LHX8

LIM homeobox 8, the group of LIM class homeoboxes

Basic information

Region (hg38): 1:75128434-75161533

Links

ENSG00000162624 ∙ NCBI:431707 ∙ OMIM:604425 ∙ HGNC:28838 ∙ Uniprot:Q68G74 ∙ 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 LHX8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LHX8 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	1	1	19
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	2

Variants in LHX8

This is a list of pathogenic ClinVar variants found in the LHX8 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-75136615-A-C		LHX8-related disorder	Likely benign (Dec 01, 2022)
1-75136633-C-T		not specified	Uncertain significance (Nov 18, 2022)
1-75136658-G-A		not specified	Uncertain significance (Aug 27, 2024)
1-75136681-G-A		not specified	Uncertain significance (Feb 23, 2025)
1-75136685-G-A		not specified	Uncertain significance (Feb 23, 2025)
1-75136698-G-A		LHX8-related disorder	Likely benign (May 10, 2019)
1-75137116-C-T		LHX8-related disorder	Benign (May 18, 2018)
1-75137158-C-T		not specified	Uncertain significance (Mar 18, 2024)
1-75137237-G-A		LHX8-related disorder	Likely benign (Apr 11, 2019)
1-75141009-C-G		not specified	Uncertain significance (Jan 01, 2025)
1-75141009-C-T		not specified	Uncertain significance (Jan 05, 2022)
1-75141010-G-A		not specified	Uncertain significance (Jun 25, 2024)
1-75141078-G-C		not specified	Uncertain significance (Nov 15, 2021)
1-75143147-G-A		not specified	Uncertain significance (Nov 13, 2023)
1-75143169-C-T		LHX8-related disorder	Benign (May 18, 2018)
1-75143198-A-G		not specified	Uncertain significance (Feb 12, 2024)
1-75143251-G-C		not specified	Uncertain significance (Aug 21, 2024)
1-75143857-G-T		not specified	Uncertain significance (Feb 28, 2024)
1-75143870-C-T		LHX8-related disorder	Likely benign (Jul 02, 2019)
1-75143884-A-G		not specified	Uncertain significance (Nov 10, 2024)
1-75143937-G-C		not specified	Uncertain significance (Nov 12, 2021)
1-75148605-G-A		not specified	Uncertain significance (May 27, 2022)
1-75148643-A-G		LHX8-related disorder	Likely benign (Jun 08, 2019)
1-75156895-G-T		LHX8-related disorder	Benign (Aug 17, 2018)
1-75156998-A-G		not specified	Uncertain significance (Jun 11, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LHX8	protein_coding	protein_coding	ENST00000294638	9	33100

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.516	0.484	125738	0	6	125744	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.61	137	201	0.681	0.00000994	2313
Missense in Polyphen		24	67.445	0.35585		780
Synonymous	-0.397	80	75.6	1.06	0.00000361	693
Loss of Function	3.23	4	19.4	0.207	8.84e-7	231

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00000881	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor involved in differentiation of certain neurons and mesenchymal cells. {ECO:0000250}.

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.277
• rvis_EVS: 0.19
• rvis_percentile_EVS: 67.03

Haploinsufficiency Scores

• pHI: 0.238
• hipred: Y
• hipred_score: 0.837

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.327

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lhx8
• 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); digestive/alimentary 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; craniofacial phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;learning or memory;female gonad development;forebrain neuron development;odontogenesis of dentin-containing tooth
• Cellular component: female germ cell nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding;sequence-specific DNA binding;metal ion binding