SBK3

SH3 domain binding kinase family member 3

Basic information

Region (hg38): 19:55540656-55545543

Links

ENSG00000231274 ∙ NCBI:100130827 ∙ ∙ HGNC:44121 ∙ Uniprot:P0C264 ∙ 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 SBK3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SBK3 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			32			32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	0	0

Variants in SBK3

This is a list of pathogenic ClinVar variants found in the SBK3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-55541172-A-C		not specified	Uncertain significance (Jan 14, 2025)
19-55541256-C-T		not specified	Uncertain significance (Apr 26, 2023)
19-55541268-G-A		not specified	Uncertain significance (Dec 13, 2023)
19-55541286-G-A		not specified	Uncertain significance (Aug 27, 2024)
19-55541288-G-A		not specified	Uncertain significance (Oct 26, 2022)
19-55541300-C-A		not specified	Uncertain significance (Jan 16, 2024)
19-55541318-G-A		not specified	Uncertain significance (Jun 02, 2024)
19-55541340-C-T		not specified	Uncertain significance (Mar 07, 2024)
19-55541364-G-A		not specified	Uncertain significance (Sep 28, 2022)
19-55541379-C-G		not specified	Uncertain significance (May 03, 2023)
19-55541381-C-T		not specified	Uncertain significance (Feb 14, 2025)
19-55541393-C-T		not specified	Uncertain significance (Aug 26, 2024)
19-55541403-C-T		not specified	Uncertain significance (Feb 22, 2025)
19-55541466-G-A		not specified	Uncertain significance (Feb 06, 2024)
19-55541486-A-C		not specified	Uncertain significance (Feb 05, 2025)
19-55541488-C-A		not specified	Uncertain significance (Feb 07, 2025)
19-55541501-C-T		not specified	Uncertain significance (Aug 21, 2024)
19-55544119-C-A		not specified	Uncertain significance (Feb 06, 2024)
19-55544137-G-A		not specified	Uncertain significance (Oct 24, 2024)
19-55544150-C-T		not specified	Uncertain significance (Feb 05, 2025)
19-55544165-G-C		not specified	Uncertain significance (Oct 28, 2024)
19-55544219-C-T		not specified	Uncertain significance (Jan 17, 2025)
19-55544224-C-T		not specified	Uncertain significance (Nov 17, 2023)
19-55544225-G-A		not specified	Uncertain significance (Jan 29, 2025)
19-55544249-A-C		not specified	Uncertain significance (May 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SBK3	protein_coding	protein_coding	ENST00000420723	4	4887

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000679	0.524	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.593	217	243	0.893	0.0000152	2661
Missense in Polyphen		77	92.814	0.82962		1018
Synonymous	0.969	93	106	0.880	0.00000680	967
Loss of Function	0.315	5	5.82	0.859	2.48e-7	80

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

Haploinsufficiency Scores

• ghis: 0.435

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sbk3

Gene ontology

• Biological process: protein phosphorylation
• Molecular function: protein serine/threonine kinase activity;ATP binding