CLK1

CDC like kinase 1, the group of CDC like kinases

Basic information

Region (hg38): 2:200853009-200864691

Links

ENSG00000013441 ∙ NCBI:1195 ∙ OMIM:601951 ∙ HGNC:2068 ∙ Uniprot:P49759 ∙ 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 CLK1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLK1 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			36	1		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4			4
Total	0	0	40	1	0

Variants in CLK1

This is a list of pathogenic ClinVar variants found in the CLK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-200853310-A-C		not specified	Uncertain significance (Aug 12, 2024)
2-200853340-T-G		not specified	Uncertain significance (Sep 20, 2024)
2-200853415-C-T		not specified	Uncertain significance (Jun 17, 2024)
2-200853416-G-A		not specified	Likely benign (Dec 15, 2023)
2-200853431-C-G		not specified	Uncertain significance (Sep 18, 2024)
2-200853967-C-A		not specified	Uncertain significance (Dec 27, 2023)
2-200853988-C-T		not specified	Uncertain significance (Nov 07, 2023)
2-200853989-G-A		not specified	Uncertain significance (Feb 13, 2025)
2-200855042-T-C		not specified	Uncertain significance (Mar 07, 2023)
2-200856703-T-C		not specified	Uncertain significance (Jan 23, 2024)
2-200856732-T-G		not specified	Uncertain significance (Nov 17, 2023)
2-200856739-C-T		not specified	Uncertain significance (Jul 30, 2024)
2-200856777-A-G		not specified	Uncertain significance (Nov 24, 2024)
2-200856783-G-A		not specified	Uncertain significance (Mar 25, 2024)
2-200856798-C-T		not specified	Uncertain significance (Dec 10, 2024)
2-200856932-A-G		not specified	Uncertain significance (May 12, 2024)
2-200857835-T-G		not specified	Uncertain significance (Jan 04, 2024)
2-200857992-T-C		not specified	Uncertain significance (Aug 21, 2023)
2-200858016-G-T		not specified	Uncertain significance (Jun 07, 2024)
2-200858027-C-T		not specified	Uncertain significance (May 12, 2024)
2-200859693-T-G		not specified	Uncertain significance (Jun 06, 2023)
2-200859738-C-T		not specified	Uncertain significance (Jun 16, 2024)
2-200861249-G-A			Uncertain significance (Aug 24, 2021)
2-200861252-G-A		not specified	Uncertain significance (Jun 09, 2022)
2-200861264-T-A		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLK1	protein_coding	protein_coding	ENST00000434813	13	11691

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.60e-7	0.995	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.468	276	299	0.924	0.0000155	3531
Missense in Polyphen		56	83.866	0.66773		1097
Synonymous	-0.818	106	95.8	1.11	0.00000496	893
Loss of Function	2.54	15	30.0	0.500	0.00000159	370

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000211	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000204	0.000202
Middle Eastern	0.000163	0.000109
South Asian	0.000131	0.000131
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, SRSF3 and PTPN1. Regulates the alternative splicing of tissue factor (F3) pre-mRNA in endothelial cells and adenovirus E1A pre-mRNA. {ECO:0000269|PubMed:10480872, ECO:0000269|PubMed:19168442}.
• Pathway: Legionellosis - Homo sapiens (human);mRNA Processing (Consensus)

Recessive Scores

• pRec: 0.154

Intolerance Scores

• loftool: 0.849
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• pHI: 0.501
• hipred: Y
• hipred_score: 0.731
• ghis: 0.585

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.979

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clk1
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: cell population proliferation;peptidyl-serine phosphorylation;peptidyl-threonine phosphorylation;peptidyl-tyrosine phosphorylation;regulation of RNA splicing;protein autophosphorylation
• Cellular component: nucleus;cytoplasm
• Molecular function: protein serine/threonine kinase activity;protein serine/threonine/tyrosine kinase activity;non-membrane spanning protein tyrosine kinase activity;protein binding;ATP binding