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.

not_specified (62 variants)
not_provided (2 variants)

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. These statistics are base on transcript: NM_000006367.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar		2 clinvar	5
missense			66 clinvar	1 clinvar		67
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	72	1	2

Loading clinvar variants...

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

loftool
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
Phenotype

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