LMTK3

lemur tyrosine kinase 3, the group of Protein phosphatase 1 regulatory subunits|Receptor tyrosine kinases

Basic information

Region (hg38): 19:48485270-48513935

Links

ENSG00000142235 ∙ NCBI:114783 ∙ OMIM:619624 ∙ HGNC:19295 ∙ Uniprot:Q96Q04 ∙ 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 LMTK3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LMTK3 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				3	3	6
missense			75	1		76
nonsense						0
start loss						0
frameshift			1			1
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1	1	2
Total	0	0	76	6	4

Variants in LMTK3

This is a list of pathogenic ClinVar variants found in the LMTK3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-48491100-T-G			Benign (May 21, 2018)
19-48491126-G-T		not specified	Uncertain significance (Jun 02, 2024)
19-48491194-G-A		not specified	Uncertain significance (Dec 18, 2023)
19-48491222-C-G		not specified	Uncertain significance (Jul 14, 2023)
19-48491234-C-G		not specified	Uncertain significance (Oct 12, 2021)
19-48491421-C-A		not specified	Uncertain significance (May 29, 2024)
19-48491478-G-A		not specified	Uncertain significance (Mar 15, 2024)
19-48491505-G-C		not specified	Uncertain significance (Aug 12, 2021)
19-48493827-G-T		not specified	Uncertain significance (Oct 02, 2023)
19-48493897-C-T		not specified	Uncertain significance (Jun 18, 2024)
19-48493906-G-C		not specified	Uncertain significance (Apr 07, 2023)
19-48493921-C-T		not specified	Uncertain significance (Dec 14, 2022)
19-48493922-GTCC-G		LMTK3-related disorder	Likely benign (Jun 21, 2023)
19-48493945-C-T		not specified	Uncertain significance (Jul 19, 2023)
19-48493953-C-T		not specified	Uncertain significance (Feb 14, 2023)
19-48493977-G-T		not specified	Uncertain significance (Feb 22, 2023)
19-48494005-C-G		not specified	Uncertain significance (Apr 07, 2023)
19-48494008-C-A		not specified	Uncertain significance (Jul 14, 2022)
19-48494043-G-A		not specified	Uncertain significance (Jan 02, 2024)
19-48494059-A-G		not specified	Uncertain significance (Jun 12, 2023)
19-48494106-C-T		not specified	Likely benign (Apr 07, 2023)
19-48497413-C-T		not specified	Uncertain significance (Sep 26, 2022)
19-48497456-G-C		not specified	Uncertain significance (Mar 20, 2024)
19-48497464-C-T		not specified	Uncertain significance (Jan 31, 2024)
19-48497481-G-T		not specified	Uncertain significance (Jun 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LMTK3	protein_coding	protein_coding	ENST00000270238	16	27919

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000315	124579	0	2	124581	0.00000803

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.32	355	669	0.531	0.0000419	9231
Missense in Polyphen		41	156.27	0.26237		1862
Synonymous	1.91	276	319	0.864	0.0000228	3345
Loss of Function	5.61	3	42.5	0.0706	0.00000213	559

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)	0.0000181	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein kinase which phosphorylates ESR1 (in vitro) and protects it against proteasomal degradation. May also regulate ESR1 levels indirectly via a PKC-AKT-FOXO3 pathway where it decreases the activity of PKC and the phosphorylation of AKT, thereby increasing binding of transcriptional activator FOXO3 to the ESR1 promoter and increasing ESR1 transcription (PubMed:21602804). Involved in endocytic trafficking of N-methyl- D-aspartate receptors (NMDAR) in neurons (By similarity). {ECO:0000250|UniProtKB:Q5XJV6, ECO:0000269|PubMed:21602804}.

Haploinsufficiency Scores

• pHI: 0.160
• ghis: 0.549

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.663

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lmtk3
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive 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)

Gene ontology

• Biological process: protein phosphorylation;negative regulation of phosphatase activity
• Cellular component: Golgi membrane;cellular_component;integral component of membrane;axon;dendrite
• Molecular function: molecular_function;protein serine/threonine kinase activity;protein binding;ATP binding;metal ion binding