CDC42SE1

CDC42 small effector 1

Basic information

Region (hg38): 1:151050971-151070325

Links

ENSG00000197622 ∙ NCBI:56882 ∙ OMIM:619456 ∙ HGNC:17719 ∙ Uniprot:Q9NRR8 ∙ 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 CDC42SE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDC42SE1 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in CDC42SE1

This is a list of pathogenic ClinVar variants found in the CDC42SE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-151054260-G-A		not specified	Uncertain significance (Aug 02, 2022)
1-151054281-C-T		not specified	Uncertain significance (Oct 25, 2022)
1-151055017-A-G		not specified	Uncertain significance (Feb 27, 2024)
1-151055043-C-A		not specified	Uncertain significance (Oct 29, 2021)
1-151055102-G-A		not specified	Uncertain significance (Jan 31, 2024)
1-151055678-G-A		not specified	Uncertain significance (Jun 16, 2022)
1-151055691-C-T		not specified	Uncertain significance (Jun 11, 2024)
1-151067323-A-G			Benign (Dec 31, 2019)
1-151067391-A-C		not specified	Uncertain significance (Nov 30, 2022)
1-151067437-C-T			Benign (Jul 04, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDC42SE1	protein_coding	protein_coding	ENST00000439374	3	19355

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00354	0.640	125725	0	20	125745	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	28	47.7	0.587	0.00000262	519
Missense in Polyphen		5	10.932	0.45739		128
Synonymous	0.595	12	14.9	0.804	7.27e-7	144
Loss of Function	0.521	4	5.29	0.756	3.10e-7	55

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000707	0.000707
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.000707	0.000707
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably involved in the organization of the actin cytoskeleton by acting downstream of CDC42, inducing actin filament assembly. Alters CDC42-induced cell shape changes. In activated T-cells, may play a role in CDC42-mediated F-actin accumulation at the immunological synapse. May play a role in early contractile events in phagocytosis in macrophages. {ECO:0000269|PubMed:10816584, ECO:0000269|PubMed:15840583, ECO:0000269|PubMed:17045588}.

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.617
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58

Haploinsufficiency Scores

• pHI: 0.219
• hipred: N
• hipred_score: 0.398
• ghis: 0.646

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Cdc42se1

Zebrafish Information Network

• Gene name: cdc42se1
• Affected structure: midbrain hindbrain boundary
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: phagocytosis;signal transduction;regulation of cell shape;negative regulation of GTPase activity;regulation of Rho protein signal transduction
• Cellular component: cytoplasm;cytoskeleton;plasma membrane
• Molecular function: GTPase inhibitor activity;structural molecule activity;Rho GTPase binding