LHX2

LIM homeobox 2, the group of LIM class homeoboxes

Basic information

Region (hg38): 9:124001669-124033301

Links

ENSG00000106689 ∙ NCBI:9355 ∙ OMIM:603759 ∙ HGNC:6594 ∙ Uniprot:P50458 ∙ 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 LHX2 gene.

• Inborn genetic diseases (11 variants)
• not provided (4 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.

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			11			11
nonsense						0
start loss						0
frameshift		1	2			3
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	13	1	1

Variants in LHX2

This is a list of pathogenic ClinVar variants found in the LHX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-124012409-A-G		not specified	Uncertain significance (Feb 17, 2023)
9-124012420-C-G		not specified	Uncertain significance (Aug 28, 2023)
9-124012460-A-G		not specified	Uncertain significance (Jun 29, 2023)
9-124013973-A-G		not specified	Uncertain significance (Feb 05, 2024)
9-124013976-AGCAGTGACCGC-A			Uncertain significance (Nov 21, 2022)
9-124014022-CGGACC-ACCT		Variable neurodevelopmental disorder	Likely pathogenic (Apr 14, 2023)
9-124014131-C-T		LHX2-related disorder	Likely benign (Aug 15, 2019)
9-124015138-C-A		not specified	Uncertain significance (Oct 04, 2022)
9-124015149-C-T		LHX2-related disorder	Likely benign (Jan 03, 2020)
9-124015305-C-A		not specified	Uncertain significance (Nov 12, 2021)
9-124015353-C-CG			Uncertain significance (Apr 09, 2023)
9-124015376-C-T		not specified	Uncertain significance (Apr 20, 2023)
9-124015379-C-G		not specified	Uncertain significance (Jun 23, 2023)
9-124015381-G-C		not specified	Uncertain significance (Feb 15, 2023)
9-124015447-G-A		LHX2-related disorder	Benign (Oct 28, 2019)
9-124015502-C-T		not specified	Uncertain significance (Sep 29, 2023)
9-124021099-C-T		not specified	Uncertain significance (Apr 10, 2023)
9-124021113-G-A		not specified	Uncertain significance (Dec 08, 2023)
9-124021136-C-T		LHX2-related disorder	Benign (Sep 25, 2019)
9-124021147-C-A		LHX2-related disorder	Likely benign (Mar 28, 2022)
9-124032503-G-C		LHX2-related disorder	Likely benign (Jun 01, 2022)
9-124032535-C-T		not specified	Uncertain significance (Dec 20, 2021)
9-124032683-A-C		not specified	Uncertain significance (Jun 11, 2021)

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
0.988	0.0119	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

Haploinsufficiency Scores

• pHI: 0.992
• hipred: Y
• hipred_score: 0.875
• ghis: 0.517

Essentials

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

Mouse Genome Informatics

• Gene name: Lhx2
• Phenotype: craniofacial phenotype; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; hematopoietic system phenotype; taste/olfaction 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); vision/eye phenotype; liver/biliary system phenotype; respiratory system phenotype; 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)

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