CAP1

cyclase associated actin cytoskeleton regulatory protein 1

Basic information

Region (hg38): 1:40040233-40072649

Links

ENSG00000131236 ∙ NCBI:10487 ∙ OMIM:617801 ∙ HGNC:20040 ∙ Uniprot:Q01518 ∙ 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 CAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAP1 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	1
missense			20	1		21
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	20	1	1

Variants in CAP1

This is a list of pathogenic ClinVar variants found in the CAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-40059368-G-A		not specified	Uncertain significance (May 03, 2023)
1-40059431-C-T		not specified	Likely benign (Apr 25, 2022)
1-40059432-G-A		not specified	Uncertain significance (Mar 07, 2024)
1-40059439-T-C			Benign (Dec 31, 2019)
1-40059450-C-T		not specified	Uncertain significance (May 01, 2022)
1-40060109-C-T		not specified	Uncertain significance (May 30, 2024)
1-40061737-G-A			Benign (Feb 26, 2018)
1-40061772-C-T		not specified	Uncertain significance (Jan 02, 2024)
1-40064275-G-T		not specified	Uncertain significance (Jan 16, 2024)
1-40064287-C-T		not specified	Uncertain significance (Mar 28, 2024)
1-40064302-G-A		not specified	Uncertain significance (Sep 27, 2022)
1-40064365-G-T		not specified	Uncertain significance (Dec 02, 2022)
1-40064520-T-C		not specified	Uncertain significance (Aug 05, 2023)
1-40064549-T-C		not specified	Uncertain significance (Feb 15, 2023)
1-40067631-C-T		not specified	Uncertain significance (Jun 02, 2023)
1-40067670-G-A		not specified	Uncertain significance (Jan 30, 2024)
1-40067684-G-A		not specified	Uncertain significance (Apr 07, 2023)
1-40067707-C-G		not specified	Uncertain significance (Jan 03, 2024)
1-40069786-C-T		not specified	Uncertain significance (Apr 22, 2022)
1-40069810-C-T		not specified	Uncertain significance (Jul 05, 2023)
1-40069819-G-A		not specified	Uncertain significance (Sep 20, 2023)
1-40069845-C-T		not specified	Uncertain significance (Dec 26, 2023)
1-40070234-G-A		not specified	Uncertain significance (Dec 22, 2023)
1-40070243-A-G		not specified	Uncertain significance (Jan 23, 2024)
1-40070273-A-G		not specified	Uncertain significance (Dec 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAP1	protein_coding	protein_coding	ENST00000372797	12	32417

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0198	0.980	124782	0	13	124795	0.0000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.27	205	263	0.779	0.0000137	3077
Missense in Polyphen		68	99.778	0.68151		1248
Synonymous	0.534	93	99.8	0.932	0.00000555	926
Loss of Function	3.32	8	26.4	0.303	0.00000147	305

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000539	0.0000530
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000654
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Directly regulates filament dynamics and has been implicated in a number of complex developmental and morphological processes, including mRNA localization and the establishment of cell polarity.
• Pathway: miR-targeted genes in adipocytes - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;Angiopoietin Like Protein 8 Regulatory Pathway;Insulin Signaling;Developmental Biology;Neutrophil degranulation;how progesterone initiates the oocyte maturation;Innate Immune System;Immune System;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis;Signaling by ROBO receptors;Axon guidance;Role of ABL in ROBO-SLIT signaling (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.77

Haploinsufficiency Scores

• pHI: 0.212
• hipred: Y
• hipred_score: 0.745
• ghis: 0.626

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.721

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cap1

Zebrafish Information Network

• Gene name: cap1
• Affected structure: adaxial cell
• Phenotype tag: abnormal
• Phenotype quality: disorganized

Gene ontology

• Biological process: cell morphogenesis;ameboidal-type cell migration;receptor-mediated endocytosis;establishment or maintenance of cell polarity;signal transduction;activation of adenylate cyclase activity;actin polymerization or depolymerization;neutrophil degranulation
• Cellular component: extracellular region;plasma membrane;focal adhesion;cortical actin cytoskeleton;azurophil granule lumen;extracellular exosome
• Molecular function: actin binding;adenylate cyclase binding