SBK2

SH3 domain binding kinase family member 2

Basic information

Region (hg38): 19:55528610-55537133

Links

ENSG00000187550 ∙ NCBI:646643 ∙ ∙ HGNC:34416 ∙ Uniprot:P0C263 ∙ 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 SBK2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SBK2 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			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	0

Variants in SBK2

This is a list of pathogenic ClinVar variants found in the SBK2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-55529741-C-T		not specified	Uncertain significance (Mar 06, 2023)
19-55529767-G-A		not specified	Uncertain significance (Jan 04, 2022)
19-55529771-C-T		not specified	Uncertain significance (Jan 09, 2024)
19-55529804-C-G		not specified	Uncertain significance (Nov 10, 2022)
19-55529804-C-T		not specified	Uncertain significance (Jun 07, 2024)
19-55529807-G-C		not specified	Uncertain significance (Mar 18, 2024)
19-55529866-C-T		not specified	Uncertain significance (May 08, 2024)
19-55529908-T-A		not specified	Uncertain significance (Aug 11, 2022)
19-55529917-T-C		not specified	Uncertain significance (Dec 01, 2022)
19-55529933-A-G		not specified	Uncertain significance (Mar 29, 2022)
19-55529973-C-G		not specified	Uncertain significance (Feb 28, 2024)
19-55530011-G-A		not specified	Uncertain significance (Aug 26, 2022)
19-55530031-C-T		not specified	Uncertain significance (Jun 27, 2022)
19-55530053-C-A		not specified	Uncertain significance (Mar 01, 2023)
19-55530092-C-T		not specified	Uncertain significance (May 26, 2024)
19-55530103-G-A		not specified	Uncertain significance (Jul 06, 2021)
19-55530151-C-A		not specified	Uncertain significance (Oct 16, 2023)
19-55530166-C-A		not specified	Uncertain significance (Dec 14, 2022)
19-55530173-C-T		not specified	Uncertain significance (Dec 20, 2021)
19-55530187-C-T		not specified	Likely benign (Jul 14, 2021)
19-55530191-G-A		not specified	Uncertain significance (Mar 29, 2023)
19-55530272-C-T		not specified	Uncertain significance (Jul 14, 2021)
19-55530292-C-A		not specified	Uncertain significance (Aug 30, 2021)
19-55530293-A-G		not specified	Uncertain significance (Aug 30, 2021)
19-55530307-G-A		not specified	Uncertain significance (Apr 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SBK2	protein_coding	protein_coding	ENST00000413299	3	7357

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000397	0.401	124593	0	42	124635	0.000169

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.141	190	196	0.972	0.0000143	2120
Missense in Polyphen		67	68.472	0.9785		854
Synonymous	1.19	87	102	0.850	0.00000884	770
Loss of Function	0.253	7	7.76	0.902	4.05e-7	95

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000373	0.000355
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000638	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000173	0.000168
Middle Eastern	0.0000638	0.0000556
South Asian	0.000447	0.000425
Other	0.000340	0.000330

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.208

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.398

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sbk2

Gene ontology

• Biological process: cell migration;signal transduction by protein phosphorylation;stress-activated protein kinase signaling cascade;activation of protein kinase activity;regulation of MAPK cascade
• Cellular component: cytoplasm
• Molecular function: protein serine/threonine kinase activity;ATP binding;Rac GTPase binding