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.

not_specified (64 variants)
not_provided (1 variants)

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. These statistics are base on transcript: NM_000004071.4. 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						0
missense			56 clinvar	2 clinvar		58
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	56	2	0

Loading clinvar variants...

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