LBX2

protein-coding

ladybird homeobox 2, the group of NKL subclass homeoboxes and pseudogenes

Gene summary

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in several processes, including positive regulation of convergent extension involved in gastrulation; positive regulation of non-canonical Wnt signaling pathway; and regulation of transcription by RNA polymerase II. Predicted to be located in chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001282430.2

Inheritance

—

ClinVar variants

U:22B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr2:74,497,517-74,503,316

External References & Databases

Ensembl (ENSG00000179528)

Transcript & Mutation Effects

hg38 • Region Span ~5.8 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 LBX2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 23

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001282430.2. 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				1 clinvar	1 clinvar	2
missense			22 clinvar	1 clinvar		23
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	22	2	1	25

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001282430.2	RefSeq	NP_001269359.1	2	MANE Select
ENST00000377566.9	Ensembl	ENSP00000366789.4	2	MANE Select
NM_001009812.2	RefSeq	NP_001009812.1	2	Standard
ENST00000341396.2	Ensembl	ENSP00000450229.1	2	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
lbx2	Danio rerio	Structure: fast muscle cell Quality: malformed abnormal

Gene / Model

Organism

Observed Phenotype

lbx2

Danio rerio

Structure: fast muscle cell

Quality: malformed

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000460508
Coding exons: 2
Length: 5800
Individuals with no LoFs: 125007
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125016
p: 0.0000360

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.158	121	116	1.04	0.00000527	1195
Missense (PolyPhen)		30	40.471	0.74128		412
Synonymous	0.234	54	56.2	0.960	0.00000257	455
Loss of Function	0.832	4	6.24	0.641	2.69e-7	60

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000045	0.000044	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Putative transcription factor. {ECO:0000250}.;

Recessive Scores

pRec: 0.0950

Intolerance Scores

LoFtool: 0.304
RVIS EVS: 0.08
RVIS percentile EVS: 60.09

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.347

Gene Damage Prediction

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