LTK

leukocyte receptor tyrosine kinase, the group of Receptor tyrosine kinases

Basic information

Region (hg38): 15:41503636-41513887

Links

ENSG00000062524 ∙ NCBI:4058 ∙ OMIM:151520 ∙ HGNC:6721 ∙ Uniprot:P29376 ∙ 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 LTK gene.

• Inborn genetic diseases (47 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LTK 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			49		1	50
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	49	1	2

Variants in LTK

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

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

Position	Type	Phenotype	Significance	ClinVar
15-41504144-C-G			Uncertain significance (Jul 01, 2018)
15-41504154-C-A			Likely benign (Aug 15, 2018)
15-41504231-A-G		not specified	Uncertain significance (Jul 14, 2023)
15-41504240-G-A		not specified	Uncertain significance (Sep 07, 2022)
15-41504355-T-C		not specified	Uncertain significance (Apr 14, 2023)
15-41504358-A-G		not specified	Uncertain significance (Apr 20, 2023)
15-41504362-G-A		not specified	Uncertain significance (Mar 06, 2023)
15-41504427-C-T		not specified	Uncertain significance (Feb 15, 2023)
15-41504539-C-T		not specified	Uncertain significance (Apr 27, 2022)
15-41504540-G-A		not specified	Uncertain significance (Dec 17, 2021)
15-41504555-C-T		not specified	Uncertain significance (Nov 17, 2022)
15-41504581-C-T		not specified	Uncertain significance (Sep 22, 2022)
15-41504608-G-A		not specified	Uncertain significance (Sep 27, 2022)
15-41504782-G-A		not specified	Uncertain significance (Jul 26, 2021)
15-41504840-G-A		not specified	Uncertain significance (May 22, 2023)
15-41504848-C-T		not specified	Uncertain significance (Jun 22, 2021)
15-41504849-G-C		not specified	Uncertain significance (Jan 11, 2023)
15-41505017-C-G		not specified	Uncertain significance (Aug 11, 2022)
15-41505023-G-A		not specified	Uncertain significance (Dec 03, 2021)
15-41505032-C-T		not specified	Uncertain significance (Aug 13, 2021)
15-41505054-C-T		not specified	Uncertain significance (Feb 10, 2022)
15-41505217-A-T		not specified	Uncertain significance (Jan 08, 2024)
15-41505281-G-A		not specified	Uncertain significance (Feb 16, 2023)
15-41505471-C-T		not specified	Uncertain significance (Dec 11, 2023)
15-41505472-G-C		not specified	Uncertain significance (Feb 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LTK	protein_coding	protein_coding	ENST00000263800	20	10250

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.29e-26	0.000860	124542	3	1203	125748	0.00481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.490	492	462	1.06	0.0000248	5421
Missense in Polyphen		201	191.11	1.0518		2333
Synonymous	-0.439	204	196	1.04	0.0000107	1858
Loss of Function	0.380	40	42.7	0.937	0.00000217	468

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00527	0.00524
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.00136	0.00136
Finnish	0.00690	0.00691
European (Non-Finnish)	0.00714	0.00703
Middle Eastern	0.00136	0.00136
South Asian	0.00170	0.00170
Other	0.00508	0.00490

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor with a tyrosine-protein kinase activity. The exact function of this protein is not known. Studies with chimeric proteins (replacing its extracellular region with that of several known growth factor receptors, such as EGFR and CSFIR) demonstrate its ability to promote growth and specifically neurite outgrowth, and cell survival. Signaling appears to involve the PI3 kinase pathway. Involved in regulation of the secretory pathway involving endoplasmic reticulum (ER) export sites (ERESs) and ER to Golgi transport. {ECO:0000269|PubMed:20548102}.
• Pathway: IL-7 signaling;JAK STAT pathway and regulation;EPO signaling;VEGF (Consensus)

Intolerance Scores

• loftool: 0.0997
• rvis_EVS: -0.77
• rvis_percentile_EVS: 13.16

Haploinsufficiency Scores

• pHI: 0.282
• hipred: N
• hipred_score: 0.342
• ghis: 0.433

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.779

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ltk

Zebrafish Information Network

• Gene name: ltk
• Affected structure: iridophore
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: protein phosphorylation;signal transduction;transmembrane receptor protein tyrosine kinase signaling pathway;cell population proliferation;positive regulation of cardiac muscle cell apoptotic process;positive regulation of neuron projection development;phosphatidylinositol 3-kinase signaling;peptidyl-tyrosine phosphorylation;negative regulation of apoptotic process;regulation of neuron differentiation;cellular response to retinoic acid
• Cellular component: plasma membrane;integral component of plasma membrane;membrane;receptor complex
• Molecular function: protein kinase activity;protein tyrosine kinase activity;transmembrane receptor protein tyrosine kinase activity;protein binding;ATP binding