SBK1

SH3 domain binding kinase 1

Basic information

Region (hg38): 16:28259246-28323849

Links

ENSG00000188322 ∙ NCBI:388228 ∙ OMIM:620212 ∙ HGNC:17699 ∙ Uniprot:Q52WX2 ∙ 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 SBK1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SBK1 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			31			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	0	0

Variants in SBK1

This is a list of pathogenic ClinVar variants found in the SBK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-28317462-G-A		not specified	Uncertain significance (Mar 23, 2023)
16-28317471-C-T		not specified	Uncertain significance (Aug 17, 2022)
16-28317479-C-A		not specified	Uncertain significance (Mar 31, 2023)
16-28319002-A-C		not specified	Uncertain significance (Feb 25, 2025)
16-28319054-C-T		not specified	Uncertain significance (Aug 02, 2023)
16-28319096-A-G		not specified	Uncertain significance (Sep 25, 2024)
16-28319103-A-G		not specified	Uncertain significance (Feb 09, 2023)
16-28319106-T-C		not specified	Uncertain significance (Nov 14, 2024)
16-28319130-A-C		not specified	Uncertain significance (Aug 02, 2023)
16-28319159-G-A		not specified	Uncertain significance (Jun 18, 2024)
16-28320095-C-T		not specified	Uncertain significance (Oct 26, 2022)
16-28320110-T-C		not specified	Uncertain significance (Sep 30, 2024)
16-28320145-G-C		not specified	Uncertain significance (Apr 25, 2022)
16-28320149-G-A		not specified	Uncertain significance (Nov 10, 2022)
16-28320272-G-C		not specified	Uncertain significance (May 09, 2024)
16-28320416-C-G		not specified	Uncertain significance (Jun 24, 2022)
16-28320448-C-T		not specified	Uncertain significance (Mar 21, 2024)
16-28320469-C-A		not specified	Uncertain significance (May 23, 2024)
16-28320500-C-G		not specified	Uncertain significance (Oct 09, 2024)
16-28320506-C-G		not specified	Uncertain significance (Aug 04, 2023)
16-28320531-A-C		not specified	Uncertain significance (Apr 07, 2023)
16-28320587-A-G		not specified	Uncertain significance (Jul 19, 2023)
16-28320610-C-G		not specified	Uncertain significance (Jun 11, 2021)
16-28320632-C-A		not specified	Uncertain significance (Dec 14, 2024)
16-28320635-G-C		not specified	Uncertain significance (Feb 08, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SBK1	protein_coding	protein_coding	ENST00000341901	3	31331

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.368	0.622	125746	0	2	125748	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.94	117	247	0.474	0.0000187	2632
Missense in Polyphen		10	67.66	0.1478		721
Synonymous	1.62	95	117	0.810	0.0000101	929
Loss of Function	2.16	2	8.97	0.223	3.83e-7	113

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)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in signal-transduction pathways related to the control of brain development. {ECO:0000250}.

Recessive Scores

• pRec: 0.122

Haploinsufficiency Scores

• pHI: 0.338
• hipred: Y
• hipred_score: 0.511
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.800

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sbk1

Gene ontology

• Biological process: peptidyl-serine phosphorylation;peptidyl-threonine phosphorylation
• Cellular component: cytoplasm
• Molecular function: protein serine/threonine kinase activity;ATP binding