LMTK3

protein-coding

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

Gene summary

Predicted to enable protein kinase activity. Predicted to be located in Golgi membrane; axon; and dendrite. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001388485.1

Inheritance

ClinVar variants

U:211B:10

Top phenotype

LMTK3-related disorder

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chr19:48,485,271-48,513,935

External References & Databases

Ensembl (ENSG00000142235)

Transcript & Mutation Effects

hg38 • Region Span ~28.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

complex neurodevelopmental disorderLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0100038

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LMTK3 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 195

not providedTotal: 20

LMTK3-related disorderTotal: 3

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001388485.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	5 clinvar	3 clinvar	10
missense			198 clinvar	2 clinvar		200
nonsense			2 clinvar			2
start loss						0
frameshift			7 clinvar			7
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	211	7	3	221

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001388485.1	RefSeq	NP_001375414.1	15	MANE Select
ENST00000600059.6	Ensembl	ENSP00000472020.1	15	MANE Select
NM_001080434.2	RefSeq	NP_001073903.2	15	Standard
ENST00000598924.1	Ensembl	ENSP00000500551.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein phosphorylation
negative regulation of phosphatase activity

Molecular Function

molecular_function
protein serine/threonine kinase activity
protein binding
ATP binding
metal ion binding

Cellular Component

Golgi membrane
cellular_component
integral component of membrane
axon
dendrite

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000270238
Coding exons: 16
Length: 27919
Individuals with no LoFs: 124579
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 124581
p: 0.00000803

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	4.32	355	669	0.531	0.0000419	9231
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.663

Gene Damage Prediction

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