CSNK1A1L

casein kinase 1 alpha 1 like, the group of casein kinase 1 family

Basic information

Region (hg38): 13:37103259-37105664

Links

ENSG00000180138 ∙ NCBI:122011 ∙ ∙ HGNC:20289 ∙ Uniprot:Q8N752 ∙ 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 CSNK1A1L gene.

• not_specified (42 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSNK1A1L gene is commonly pathogenic or not. These statistics are base on transcript: NM_000145203.6. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			42			42
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	42	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSNK1A1L	protein_coding	protein_coding	ENST00000379800	1	2406

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0132	0.872	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.172	178	185	0.964	0.0000111	2248
Missense in Polyphen		73	75.343	0.9689		988
Synonymous	-1.09	84	72.2	1.16	0.00000470	624
Loss of Function	1.31	4	7.98	0.501	6.29e-7	94

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Casein kinases are operationally defined by their preferential utilization of acidic proteins such as caseins as substrates. It can phosphorylate a large number of proteins. Participates in Wnt signaling (By similarity). {ECO:0000250}.
• Pathway: Gastric cancer - Homo sapiens (human);Breast cancer - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Hedgehog signaling pathway - Homo sapiens (human);WNT-Core;HH-Core;Chromosomal and microsatellite instability in colorectal cancer;Hedgehog Signaling Pathway;Wnt Signaling Pathway (Consensus)

Recessive Scores

• pRec: 0.171

Intolerance Scores

• loftool: 0.908
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.48

Haploinsufficiency Scores

• pHI: 0.0957
• hipred: N
• hipred_score: 0.168

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.914

Gene Damage Prediction

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

Gene ontology

• Biological process: Wnt signaling pathway;peptidyl-serine phosphorylation;peptidyl-threonine phosphorylation;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;negative regulation of canonical Wnt signaling pathway
• Cellular component: nucleus;cytoplasm;cytosol
• Molecular function: protein serine/threonine kinase activity;ATP binding