LBX2

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

Basic information

Region (hg38): 2:74497517-74503316

Links

ENSG00000179528 ∙ NCBI:85474 ∙ OMIM:607164 ∙ HGNC:15525 ∙ Uniprot:Q6XYB7 ∙ 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 LBX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LBX2 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	2
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	1

Variants in LBX2

This is a list of pathogenic ClinVar variants found in the LBX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-74497940-T-G		not specified	Uncertain significance (Oct 06, 2021)
2-74497982-G-A		not specified	Uncertain significance (Jan 31, 2023)
2-74497989-C-T		not specified	Uncertain significance (Sep 16, 2021)
2-74498046-C-T		not specified	Uncertain significance (Apr 23, 2024)
2-74498048-G-A		not specified	Uncertain significance (Aug 16, 2022)
2-74498137-C-G			Likely benign (Jul 27, 2018)
2-74498160-G-A		not specified	Uncertain significance (May 18, 2023)
2-74498264-T-C		not specified	Uncertain significance (Jan 22, 2024)
2-74498286-G-A		not specified	Uncertain significance (Dec 28, 2023)
2-74498310-C-G		not specified	Uncertain significance (May 16, 2024)
2-74499487-T-A			Benign (Jul 27, 2018)
2-74502817-C-G		not specified	Uncertain significance (Oct 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LBX2	protein_coding	protein_coding	ENST00000460508	2	5800

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00588	0.745	125007	0	9	125016	0.0000360

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.158	121	116	1.04	0.00000527	1195
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000117	0.000117
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000452	0.0000443
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0872
• hipred: N
• hipred_score: 0.322
• ghis: 0.392

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.347

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lbx2
• Phenotype: homeostasis/metabolism phenotype; embryo phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: lbx2
• Affected structure: fast muscle cell
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding