CDC42BPG

protein-coding

CDC42 binding protein kinase gamma, the group of Pleckstrin homology domain containing|AGC family kinases

Gene summary

Enables ATP binding activity; magnesium ion binding activity; and protein serine/threonine kinase activity. Involved in protein phosphorylation. Located in cell leading edge and cytosol. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_017525.3

Inheritance

—

ClinVar variants

U:299B:26

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chr11:64,823,052-64,844,653

External References & Databases

Ensembl (ENSG00000171219)

Transcript & Mutation Effects

hg38 • Region Span ~21.6 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 CDC42BPG variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 290

not providedTotal: 6

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017525.3. 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			6 clinvar	2 clinvar	3 clinvar	11
missense			281 clinvar	20 clinvar	1 clinvar	302
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			11 clinvar			11
Total	0	0	299	22	4	325

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017525.3	RefSeq	NP_059995.2	37	MANE Select
ENST00000342711.6	Ensembl	ENSP00000345133.5	37	MANE Select
ENST00000904236.1	Ensembl	ENSP00000574295.1	37	Standard
ENST00000904236.2	Ensembl	ENSP00000574295.1	37	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein phosphorylation
actin cytoskeleton reorganization
intracellular signal transduction

Molecular Function

magnesium ion binding
protein serine/threonine kinase activity
protein binding
ATP binding

Cellular Component

microtubule organizing center
cytosol
cell leading edge

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000342711
Coding exons: 37
Length: 21183
Individuals with no LoFs: 125635
Homozygous LoFs: 0
Heterozygous LoFs: 113
Defined: 125748
p: 0.000449

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.34	836	952	0.878	0.0000665	9736
Missense (PolyPhen)		356	429.11	0.82963		4422
Synonymous	-1.19	453	422	1.07	0.0000295	3292
Loss of Function	2.75	53	79.4	0.667	0.00000398	867

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00058	0.00055	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00044	0.00044	rare
Finnish	0.00050	0.00042	rare
European (Non-Finnish)	0.00046	0.00044	rare
South Asian	0.00082	0.00082	rare
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as a downstream effector of CDC42 in cytoskeletal reorganization. Contributes to the actomyosin contractility required for cell invasion, through the regulation of MYPT1 and thus MLC2 phosphorylation (By similarity). {ECO:0000250|UniProtKB:Q5VT25, ECO:0000269|PubMed:15194684}.;

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.862
RVIS EVS: -1.46
RVIS percentile EVS: 3.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.908

Gene Damage Prediction

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