LIMK2

LIM domain kinase 2, the group of LIM domain containing|PDZ domain containing|LIMK/TESK kinase family

Basic information

Region (hg38): 22:31212239-31280080

Links

ENSG00000182541

∙ NCBI:3985 ∙ OMIM:601988 ∙ HGNC:6614 ∙ Uniprot:P53671 ∙ 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 LIMK2 gene.

not_specified (94 variants)
not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIMK2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005569.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					2 clinvar	2
missense			62 clinvar	3 clinvar		65
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	62	3	2

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LIMK2	protein_coding	protein_coding	ENST00000340552	15	67842

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0156	0.984	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	342	423	0.809	0.0000259	4503
Missense in Polyphen		68	124.49	0.54621		1397
Synonymous	-0.114	170	168	1.01	0.0000103	1341
Loss of Function	3.57	9	30.2	0.298	0.00000156	355

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000308	0.000308
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000480	0.0000462
European (Non-Finnish)	0.0000462	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.000272	0.000261
Other	0.000349	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Displays serine/threonine-specific phosphorylation of myelin basic protein and histone (MBP) in vitro. {ECO:0000269|PubMed:10436159, ECO:0000269|PubMed:11018042}.;
Pathway: Fc gamma R-mediated phagocytosis - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Axon guidance - Homo sapiens (human);Androgen receptor signaling pathway;TGF-beta Signaling Pathway;EGF-EGFR Signaling Pathway;Developmental Biology;Signal Transduction;EPH-Ephrin signaling;EPHB-mediated forward signaling;RHO GTPases Activate ROCKs;RHO GTPase Effectors;Signaling by Rho GTPases;Sema4D induced cell migration and growth-cone collapse;Sema4D in semaphorin signaling;Semaphorin interactions;Axon guidance;CDC42 signaling events;RhoA signaling pathway (Consensus)

Recessive Scores

pRec: 0.206

Intolerance Scores

loftool: 0.117
rvis_EVS: 0.11
rvis_percentile_EVS: 62.14

Haploinsufficiency Scores

pHI: 0.266
hipred: Y
hipred_score: 0.756
ghis: 0.489

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Limk2
Phenotype: reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; renal/urinary system phenotype; skeleton phenotype; limbs/digits/tail phenotype; vision/eye phenotype; craniofacial phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype;

Gene ontology

Biological process: protein phosphorylation;spermatogenesis;phosphorylation;actin cytoskeleton organization;head development;cornea development in camera-type eye
Cellular component: nucleus;cytoplasm;cis-Golgi network
Molecular function: protein serine/threonine kinase activity;protein binding;ATP binding;metal ion binding;protein heterodimerization activity