LGALS12

protein-coding

galectin 12, the group of Galectins

Gene summary

This gene encodes a member of the galectin superfamily, a group of beta-galactoside-binding proteins with conserved carbohydrate recognition domains. The related mouse protein is a primary regulator of the early stages of adipose tissue development. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, May 2010]

MANE transcript

NM_033101.4

Inheritance

—

ClinVar variants

U:59B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.07

Max pathogenic AF

—

Genomic locus

chr11:63,506,052-63,516,774

External References & Databases

Ensembl (ENSG00000133317)

Transcript & Mutation Effects

hg38 • Region Span ~10.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LGALS12 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 61

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033101.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			55 clinvar	5 clinvar		60
nonsense						0
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	59	5	0	64

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033101.4	RefSeq	NP_149092.3	9	MANE Select
ENST00000394618.9	Ensembl	ENSP00000378116.4	9	MANE Select
NM_001142535.2	RefSeq	NP_001136007.2	9	Standard
NM_001142536.2	RefSeq	NP_001136008.2	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of fat cell differentiation
regulation of lipid catabolic process
intrinsic apoptotic signaling pathway

Molecular Function

lactose binding

Cellular Component

nucleus
mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000340246
Coding exons: 9
Length: 10691
Individuals with no LoFs: 125535
Homozygous LoFs: 1
Heterozygous LoFs: 212
Defined: 125748
p: 0.000847

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0302	198	197	1.01	0.0000110	2182
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0055	0.0056	notable
Latino/Admixed American	0.00064	0.00064	rare
Ashkenazi Jewish	0.00060	0.00060	rare
East Asian	0.00011	0.00011	rare
Finnish	0.000094	0.000092	rare
European (Non-Finnish)	0.00068	0.00068	rare
South Asian	0.00036	0.00033	rare
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.194

Gene Damage Prediction

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