LIMK2

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

Basic information

Region (hg38): 22:31212238-31280080

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.

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.

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	2
missense			42	2		44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	2	2

Variants in LIMK2

This is a list of pathogenic ClinVar variants found in the LIMK2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-31225727-T-A		not specified	Uncertain significance (Sep 06, 2022)
22-31225729-T-A		not specified	Uncertain significance (Dec 16, 2022)
22-31225734-A-G		not specified	Uncertain significance (Jun 24, 2022)
22-31225750-G-A		not specified	Uncertain significance (Jun 29, 2022)
22-31225809-T-C		not specified	Uncertain significance (Oct 26, 2022)
22-31225815-T-G		not specified	Uncertain significance (Jun 03, 2022)
22-31248753-T-G		not specified	Uncertain significance (Dec 22, 2023)
22-31259210-G-A			Benign (Jun 01, 2023)
22-31260014-G-A		not specified	Uncertain significance (Apr 22, 2024)
22-31260041-C-G		not specified	Uncertain significance (Jan 30, 2024)
22-31260064-G-A		not specified	Uncertain significance (Feb 27, 2023)
22-31262189-C-T		not specified	Uncertain significance (Oct 04, 2022)
22-31262216-G-A		not specified	Uncertain significance (Sep 07, 2022)
22-31262679-C-T		not specified	Uncertain significance (May 02, 2023)
22-31262691-C-T		not specified	Uncertain significance (Dec 01, 2022)
22-31262692-G-A		not specified	Likely benign (Dec 20, 2023)
22-31262718-G-A		not specified	Uncertain significance (Jun 03, 2024)
22-31262730-G-A		not specified	Likely benign (Sep 22, 2023)
22-31262776-G-A		not specified	Uncertain significance (Mar 31, 2024)
22-31262781-C-T		not specified	Uncertain significance (Aug 02, 2023)
22-31265995-C-T		not specified	Uncertain significance (Feb 27, 2024)
22-31266011-G-A		not specified	Uncertain significance (Sep 21, 2021)
22-31266019-A-G		not specified	Uncertain significance (Mar 28, 2024)
22-31266022-C-T		not specified	Uncertain significance (Mar 01, 2023)
22-31266038-G-A		not specified	Uncertain significance (Dec 22, 2023)

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