LHX5

LIM homeobox 5, the group of LIM class homeoboxes

Basic information

Region (hg38): 12:113462033-113472280

Links

ENSG00000089116 ∙ NCBI:64211 ∙ OMIM:605992 ∙ HGNC:14216 ∙ Uniprot:Q9H2C1 ∙ 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 LHX5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LHX5 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						0
missense			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	17	1	0

Variants in LHX5

This is a list of pathogenic ClinVar variants found in the LHX5 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-113463213-G-T		not specified	Uncertain significance (Mar 15, 2024)
12-113463249-C-T		not specified	Uncertain significance (Mar 07, 2024)
12-113463300-C-T		not specified	Uncertain significance (Jul 20, 2021)
12-113463309-T-C		not specified	Uncertain significance (Apr 07, 2023)
12-113463312-G-T		not specified	Uncertain significance (Feb 10, 2022)
12-113463326-G-T		not specified	Uncertain significance (Oct 25, 2023)
12-113463332-C-T		not specified	Uncertain significance (Sep 27, 2022)
12-113463425-G-T		not specified	Uncertain significance (May 15, 2024)
12-113463485-T-G		not specified	Uncertain significance (Jul 25, 2023)
12-113463504-C-G		not specified	Uncertain significance (Jan 19, 2024)
12-113463528-T-C		not specified	Likely benign (Sep 06, 2022)
12-113467276-G-C		not specified	Uncertain significance (Mar 20, 2023)
12-113467325-T-A		not specified	Uncertain significance (Jun 17, 2024)
12-113467325-T-G		not specified	Uncertain significance (Jun 14, 2023)
12-113467343-A-G		not specified	Uncertain significance (Dec 07, 2021)
12-113467349-C-G		not specified	Uncertain significance (Dec 21, 2023)
12-113468123-G-T		not specified	Likely benign (Jul 24, 2017)
12-113468177-T-C		not specified	Uncertain significance (Aug 02, 2021)
12-113469209-C-G		not specified	Uncertain significance (Aug 26, 2022)
12-113469286-C-A		not specified	Uncertain significance (Jan 24, 2024)
12-113471356-C-T		not specified	Uncertain significance (Feb 11, 2022)
12-113471386-T-C		not specified	Uncertain significance (Oct 06, 2023)
12-113471470-C-A		not specified	Uncertain significance (Jun 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LHX5	protein_coding	protein_coding	ENST00000261731	5	10247

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.946	0.0541	121783	0	1	121784	0.00000411

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.17	130	221	0.589	0.0000100	2584
Missense in Polyphen		20	69.69	0.28698		770
Synonymous	0.961	86	98.1	0.877	0.00000476	786
Loss of Function	3.17	1	13.6	0.0735	5.84e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000554	0.0000554
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000554	0.0000554
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an essential role in the regulation of neuronal differentiation and migration during development of the central nervous system.
• Pathway: Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);Neural Crest Differentiation (Consensus)

Recessive Scores

• pRec: 0.186

Intolerance Scores

• loftool: 0.0577
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

• pHI: 0.552
• hipred: Y
• hipred_score: 0.789
• ghis: 0.432

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.640

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lhx5
• 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); 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); homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;spinal cord association neuron differentiation;cerebellar Purkinje cell differentiation;hippocampus development;cell proliferation in forebrain;forebrain neuron differentiation;cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation;positive regulation of transcription, DNA-templated
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding;metal ion binding