TLX1

T cell leukemia homeobox 1, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 10:101131299-101137789

Previous symbols: [ "TCL3", "HOX11" ]

Links

ENSG00000107807 ∙ NCBI:3195 ∙ OMIM:186770 ∙ HGNC:5056 ∙ Uniprot:P31314 ∙ 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 TLX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TLX1 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in TLX1

This is a list of pathogenic ClinVar variants found in the TLX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-101131563-C-T		not specified	Uncertain significance (Jun 18, 2021)
10-101131674-T-C		not specified	Uncertain significance (Feb 14, 2024)
10-101131680-C-A		not specified	Uncertain significance (Nov 30, 2022)
10-101131731-G-A		not specified	Uncertain significance (Sep 22, 2022)
10-101131734-G-T		not specified	Uncertain significance (Mar 12, 2024)
10-101131737-A-C		not specified	Uncertain significance (Jul 09, 2021)
10-101131749-G-A		not specified	Uncertain significance (May 10, 2024)
10-101131777-C-T		not specified	Uncertain significance (Apr 22, 2022)
10-101131795-C-G		not specified	Uncertain significance (Jan 04, 2022)
10-101131876-G-C		not specified	Uncertain significance (Feb 15, 2023)
10-101131878-C-T		not specified	Uncertain significance (Mar 29, 2022)
10-101131896-A-G		not specified	Likely benign (Dec 28, 2022)
10-101131905-G-A		not specified	Uncertain significance (Feb 21, 2024)
10-101131941-G-A		not specified	Uncertain significance (May 30, 2024)
10-101131975-C-T		not specified	Uncertain significance (Dec 28, 2022)
10-101131978-A-C		not specified	Uncertain significance (Dec 07, 2021)
10-101134217-C-T		not specified	Uncertain significance (Sep 28, 2021)
10-101136717-C-T		not specified	Uncertain significance (Oct 26, 2021)
10-101136821-T-C		not specified	Uncertain significance (May 05, 2023)
10-101136891-C-T		not specified	Uncertain significance (Feb 28, 2024)
10-101136906-G-T		not specified	Uncertain significance (Mar 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TLX1	protein_coding	protein_coding	ENST00000370196	3	8289

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.742	0.256	123490	0	2	123492	0.00000810

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.93	85	152	0.560	0.00000709	2053
Missense in Polyphen		19	52.994	0.35853		638
Synonymous	0.560	64	70.0	0.915	0.00000342	708
Loss of Function	2.44	1	8.80	0.114	3.81e-7	110

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000549	0.0000546
Finnish	0.00	0.00
European (Non-Finnish)	0.00000911	0.00000910
Middle Eastern	0.0000549	0.0000546
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Controls the genesis of the spleen. Binds to the DNA sequence 5'-GGCGGTAAGTGG-3'.
• Disease: DISEASE: Note=A chromosomal aberration involving TLX1 may be a cause of a form of T-cell acute lymphoblastic leukemia (T-ALL). Translocation t(10;14)(q24;q11) with TCRD. {ECO:0000269|PubMed:1676542, ECO:0000269|PubMed:1681546, ECO:0000269|PubMed:1717256}.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human);Cell Differentiation - Index expanded;Cell Differentiation - Index (Consensus)

Recessive Scores

• pRec: 0.232

Intolerance Scores

• loftool: 0.138
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.4

Haploinsufficiency Scores

• pHI: 0.471
• hipred: Y
• hipred_score: 0.736
• ghis: 0.423

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.891

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tlx1
• Phenotype: cellular phenotype; hematopoietic system 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); immune system phenotype

Gene ontology

• Biological process: multicellular organism development;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;protein binding