CDC42BPA

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

Basic information

Region (hg38): 1:226989865-227318492

Links

ENSG00000143776 ∙ NCBI:8476 ∙ OMIM:603412 ∙ HGNC:1737 ∙ Uniprot:Q5VT25 ∙ 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 CDC42BPA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDC42BPA 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				3	3	6
missense			56	4	2	62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	56	7	5

Variants in CDC42BPA

This is a list of pathogenic ClinVar variants found in the CDC42BPA region.

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

Position	Type	Phenotype	Significance	ClinVar
1-226994288-G-C		not specified	Uncertain significance (May 20, 2024)
1-226994323-C-T		not specified	Uncertain significance (Feb 16, 2023)
1-226994330-A-T		not specified	Uncertain significance (Dec 15, 2022)
1-226994341-G-C		not specified	Uncertain significance (Apr 28, 2022)
1-226994386-G-A		not specified	Uncertain significance (Apr 28, 2022)
1-226994399-C-T		not specified	Uncertain significance (Jan 26, 2022)
1-226994854-C-T		not specified	Uncertain significance (Apr 17, 2024)
1-226994897-G-T		not specified	Uncertain significance (Jan 29, 2024)
1-226994914-C-T		not specified	Uncertain significance (Mar 01, 2023)
1-226994915-G-A		not specified	Uncertain significance (Apr 09, 2024)
1-226994921-C-A		not specified	Uncertain significance (May 18, 2022)
1-226994972-C-T		not specified	Uncertain significance (Jan 03, 2024)
1-226994973-G-A			Benign (Jan 24, 2018)
1-227005007-A-C		not specified	Uncertain significance (Apr 06, 2024)
1-227016124-T-C		not specified	Uncertain significance (Apr 04, 2024)
1-227016972-C-T		not specified	Uncertain significance (May 10, 2022)
1-227017008-C-T		not specified	Uncertain significance (Dec 16, 2022)
1-227023331-T-C		not specified	Likely benign (Jul 14, 2021)
1-227026060-T-G		not specified	Uncertain significance (May 23, 2023)
1-227026065-G-A		not specified	Uncertain significance (Apr 19, 2023)
1-227026130-C-T			Likely benign (Dec 31, 2019)
1-227026131-G-A		not specified	Uncertain significance (Feb 15, 2023)
1-227028662-G-C		not specified	Uncertain significance (Mar 29, 2022)
1-227028707-C-T		not specified	Uncertain significance (Sep 17, 2021)
1-227028866-T-C		not specified	Uncertain significance (Apr 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDC42BPA	protein_coding	protein_coding	ENST00000366769	36	328610

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00691	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.39	684	884	0.774	0.0000456	11307
Missense in Polyphen		162	283.05	0.57234		3558
Synonymous	0.646	295	309	0.953	0.0000158	3137
Loss of Function	7.28	18	94.2	0.191	0.00000511	1192

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000523	0.000522
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000572	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000160	0.000158
Middle Eastern	0.0000572	0.0000544
South Asian	0.0000703	0.0000653
Other	0.000164	0.000163

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 (PubMed:15723050, PubMed:9418861, PubMed:9092543). Regulates actin cytoskeletal reorganization via phosphorylation of PPP1R12C and MYL9/MLC2 (PubMed:21457715). 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, LIMK1 and LIMK2 (PubMed:11340065, PubMed:11399775). May play a role in TFRC-mediated iron uptake (PubMed:20188707). 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:Q3UU96, ECO:0000269|PubMed:11340065, ECO:0000269|PubMed:11399775, ECO:0000269|PubMed:15723050, ECO:0000269|PubMed:18854160, ECO:0000269|PubMed:20188707, ECO:0000269|PubMed:21457715, ECO:0000269|PubMed:9092543, ECO:0000269|PubMed:9418861}.
• Pathway: CDC42 signaling events (Consensus)

Recessive Scores

• pRec: 0.161

Intolerance Scores

• loftool: 0.607
• rvis_EVS: -1.54
• rvis_percentile_EVS: 3.32

Haploinsufficiency Scores

• pHI: 0.347
• hipred: Y
• hipred_score: 0.652
• ghis: 0.600

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.655

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdc42bpa

Gene ontology

• Biological process: protein phosphorylation;cell migration;actomyosin structure organization;actin cytoskeleton reorganization;intracellular signal transduction
• Cellular component: cytoplasm;cell-cell junction;lamellipodium;cell leading edge;actomyosin;extracellular exosome
• Molecular function: magnesium ion binding;protein serine/threonine kinase activity;protein binding;ATP binding;identical protein binding