	0.0173	125535	1	212	125748	0.000847

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0302	198	197	1.01	0.0000110	2182
Missense in Polyphen		65	62.986	1.032		723
Synonymous	0.668	70	77.5	0.903	0.00000404	695
Loss of Function	-0.283	18	16.8	1.07	7.99e-7	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00618	0.00619
Ashkenazi Jewish	0.000595	0.000595
East Asian	0.000109	0.000109
Finnish	0.0000936	0.0000924
European (Non-Finnish)	0.000677	0.000677
Middle Eastern	0.000109	0.000109
South Asian	0.000360	0.000327
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds lactose. May participate in the apoptosis of adipocytes.

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.987
• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.55

Haploinsufficiency Scores

• pHI: 0.0767
• hipred: N
• hipred_score: 0.170
• ghis: 0.393

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.194

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lgals12
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of fat cell differentiation;regulation of lipid catabolic process;intrinsic apoptotic signaling pathway
• Cellular component: nucleus;mitochondrion
• Molecular function: lactose binding