CLK3

CDC like kinase 3, the group of CDC like kinases

Basic information

Region (hg38): 15:74598500-74645414

Links

ENSG00000179335 ∙ NCBI:1198 ∙ OMIM:602990 ∙ HGNC:2071 ∙ Uniprot:P49761 ∙ 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 CLK3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLK3 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						0
missense			38			38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			17	1		18
Total	0	0	55	1	0

Variants in CLK3

This is a list of pathogenic ClinVar variants found in the CLK3 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-74615513-G-C		not specified	Uncertain significance (Apr 07, 2023)
15-74615543-G-A		not specified	Uncertain significance (Jan 07, 2025)
15-74615615-G-A		not specified	Uncertain significance (Mar 08, 2024)
15-74615626-G-A		not specified	Uncertain significance (Feb 06, 2023)
15-74615635-G-T		not specified	Uncertain significance (Oct 06, 2021)
15-74615642-G-T		not specified	Uncertain significance (Dec 19, 2022)
15-74615650-C-T		not specified	Uncertain significance (May 05, 2023)
15-74615659-G-A		not specified	Uncertain significance (Apr 28, 2022)
15-74615659-G-C		not specified	Uncertain significance (Apr 08, 2024)
15-74615665-C-T		not specified	Uncertain significance (Feb 05, 2025)
15-74615677-C-T		not specified	Uncertain significance (Aug 02, 2022)
15-74615687-G-T		not specified	Uncertain significance (Feb 23, 2023)
15-74615699-G-A		not specified	Uncertain significance (Apr 20, 2024)
15-74615705-G-T		not specified	Uncertain significance (Jan 26, 2025)
15-74615716-T-G		not specified	Uncertain significance (Dec 09, 2024)
15-74615720-C-G		not specified	Uncertain significance (Jul 27, 2022)
15-74615747-C-T		not specified	Uncertain significance (Jan 27, 2025)
15-74615813-T-A		not specified	Uncertain significance (Dec 14, 2023)
15-74615848-G-A		not specified	Likely benign (Jun 03, 2024)
15-74615851-G-A		not specified	Uncertain significance (Aug 14, 2023)
15-74615852-C-G		not specified	Uncertain significance (Oct 01, 2024)
15-74615864-A-C		not specified	Uncertain significance (May 26, 2024)
15-74619213-G-A		not specified	Uncertain significance (Jun 23, 2023)
15-74619279-G-A		not specified	Uncertain significance (Oct 11, 2024)
15-74619312-G-A		not specified	Uncertain significance (Apr 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLK3	protein_coding	protein_coding	ENST00000395066	13	41217

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.230	0.770	125732	0	15	125747	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.03	228	332	0.686	0.0000225	4104
Missense in Polyphen		60	121.16	0.49523		1339
Synonymous	0.128	118	120	0.985	0.00000687	1286
Loss of Function	4.09	8	33.6	0.238	0.00000221	365

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000182	0.000182
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000796	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dual specificity kinase acting on both serine/threonine and tyrosine-containing substrates. Phosphorylates serine- and arginine-rich (SR) proteins of the spliceosomal complex. May be a constituent of a network of regulatory mechanisms that enable SR proteins to control RNA splicing and can cause redistribution of SR proteins from speckles to a diffuse nucleoplasmic distribution. Phosphorylates SRSF1 and SRSF3. Regulates the alternative splicing of tissue factor (F3) pre-mRNA in endothelial cells. {ECO:0000269|PubMed:19168442, ECO:0000269|PubMed:9637771}.
• Pathway: mRNA Processing (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.682
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.62

Haploinsufficiency Scores

• pHI: 0.203
• hipred: Y
• hipred_score: 0.520
• ghis: 0.568

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.983

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clk3

Gene ontology

• Biological process: protein phosphorylation;peptidyl-tyrosine phosphorylation;regulation of RNA splicing;protein autophosphorylation
• Cellular component: acrosomal vesicle;nucleus;nucleoplasm;membrane;nuclear speck;intermediate filament cytoskeleton
• Molecular function: RNA binding;protein serine/threonine kinase activity;protein serine/threonine/tyrosine kinase activity;protein tyrosine kinase activity;protein binding;ATP binding;identical protein binding