LHX6

LIM homeobox 6, the group of LIM class homeoboxes

Basic information

Region (hg38): 9:122202577-122229626

Links

ENSG00000106852NCBI:26468OMIM:608215HGNC:21735Uniprot:Q9UPM6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LHX6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LHX6 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
10
clinvar
10
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
1
clinvar
1
Total 0 0 10 1 0

Variants in LHX6

This is a list of pathogenic ClinVar variants found in the LHX6 region.

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

Position Type Phenotype Significance ClinVar
9-122209672-G-A not specified Uncertain significance (Dec 28, 2022)2357263
9-122213705-G-T not specified Uncertain significance (Jan 16, 2024)3118681
9-122213716-G-A not specified Uncertain significance (Aug 02, 2022)2304747
9-122214003-T-G not specified Uncertain significance (Jan 03, 2024)3118680
9-122214344-T-C not specified Uncertain significance (Dec 01, 2022)3118679
9-122226990-T-C not specified Uncertain significance (Mar 31, 2022)2281131
9-122227440-C-T not specified Uncertain significance (Apr 20, 2024)3290635
9-122227471-G-C not specified Uncertain significance (Apr 09, 2024)3290634
9-122227488-A-G Likely benign (Mar 29, 2018)778380
9-122228662-C-A not specified Uncertain significance (Feb 27, 2023)2489275
9-122228674-C-T not specified Uncertain significance (Dec 21, 2023)3118678
9-122228719-C-T not specified Uncertain significance (Dec 28, 2022)2340629
9-122228720-G-C not specified Uncertain significance (Jul 26, 2022)2303077

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
LHX6protein_codingprotein_codingENST00000394319 1027050
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9660.0343124269011242700.00000402
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.931042280.4550.00001222522
Missense in Polyphen2490.1520.26622913
Synonymous1.01881010.8720.00000591770
Loss of Function3.65219.30.1048.80e-7227

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002890.0000289
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Probable transcription factor required for the expression of a subset of genes involved in interneurons migration and development. Functions in the specification of cortical interneuron subtypes and in the migration of GABAergic interneuron precursors from the subpallium to the cerebral cortex (By similarity). {ECO:0000250}.;

Recessive Scores

pRec
0.148

Intolerance Scores

loftool
0.0293
rvis_EVS
0.19
rvis_percentile_EVS
66.82

Haploinsufficiency Scores

pHI
0.671
hipred
Y
hipred_score
0.837
ghis
0.536

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.911

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Lhx6
Phenotype
homeostasis/metabolism phenotype; cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); normal 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);

Gene ontology

Biological process
regulation of transcription by RNA polymerase II;cerebral cortex radially oriented cell migration;cerebral cortex tangential migration;cerebral cortex GABAergic interneuron migration;cell maturation
Cellular component
nucleus
Molecular function
DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;sequence-specific DNA binding;metal ion binding