SBK1

protein-coding

SH3 domain binding kinase 1

Gene summary

Predicted to enable protein serine/threonine kinase activity. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001024401.3

Inheritance

—

ClinVar variants

U:53

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr16:28,259,246-28,323,849

External References & Databases

Ensembl (ENSG00000188322)

Transcript & Mutation Effects

hg38 • Region Span ~64.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SBK1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 51

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001024401.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			53 clinvar			53
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	53	0	0	53

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001024401.3	RefSeq	NP_001019572.1	3	MANE Select
ENST00000341901.5	Ensembl	ENSP00000343248.4	3	MANE Select
ENST00000671413.3	Ensembl	ENSP00000499661.3	4	Standard
ENST00001134229.1	Ensembl	ENSP00000808052.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

peptidyl-serine phosphorylation
peptidyl-threonine phosphorylation

Molecular Function

protein serine/threonine kinase activity
ATP binding

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000341901
Coding exons: 3
Length: 31331
Individuals with no LoFs: 125746
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125748
p: 0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.94	117	247	0.474	0.0000187	2632
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.800

Gene Damage Prediction

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