CDC42BPB

CDC42 binding protein kinase beta, the group of AGC family kinases

Basic information

Region (hg38): 14:102932380-103057549

Links

ENSG00000198752 ∙ NCBI:9578 ∙ OMIM:614062 ∙ HGNC:1738 ∙ Uniprot:Q9Y5S2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Moderate), mode of inheritance: AD
• Chilton-Okur-Chung neurodevelopmental syndrome (Strong), mode of inheritance: AD
• Chilton-Okur-Chung neurodevelopmental syndrome (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Chilton-Okur-Chung neurodevelopmental syndrome	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	32031333

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CDC42BPB gene.

• Inborn_genetic_diseases (147 variants)
• not_provided (136 variants)
• CDC42BPB-related_disorder (43 variants)
• Chilton-Okur-Chung_neurodevelopmental_syndrome (42 variants)
• not_specified (14 variants)
• CDC42BPB-related_neurodevelopmental_syndrome (12 variants)
• See_cases (6 variants)
• Neurodevelopmental_disorder (3 variants)
• Autism_spectrum_disorder (2 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
• CDC42BPB-related_Neurodevelopmental_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDC42BPB gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006035.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	30	6	38
missense		13	234	42	2	291
nonsense	4	3	4			11
start loss		1				1
frameshift	1	4	2			7
splice donor/acceptor (+/-2bp)		4	1			5
Total	5	25	243	72	8

Highest pathogenic variant AF is 0.0000037233917

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDC42BPB	protein_coding	protein_coding	ENST00000361246	37	125084

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	3.63e-12	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.66	686	1.01e+3	0.677	0.0000638	11188
Missense in Polyphen		182	393.59	0.46241		4336
Synonymous	-0.553	433	419	1.03	0.0000295	3268
Loss of Function	8.63	6	98.4	0.0610	0.00000557	1083

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000907	0.0000905
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000619	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine/threonine-protein kinase which is an important downstream effector of CDC42 and plays a role in the regulation of cytoskeleton reorganization and cell migration. Regulates actin cytoskeletal reorganization via phosphorylation of PPP1R12C and MYL9/MLC2 (PubMed:21457715, PubMed:21949762). In concert with MYO18A and LURAP1, is involved in modulating lamellar actomyosin retrograde flow that is crucial to cell protrusion and migration (PubMed:18854160). Phosphorylates PPP1R12A (PubMed:21457715). In concert with FAM89B/LRAP25 mediates the targeting of LIMK1 to the lamellipodium resulting in its activation and subsequent phosphorylation of CFL1 which is important for lamellipodial F- actin regulation (By similarity). {ECO:0000250|UniProtKB:Q7TT50, ECO:0000269|PubMed:18854160, ECO:0000269|PubMed:21457715, ECO:0000269|PubMed:21949762}.

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.0187
• rvis_EVS: -3.29
• rvis_percentile_EVS: 0.42

Haploinsufficiency Scores

• pHI: 0.248
• hipred: Y
• hipred_score: 0.707
• ghis: 0.625

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.437

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdc42bpb

Gene ontology

• Biological process: protein phosphorylation;cytoskeleton organization;establishment or maintenance of cell polarity;signal transduction;cell migration;actomyosin structure organization;actin cytoskeleton reorganization;intracellular signal transduction
• Cellular component: cytoplasm;cytoskeleton;plasma membrane;cell-cell junction;lamellipodium;cell leading edge;actomyosin;extracellular exosome
• Molecular function: magnesium ion binding;protein kinase activity;protein serine/threonine kinase activity;ATP binding;Rho GTPase binding;protein-containing complex binding