LMTK2

lemur tyrosine kinase 2, the group of Protein phosphatase 1 regulatory subunits|Receptor tyrosine kinases

Basic information

Region (hg38): 7:98106861-98209638

Links

ENSG00000164715 ∙ NCBI:22853 ∙ OMIM:610989 ∙ HGNC:17880 ∙ Uniprot:Q8IWU2 ∙ 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 LMTK2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LMTK2 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				2	5	7
missense			73	2	1	76
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	73	4	6

Variants in LMTK2

This is a list of pathogenic ClinVar variants found in the LMTK2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-98107239-C-T		not specified	Uncertain significance (Oct 03, 2022)
7-98141521-C-T		not specified	Uncertain significance (May 23, 2024)
7-98141530-A-G		not specified	Uncertain significance (Oct 03, 2022)
7-98151384-G-A		not specified	Uncertain significance (Aug 11, 2022)
7-98154791-G-A		not specified	Uncertain significance (Jul 26, 2021)
7-98154806-G-A		not specified	Uncertain significance (Aug 12, 2021)
7-98154806-G-C		not specified	Uncertain significance (Jan 03, 2024)
7-98159405-G-A		not specified	Uncertain significance (Apr 19, 2024)
7-98159411-G-C		not specified	Uncertain significance (Sep 22, 2023)
7-98159416-CTG-C		Malignant tumor of prostate	Uncertain significance (-)
7-98171580-A-T		not specified	Uncertain significance (Oct 03, 2022)
7-98171584-G-C		not specified	Uncertain significance (Sep 14, 2022)
7-98171625-G-C		not specified	Uncertain significance (Jan 09, 2024)
7-98185092-A-G		not specified	Uncertain significance (May 27, 2022)
7-98186988-A-G		not specified	Uncertain significance (Oct 29, 2021)
7-98190763-A-G		not specified	Uncertain significance (Feb 23, 2023)
7-98190764-T-G		not specified	Uncertain significance (Feb 06, 2023)
7-98191661-C-T		not specified	Uncertain significance (Sep 16, 2021)
7-98191697-G-A		not specified	Uncertain significance (Apr 15, 2024)
7-98191723-G-A		not specified	Uncertain significance (Aug 28, 2023)
7-98191827-G-A			Likely benign (Feb 08, 2018)
7-98191915-G-A		not specified	Uncertain significance (Sep 23, 2023)
7-98191934-G-T		not specified	Uncertain significance (Feb 21, 2024)
7-98192023-G-A		not specified	Uncertain significance (Nov 21, 2022)
7-98192066-C-T		not specified	Uncertain significance (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LMTK2	protein_coding	protein_coding	ENST00000297293	14	102749

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000217	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.29	770	877	0.878	0.0000536	9842
Missense in Polyphen		184	318.08	0.57847		3657
Synonymous	-0.434	412	401	1.03	0.0000299	2994
Loss of Function	6.00	7	55.0	0.127	0.00000261	680

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.000218	0.000163
South Asian	0.0000981	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Phosphorylates PPP1C, phosphorylase b and CFTR.

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.103
• rvis_EVS: -2.42
• rvis_percentile_EVS: 1.05

Haploinsufficiency Scores

• pHI: 0.321
• hipred: Y
• hipred_score: 0.540
• ghis: 0.514

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.869

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lmtk2
• Phenotype: reproductive system 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); cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: receptor recycling;protein phosphorylation;transmembrane receptor protein tyrosine kinase signaling pathway;peptidyl-serine phosphorylation;peptidyl-threonine phosphorylation;peptidyl-tyrosine phosphorylation;endocytic recycling;negative regulation of phosphoprotein phosphatase activity;transferrin transport;early endosome to late endosome transport;protein autophosphorylation
• Cellular component: early endosome;Golgi apparatus;cytosol;integral component of plasma membrane;integral component of membrane;growth cone;neuronal cell body;receptor complex;perinuclear region of cytoplasm;recycling endosome
• Molecular function: protein serine/threonine kinase activity;transmembrane receptor protein tyrosine kinase activity;protein phosphatase inhibitor activity;protein binding;ATP binding;myosin VI binding