LEUTX

leucine twenty homeobox, the group of PRD class homeoboxes and pseudogenes

Basic information

Region (hg38): 19:39776595-39786291

Links

ENSG00000213921 ∙ NCBI:342900 ∙ OMIM:618701 ∙ HGNC:31953 ∙ Uniprot:A8MZ59 ∙ 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 LEUTX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LEUTX 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			8	3		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	3	0

Variants in LEUTX

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

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

Position	Type	Phenotype	Significance	ClinVar
19-39784614-A-G		not specified	Uncertain significance (Dec 12, 2023)
19-39784670-G-A		not specified	Uncertain significance (Oct 29, 2021)
19-39785698-A-T		not specified	Uncertain significance (Apr 20, 2023)
19-39785758-C-T		not specified	Likely benign (Dec 16, 2023)
19-39785783-A-C		not specified	Uncertain significance (Jun 07, 2024)
19-39785840-G-A		not specified	Likely benign (Mar 02, 2023)
19-39785879-A-G		not specified	Uncertain significance (Oct 05, 2023)
19-39785884-C-T		not specified	Uncertain significance (Nov 01, 2022)
19-39785930-C-T		not specified	Likely benign (Feb 28, 2023)
19-39785983-G-C		not specified	Uncertain significance (Apr 26, 2024)
19-39786023-T-G		not specified	Uncertain significance (Feb 27, 2024)
19-39786051-G-T		not specified	Uncertain significance (Jan 19, 2022)
19-39786084-A-T		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LEUTX	protein_coding	protein_coding	ENST00000396841	2	9541

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00160	0.278	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.946	66	91.5	0.722	0.00000499	1079
Missense in Polyphen		8	12.496	0.64021		144
Synonymous	0.892	26	32.5	0.801	0.00000162	341
Loss of Function	-1.87	3	0.991	3.03	4.18e-8	13

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	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: Preimplantation Embryo (Consensus)

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0344

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding