CDC42BPG

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

Basic information

Region (hg38): 11:64823051-64844653

Links

ENSG00000171219 ∙ NCBI:55561 ∙ OMIM:613991 ∙ HGNC:29829 ∙ Uniprot:Q6DT37 ∙ 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 CDC42BPG gene.

• Inborn genetic diseases (103 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDC42BPG 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				1	3	4
missense			94	9	1	104
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	94	10	4

Variants in CDC42BPG

This is a list of pathogenic ClinVar variants found in the CDC42BPG region.

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

Position	Type	Phenotype	Significance	ClinVar
11-64826489-G-C		not specified	Uncertain significance (Dec 13, 2022)
11-64826674-G-C		not specified	Uncertain significance (Feb 28, 2023)
11-64826719-G-C		not specified	Uncertain significance (Oct 12, 2022)
11-64827055-A-T		not specified	Uncertain significance (Nov 07, 2022)
11-64827079-C-A		not specified	Uncertain significance (Jul 21, 2021)
11-64827105-T-C		not specified	Uncertain significance (Oct 25, 2022)
11-64827117-G-C		not specified	Uncertain significance (Oct 03, 2023)
11-64827150-G-C		not specified	Uncertain significance (Apr 05, 2023)
11-64827309-C-A		not specified	Uncertain significance (Aug 10, 2023)
11-64827321-A-C		not specified	Uncertain significance (Jan 25, 2023)
11-64827332-C-T		not specified	Uncertain significance (Feb 09, 2023)
11-64827366-C-G		not specified	Uncertain significance (Feb 28, 2023)
11-64827372-G-A		not specified	Uncertain significance (Jul 12, 2022)
11-64827539-T-C		not specified	Uncertain significance (Mar 01, 2023)
11-64827581-A-C		not specified	Uncertain significance (Mar 05, 2024)
11-64827586-G-T		not specified	Uncertain significance (Jan 10, 2022)
11-64827595-G-C		not specified	Uncertain significance (Dec 16, 2022)
11-64827694-G-A		not specified	Uncertain significance (Dec 26, 2023)
11-64827700-C-T		not specified	Uncertain significance (Nov 08, 2021)
11-64829507-G-A		not specified	Uncertain significance (May 24, 2023)
11-64829654-C-T		not specified	Uncertain significance (Jan 24, 2024)
11-64829667-C-T			Benign (Jun 08, 2018)
11-64829711-C-T		not specified	Uncertain significance (Jan 10, 2023)
11-64829785-C-T		not specified	Uncertain significance (Sep 27, 2021)
11-64829786-G-A		not specified	Uncertain significance (Mar 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDC42BPG	protein_coding	protein_coding	ENST00000342711	37	21183

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.56e-26	0.934	125635	0	113	125748	0.000449

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.34	836	952	0.878	0.0000665	9736
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000727	0.000702
Ashkenazi Jewish	0.000301	0.000298
East Asian	0.000436	0.000435
Finnish	0.000501	0.000416
European (Non-Finnish)	0.000459	0.000440
Middle Eastern	0.000436	0.000435
South Asian	0.000820	0.000817
Other	0.000653	0.000652

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.120
• hipred: N
• hipred_score: 0.484
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.908

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdc42bpg

Gene ontology

• Biological process: protein phosphorylation;actin cytoskeleton reorganization;intracellular signal transduction
• Cellular component: microtubule organizing center;cytosol;cell leading edge
• Molecular function: magnesium ion binding;protein serine/threonine kinase activity;protein binding;ATP binding