LHX9

LIM homeobox 9, the group of LIM class homeoboxes

Basic information

Region (hg38): 1:197911902-197935478

Links

ENSG00000143355 ∙ NCBI:56956 ∙ OMIM:606066 ∙ HGNC:14222 ∙ Uniprot:Q9NQ69 ∙ 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 LHX9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LHX9 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
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	1

Variants in LHX9

This is a list of pathogenic ClinVar variants found in the LHX9 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-197917875-C-G		not specified	Uncertain significance (Aug 04, 2023)
1-197917875-C-T		not specified	Uncertain significance (Jan 30, 2024)
1-197917959-C-A		not specified	Uncertain significance (Aug 02, 2021)
1-197917975-C-T		not specified	Uncertain significance (Mar 06, 2023)
1-197919982-C-G		not specified	Uncertain significance (Jun 29, 2023)
1-197920024-G-A		not specified	Uncertain significance (Jun 19, 2024)
1-197921522-T-C		not specified	Uncertain significance (Mar 06, 2023)
1-197921567-C-T		not specified	Uncertain significance (Oct 03, 2022)
1-197921626-G-T		not specified	Uncertain significance (Jan 16, 2024)
1-197927621-A-G		not specified	Uncertain significance (Dec 18, 2023)
1-197927648-C-T		not specified	Uncertain significance (May 03, 2023)
1-197929012-A-G		Inborn genetic diseases	Uncertain significance (Apr 08, 2019)
1-197929048-G-A		not specified	Uncertain significance (Nov 22, 2021)
1-197929098-C-T		not specified	Uncertain significance (Mar 29, 2022)
1-197929128-C-A		Pituitary stalk interruption syndrome	Uncertain significance (-)
1-197929155-G-C		not specified	Uncertain significance (Mar 15, 2023)
1-197929161-A-T		not specified	Uncertain significance (May 16, 2023)
1-197929162-C-A		not specified	Uncertain significance (Mar 02, 2023)
1-197929226-C-T			Benign (Jul 21, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LHX9	protein_coding	protein_coding	ENST00000367387	5	23572

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.981	0.0194	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	189	235	0.803	0.0000118	2577
Missense in Polyphen		29	79.245	0.36595		875
Synonymous	-0.192	101	98.6	1.02	0.00000507	801
Loss of Function	3.53	1	16.5	0.0608	8.52e-7	185

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000294	0.0000294
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in gonadal development. {ECO:0000250}.
• Pathway: Developmental Biology;Regulation of expression of SLITs and ROBOs;Signaling by ROBO receptors;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.221

Intolerance Scores

• loftool: 0.0925
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.89

Haploinsufficiency Scores

• pHI: 0.736
• hipred: Y
• hipred_score: 0.837
• ghis: 0.441

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.271

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lhx9
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; endocrine/exocrine gland 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); reproductive system phenotype

Zebrafish Information Network

• Gene name: lhx9
• Affected structure: hypocretin-secreting neuron
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;cell population proliferation;male gonad development;female gonad development;gonad morphogenesis;negative regulation of transcription, DNA-templated;dorsal spinal cord interneuron anterior axon guidance
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;transcription corepressor activity;protein binding;sequence-specific DNA binding;metal ion binding