SIK2

salt inducible kinase 2, the group of SIK family kinases

Basic information

Region (hg38): 11:111602448-111730855

Previous symbols: [ "SNF1LK2" ]

Links

ENSG00000170145 ∙ NCBI:23235 ∙ OMIM:608973 ∙ HGNC:21680 ∙ Uniprot:Q9H0K1 ∙ 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 SIK2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIK2 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	2
missense			36	1		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	3		4
Total	0	0	37	5	1

Variants in SIK2

This is a list of pathogenic ClinVar variants found in the SIK2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-111602603-C-G		not specified	Uncertain significance (May 31, 2023)
11-111602624-G-A		not specified	Uncertain significance (Dec 01, 2022)
11-111602691-A-G		not specified	Uncertain significance (Apr 07, 2023)
11-111701507-C-T		not specified	Uncertain significance (Nov 03, 2023)
11-111703217-A-G		not specified	Uncertain significance (Jun 27, 2022)
11-111703244-T-C		not specified	Uncertain significance (May 13, 2024)
11-111703311-G-A		not specified	Uncertain significance (Jul 05, 2023)
11-111703323-A-G		not specified	Uncertain significance (May 07, 2024)
11-111703419-T-C		not specified	Uncertain significance (Apr 12, 2024)
11-111712271-G-T		not specified	Uncertain significance (Sep 17, 2021)
11-111712302-C-A		not specified	Uncertain significance (Jul 14, 2021)
11-111712349-G-A		not specified	Uncertain significance (Nov 07, 2022)
11-111719782-G-T		not specified	Uncertain significance (Jan 27, 2022)
11-111719976-A-G		not specified	Uncertain significance (Oct 24, 2023)
11-111720624-A-G		not specified	Uncertain significance (Oct 14, 2023)
11-111720918-A-G			Benign (Jul 30, 2018)
11-111720995-C-T		not specified	Uncertain significance (Mar 04, 2024)
11-111720996-G-A		not specified	Likely benign (Mar 01, 2024)
11-111720997-G-C		not specified	Uncertain significance (Jan 23, 2024)
11-111721022-C-T		not specified	Uncertain significance (Oct 26, 2022)
11-111721843-A-G		not specified	Uncertain significance (Feb 28, 2024)
11-111721900-G-A		not specified	Uncertain significance (Nov 08, 2022)
11-111722669-C-T		not specified	Uncertain significance (May 25, 2022)
11-111722723-C-T		not specified	Uncertain significance (Mar 29, 2022)
11-111723510-G-A		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIK2	protein_coding	protein_coding	ENST00000304987	15	128463

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00349	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.55	360	524	0.686	0.0000295	6046
Missense in Polyphen		93	215.78	0.43099		2432
Synonymous	1.16	183	204	0.897	0.0000120	1853
Loss of Function	5.45	7	47.5	0.147	0.00000272	491

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000643	0.0000615
Middle Eastern	0.000163	0.000163
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Phosphorylates 'Ser-794' of IRS1 in insulin-stimulated adipocytes, potentially modulating the efficiency of insulin signal transduction. Inhibits CREB activity by phosphorylating and repressing TORCs, the CREB-specific coactivators. {ECO:0000269|PubMed:15454081}.
• Pathway: Glucagon signaling pathway - Homo sapiens (human);LKB1 signaling events (Consensus)

Recessive Scores

• pRec: 0.172

Intolerance Scores

• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.79

Haploinsufficiency Scores

• pHI: 0.266
• hipred: Y
• hipred_score: 0.809
• ghis: 0.510

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.522

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sik2
• Phenotype: pigmentation phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; muscle phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein phosphorylation;negative regulation of TOR signaling;intracellular signal transduction;cellular response to glucose starvation;regulation of insulin receptor signaling pathway;protein autophosphorylation
• Cellular component: nucleus;cytoplasm;nucleotide-activated protein kinase complex
• Molecular function: magnesium ion binding;protein serine/threonine kinase activity;protein binding;ATP binding