CDC42EP4

CDC42 effector protein 4, the group of CDC42 effector proteins

Basic information

Region (hg38): 17:73283624-73312005

Links

ENSG00000179604 ∙ NCBI:23580 ∙ OMIM:605468 ∙ HGNC:17147 ∙ Uniprot:Q9H3Q1 ∙ 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 CDC42EP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDC42EP4 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			38	5		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	5	0

Variants in CDC42EP4

This is a list of pathogenic ClinVar variants found in the CDC42EP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-73285438-G-A		not specified	Uncertain significance (May 18, 2023)
17-73285453-C-T		not specified	Uncertain significance (Sep 15, 2021)
17-73285498-C-G		not specified	Likely benign (Aug 10, 2021)
17-73285516-C-A		not specified	Uncertain significance (Mar 01, 2023)
17-73285525-G-A		not specified	Uncertain significance (Feb 28, 2023)
17-73285526-G-C		not specified	Uncertain significance (Jun 21, 2023)
17-73285530-G-T		not specified	Uncertain significance (Dec 16, 2023)
17-73285539-C-T		not specified	Uncertain significance (Nov 20, 2023)
17-73285578-C-A		not specified	Uncertain significance (Nov 21, 2023)
17-73285588-G-A		not specified	Uncertain significance (May 04, 2022)
17-73285588-G-C		not specified	Uncertain significance (Oct 14, 2023)
17-73285604-C-T		not specified	Uncertain significance (Aug 17, 2022)
17-73285612-G-A		not specified	Uncertain significance (Feb 15, 2023)
17-73285621-C-T		not specified	Uncertain significance (Nov 09, 2021)
17-73285633-C-T		not specified	Uncertain significance (Aug 02, 2021)
17-73285643-C-G		not specified	Uncertain significance (Nov 09, 2022)
17-73285720-G-A		not specified	Uncertain significance (Nov 21, 2022)
17-73285735-C-T		not specified	Likely benign (Jan 29, 2024)
17-73285740-G-A		not specified	Likely benign (Aug 01, 2022)
17-73285770-C-G		not specified	Uncertain significance (Jan 09, 2024)
17-73285797-C-T		not specified	Likely benign (Jun 18, 2021)
17-73285814-C-G		not specified	Uncertain significance (Jan 02, 2024)
17-73285893-G-A		not specified	Uncertain significance (Sep 01, 2021)
17-73285895-A-T		not specified	Uncertain significance (Sep 29, 2023)
17-73285911-G-A		not specified	Uncertain significance (Apr 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDC42EP4	protein_coding	protein_coding	ENST00000335793	1	28552

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.212	0.752	125713	0	11	125724	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.330	235	250	0.941	0.0000175	2294
Missense in Polyphen		69	91.229	0.75634		912
Synonymous	-0.0329	116	116	1.00	0.00000871	775
Loss of Function	1.75	2	6.99	0.286	3.84e-7	79

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000304	0.000300
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000690	0.0000653
Other	0.00	0.00

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, when overexpressed in fibroblasts.

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.349
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.73

Haploinsufficiency Scores

• pHI: 0.164
• hipred: N
• hipred_score: 0.322
• ghis: 0.624

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.716

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdc42ep4
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: Rho protein signal transduction;regulation of cell shape;positive regulation of actin filament polymerization;positive regulation of pseudopodium assembly;cellular response to interferon-gamma
• Cellular component: cytoplasm;plasma membrane;cell-cell adherens junction;endomembrane system;actin cytoskeleton;microtubule cytoskeleton;phagocytic vesicle
• Molecular function: RNA binding;protein binding;GTP-Rho binding