CDC42EP3

CDC42 effector protein 3, the group of CDC42 effector proteins

Basic information

Region (hg38): 2:37641882-37738468

Links

ENSG00000163171 ∙ NCBI:10602 ∙ OMIM:606133 ∙ HGNC:16943 ∙ Uniprot:Q9UKI2 ∙ 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 CDC42EP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDC42EP3 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						0
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in CDC42EP3

This is a list of pathogenic ClinVar variants found in the CDC42EP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-37645933-T-C		not specified	Uncertain significance (Jul 14, 2023)
2-37645947-A-G		not specified	Uncertain significance (Jan 26, 2022)
2-37645960-G-T		not specified	Uncertain significance (Apr 20, 2023)
2-37645965-G-C		not specified	Uncertain significance (Jul 26, 2023)
2-37645974-A-C		not specified	Uncertain significance (Aug 02, 2021)
2-37645984-C-T		not specified	Uncertain significance (Apr 27, 2024)
2-37645996-C-T		not specified	Uncertain significance (Feb 08, 2023)
2-37646062-C-T		not specified	Uncertain significance (Dec 15, 2023)
2-37646127-T-A		not specified	Uncertain significance (May 24, 2023)
2-37646143-T-A		not specified	Uncertain significance (Apr 15, 2024)
2-37646153-G-C		not specified	Uncertain significance (Jan 06, 2023)
2-37646182-C-G		not specified	Uncertain significance (Jun 17, 2024)
2-37646182-C-T		not specified	Uncertain significance (Apr 04, 2023)
2-37646218-A-C		not specified	Uncertain significance (Dec 22, 2023)
2-37646295-G-A		not specified	Uncertain significance (Apr 05, 2023)
2-37646311-A-G		not specified	Uncertain significance (Jul 06, 2021)
2-37646322-C-T		not specified	Uncertain significance (Oct 02, 2023)
2-37646324-G-T		not specified	Uncertain significance (Apr 28, 2022)
2-37646420-A-C		not specified	Uncertain significance (May 14, 2024)
2-37646421-A-G		not specified	Uncertain significance (Oct 12, 2022)
2-37646430-A-G		CDC42EP3-related condition	Uncertain significance (May 13, 2024)
2-37646451-T-C		not specified	Uncertain significance (Sep 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDC42EP3	protein_coding	protein_coding	ENST00000295324	1	96580

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.186	0.768	125741	0	6	125747	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0558	146	144	1.01	0.00000768	1672
Missense in Polyphen		40	56.016	0.71408		668
Synonymous	-0.793	74	65.8	1.12	0.00000422	515
Loss of Function	1.65	2	6.57	0.304	2.79e-7	79

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000395	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably involved in the organization of the actin cytoskeleton. May act downstream of CDC42 to induce actin filament assembly leading to cell shape changes. Induces pseudopodia formation in fibroblasts. {ECO:0000269|PubMed:10490598, ECO:0000269|PubMed:11035016}.
• Pathway: Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Signal Transduction;MAPK6/MAPK4 signaling;MAPK family signaling cascades (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.249
• rvis_EVS: -0.29
• rvis_percentile_EVS: 32.94

Haploinsufficiency Scores

• pHI: 0.119
• hipred: Y
• hipred_score: 0.767
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdc42ep3

Gene ontology

• Biological process: signal transduction;Rho protein signal transduction;regulation of cell shape;positive regulation of actin filament polymerization;positive regulation of pseudopodium assembly
• Cellular component: cytoplasm;cytosol;plasma membrane;endomembrane system;actin cytoskeleton
• Molecular function: protein binding;cytoskeletal regulatory protein binding;GTP-Rho binding