LBX1

ladybird homeobox 1, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 10:101226994-101229463

Links

ENSG00000138136 ∙ NCBI:10660 ∙ OMIM:604255 ∙ HGNC:16960 ∙ Uniprot:P52954 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Central hypoventilation syndrome, congenital 3	AR	Neurologic	In Central hypoventilation syndrome, congenital, early recognition and interventions to support ventilation may reduce morbidity and mortality	Gastrointestinal; Neurologic	30487221

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LBX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LBX1 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					2	2
missense			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	9	1	3

Variants in LBX1

This is a list of pathogenic ClinVar variants found in the LBX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-101227296-C-T		not specified	Uncertain significance (Oct 26, 2022)
10-101227340-G-A		not specified	Uncertain significance (Dec 14, 2023)
10-101227346-G-A		not specified	Uncertain significance (Sep 16, 2021)
10-101227394-G-T		not specified	Uncertain significance (Aug 21, 2023)
10-101227402-G-C			Benign (Dec 31, 2019)
10-101227403-G-T		not specified	Uncertain significance (Sep 30, 2021)
10-101227517-C-T		not specified	Uncertain significance (Aug 26, 2022)
10-101227977-G-T			Benign (May 21, 2021)
10-101228496-G-A			Uncertain significance (May 01, 2022)
10-101228588-G-A			Benign (May 04, 2021)
10-101228590-G-A		not specified	Uncertain significance (Jan 04, 2022)
10-101228613-T-G		not specified	Likely benign (Apr 07, 2023)
10-101228650-C-A			Uncertain significance (Dec 01, 2022)
10-101228674-G-C		not specified	Uncertain significance (Mar 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LBX1	protein_coding	protein_coding	ENST00000370193	2	2819

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.679	0.317	118177	0	1	118178	0.00000423

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.11	121	161	0.753	0.00000728	1763
Missense in Polyphen		29	63.395	0.45745		666
Synonymous	0.0602	77	77.7	0.991	0.00000364	595
Loss of Function	2.29	1	8.00	0.125	3.41e-7	90

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000172	0.000172

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor required for the development of GABAergic interneurons in the dorsal horn of the spinal cord and migration and further development of hypaxial muscle precursor cells for limb muscles, diaphragm and hypoglossal cord. {ECO:0000250}.

Recessive Scores

• pRec: 0.268

Intolerance Scores

• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.62

Haploinsufficiency Scores

• pHI: 0.435
• hipred: Y
• hipred_score: 0.735
• ghis: 0.631

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.225

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lbx1
• 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); limbs/digits/tail phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; muscle phenotype; cellular phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: heart looping;muscle organ development;negative regulation of cell population proliferation;anatomical structure morphogenesis;spinal cord motor neuron differentiation;regulation of transcription from RNA polymerase II promoter involved in spinal cord association neuron specification;negative regulation of neuron differentiation;neuron fate determination
• Cellular component: nucleus;transcription factor complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding