TLX2

T cell leukemia homeobox 2, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 2:74513463-74517148

Previous symbols: [ "HOX11L1" ]

Links

ENSG00000115297 ∙ NCBI:3196 ∙ OMIM:604240 ∙ HGNC:5057 ∙ Uniprot:O43763 ∙ 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 TLX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TLX2 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			14	1	1	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	2

Variants in TLX2

This is a list of pathogenic ClinVar variants found in the TLX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-74514813-C-T		not specified	Uncertain significance (May 20, 2024)
2-74514845-C-A		not specified	Uncertain significance (Jan 23, 2024)
2-74514864-G-C		not specified	Uncertain significance (May 31, 2023)
2-74514871-A-G		not specified	Uncertain significance (Jun 28, 2023)
2-74514904-G-A		not specified	Uncertain significance (May 04, 2022)
2-74514906-G-C		not specified	Uncertain significance (Nov 03, 2023)
2-74514939-G-A		not specified	Uncertain significance (Sep 26, 2022)
2-74515006-C-T		not specified	Uncertain significance (Mar 01, 2024)
2-74515055-C-G			Benign (Feb 25, 2018)
2-74515093-G-C		not specified	Likely benign (Jun 29, 2023)
2-74515093-G-T		not specified	Uncertain significance (Jan 06, 2023)
2-74515149-G-A		not specified	Uncertain significance (Dec 13, 2023)
2-74515203-A-T		not specified	Uncertain significance (Sep 09, 2021)
2-74515204-C-T		not specified	Uncertain significance (Aug 12, 2022)
2-74515815-C-G		not specified	Uncertain significance (Apr 23, 2024)
2-74516012-C-T			Benign (Jan 23, 2018)
2-74516031-C-T		not specified	Uncertain significance (Aug 17, 2022)
2-74516109-C-T		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TLX2	protein_coding	protein_coding	ENST00000233638	3	3685

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.255	0.720	125573	0	3	125576	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.495	135	152	0.887	0.00000699	1732
Missense in Polyphen		48	52.893	0.9075		594
Synonymous	-0.948	83	72.7	1.14	0.00000342	661
Loss of Function	1.88	2	7.59	0.263	3.30e-7	88

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription activator that binds DNA elements with the consensus sequence 5'-CGGTAATTGG-3'. Binds DNA via its homeobox. Required for normal cell death of enteric neurons in the gastrointestinal tract. Required for normal development of the enteric nervous system, and for proper development of normal motility of the gastrointestinal tract (By similarity). {ECO:0000250}.
• Pathway: Cell Differentiation - Index expanded;Cell Differentiation - Index;Neural Crest Differentiation;ALK1 signaling events;ALK2 signaling events (Consensus)

Recessive Scores

• pRec: 0.233

Haploinsufficiency Scores

• pHI: 0.226
• hipred: N
• hipred_score: 0.482
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.576

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tlx2
• 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); growth/size/body region 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; embryo phenotype

Gene ontology

• Biological process: mesoderm formation;positive regulation of transcription by RNA polymerase II;enteric nervous system development;negative regulation of dendrite morphogenesis
• Cellular component: cellular_component;nucleus;cytoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;sequence-specific DNA binding