TLX3

T cell leukemia homeobox 3, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 5:171309248-171312139

Previous symbols: [ "HOX11L2" ]

Links

ENSG00000164438

∙ NCBI:30012 ∙ OMIM:604640 ∙ HGNC:13532 ∙ Uniprot:O43711 ∙ 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 TLX3 gene.

not_specified (31 variants)
Hereditary_breast_ovarian_cancer_syndrome (1 variants)
TLX3-related_condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TLX3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021025.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			33 clinvar			33
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	33	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TLX3	protein_coding	protein_coding	ENST00000296921	3	2851

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.260	0.716	122477	0	1	122478	0.00000408

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	119	170	0.698	0.00000777	1842
Missense in Polyphen		20	34.404	0.58132		369
Synonymous	-0.941	85	74.7	1.14	0.00000353	609
Loss of Function	1.90	2	7.66	0.261	3.29e-7	82

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000640	0.0000640
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

Pathway: Transcriptional misregulation in cancer - Homo sapiens (human);Cell Differentiation - Index expanded;Cell Differentiation - Index;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways (Consensus)

Recessive Scores

pRec: 0.163

Intolerance Scores

loftool: 0.0391
rvis_EVS: -0.1
rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

pHI: 0.690
hipred: Y
hipred_score: 0.665
ghis

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.974

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Tlx3
Phenotype: homeostasis/metabolism phenotype; respiratory system 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); 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); neoplasm;

Gene ontology

Biological process: neuron migration;regulation of respiratory gaseous exchange by neurological system process;regulation of transcription by RNA polymerase II;central nervous system development;respiratory gaseous exchange;negative regulation of neuron differentiation;neuron fate specification
Cellular component: nucleoplasm
Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding;sequence-specific DNA binding