LHX2

LIM homeobox 2, the group of LIM class homeoboxes

Basic information

Region (hg38): 9:124001670-124033301

Links

ENSG00000106689 ∙ NCBI:9355 ∙ OMIM:603759 ∙ HGNC:6594 ∙ Uniprot:P50458 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Strong), mode of inheritance: AD
• complex neurodevelopmental disorder (Moderate), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LHX2 gene.

• not_specified (33 variants)
• not_provided (31 variants)
• LHX2-related_disorder (6 variants)
• Neurodevelopmental_disorder (1 variants)
• LHX2-associated_neurodevelopmental_disorder (1 variants)
• Variable_neurodevelopmental_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LHX2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004789.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	3	1	5
missense	2	1	50	2	1	56
nonsense			1			1
start loss						0
frameshift	3	1	4			8
splice donor/acceptor (+/-2bp)						0
Total	5	2	56	5	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LHX2	protein_coding	protein_coding	ENST00000373615	5	31632

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.27	143	243	0.589	0.0000126	2638
Missense in Polyphen		47	102.86	0.45692		1060
Synonymous	-1.17	121	106	1.14	0.00000563	818
Loss of Function	3.39	0	13.4	0.00	6.23e-7	161

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	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional activator. Stimulates the promoter of the alpha-glycoprotein gene. Transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types (By similarity). {ECO:0000250}.
• Pathway: Neural Crest Differentiation;Developmental Biology;Regulation of expression of SLITs and ROBOs;Signaling by ROBO receptors;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.238

Intolerance Scores

• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.89

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.926

Zebrafish Information Network

• Gene name: lhx2b
• Affected structure: retinal ganglion cell
• Phenotype tag: abnormal
• Phenotype quality: misrouted

Gene ontology

• Biological process: neural tube closure;hair follicle development;axon guidance;mesoderm development;dorsal/ventral pattern formation;olfactory bulb development;telencephalon regionalization;cerebral cortex development;maintenance of epithelial cell apical/basal polarity;negative regulation of gene expression, epigenetic;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;axon extension;negative regulation of neurogenesis;retina development in camera-type eye;positive regulation of neural precursor cell proliferation;negative regulation of transcription regulatory region DNA binding
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;chromatin binding;metal ion binding