CLK4

CDC like kinase 4, the group of CDC like kinases

Basic information

Region (hg38): 5:178602664-178630615

Links

ENSG00000113240 ∙ NCBI:57396 ∙ OMIM:607969 ∙ HGNC:13659 ∙ Uniprot:Q9HAZ1 ∙ 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 CLK4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLK4 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					1	1
missense			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	1

Variants in CLK4

This is a list of pathogenic ClinVar variants found in the CLK4 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-178603622-T-C		not specified	Uncertain significance (Aug 01, 2024)
5-178603657-G-C		not specified	Uncertain significance (Jan 18, 2025)
5-178603705-C-T		not specified	Uncertain significance (Dec 13, 2024)
5-178603741-T-C		not specified	Uncertain significance (Nov 14, 2024)
5-178603753-A-C		not specified	Uncertain significance (May 09, 2023)
5-178603861-G-A		not specified	Uncertain significance (May 07, 2024)
5-178605313-G-C		not specified	Uncertain significance (Dec 06, 2022)
5-178605319-T-A		not specified	Uncertain significance (Feb 12, 2024)
5-178612457-A-G		not specified	Uncertain significance (Jul 05, 2023)
5-178612475-T-C		not specified	Uncertain significance (Sep 08, 2024)
5-178612484-G-A		not specified	Uncertain significance (Sep 27, 2024)
5-178612885-G-A		not specified	Uncertain significance (Jan 05, 2022)
5-178613479-T-C		not specified	Uncertain significance (Jan 22, 2024)
5-178613511-A-T		not specified	Uncertain significance (Jan 24, 2025)
5-178613635-A-G		not specified	Uncertain significance (Sep 30, 2024)
5-178613637-C-T		not specified	Uncertain significance (Nov 14, 2024)
5-178613794-G-A		not specified	Uncertain significance (Nov 17, 2022)
5-178613815-C-T		not specified	Uncertain significance (Oct 28, 2024)
5-178613836-T-C		not specified	Uncertain significance (Jan 10, 2023)
5-178613841-T-C		not specified	Uncertain significance (Aug 02, 2022)
5-178617352-C-T		not specified	Uncertain significance (Sep 01, 2021)
5-178618590-C-T		not specified	Uncertain significance (Dec 12, 2022)
5-178618612-T-C		not specified	Uncertain significance (Jan 27, 2025)
5-178618643-G-A			Benign (Sep 01, 2017)
5-178618723-C-T		not specified	Likely benign (Aug 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLK4	protein_coding	protein_coding	ENST00000316308	12	27952

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000619	0.999	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.11	181	280	0.645	0.0000161	3235
Missense in Polyphen		40	96.906	0.41277		1186
Synonymous	-0.0430	90	89.5	1.01	0.00000485	807
Loss of Function	2.87	12	28.6	0.420	0.00000159	346

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000343	0.000333
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.0000513	0.0000462
European (Non-Finnish)	0.000178	0.000176
Middle Eastern	0.000111	0.000109
South Asian	0.0000985	0.0000980
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 and may be a constituent of a network of regulatory mechanisms that enable SR proteins to control RNA splicing. Phosphorylates SRSF1 and SRSF3. Required for the regulation of alternative splicing of MAPT/TAU. Regulates the alternative splicing of tissue factor (F3) pre-mRNA in endothelial cells. {ECO:0000269|PubMed:11170754, ECO:0000269|PubMed:19168442}.
• Pathway: mRNA Processing (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.581
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.22

Haploinsufficiency Scores

• pHI: 0.201
• hipred: Y
• hipred_score: 0.639
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• 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: Clk4

Gene ontology

• Biological process: peptidyl-tyrosine phosphorylation;regulation of RNA splicing;protein autophosphorylation
• Cellular component: nucleus
• Molecular function: protein serine/threonine kinase activity;protein serine/threonine/tyrosine kinase activity;protein tyrosine kinase activity;protein binding;ATP binding