CAPZA1

capping actin protein of muscle Z-line subunit alpha 1, the group of Dynactin subunits

Basic information

Region (hg38): 1:112619804-112671616

Links

ENSG00000116489 ∙ NCBI:829 ∙ OMIM:601580 ∙ HGNC:1488 ∙ Uniprot:P52907 ∙ 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 CAPZA1 gene.

• Inborn genetic diseases (15 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAPZA1 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			15			15
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	15	0	0

Variants in CAPZA1

This is a list of pathogenic ClinVar variants found in the CAPZA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-112619857-G-A		not specified	Uncertain significance (Jun 07, 2023)
1-112619878-G-A		not specified	Benign/Likely benign (-)
1-112647213-C-T		not specified	Uncertain significance (Jan 18, 2023)
1-112647216-A-G		not specified	Uncertain significance (Dec 06, 2022)
1-112647239-T-G		not specified	Uncertain significance (Feb 26, 2024)
1-112653620-G-A		not specified	Uncertain significance (Mar 21, 2022)
1-112653625-G-C		not specified	Uncertain significance (Dec 02, 2021)
1-112653630-C-T		not specified	Uncertain significance (Sep 16, 2021)
1-112653642-T-C		not specified	Uncertain significance (Sep 17, 2021)
1-112654557-A-C		not specified	Uncertain significance (Jan 24, 2023)
1-112654579-G-A		not specified	Uncertain significance (Dec 28, 2023)
1-112654660-G-A		not specified	Uncertain significance (Dec 28, 2023)
1-112659709-G-A		not specified	Uncertain significance (May 27, 2022)
1-112659765-G-A		not specified	Uncertain significance (Sep 14, 2023)
1-112667121-T-A		not specified	Uncertain significance (Dec 26, 2023)
1-112667126-A-G		not specified	Uncertain significance (May 30, 2023)
1-112667143-T-A		not specified	Uncertain significance (Jul 14, 2022)
1-112667152-A-G			Likely benign (Aug 01, 2022)
1-112669562-A-G		not specified	Uncertain significance (Sep 14, 2022)
1-112669573-A-G		not specified	Uncertain significance (Jun 11, 2021)
1-112670028-A-G		not specified	Uncertain significance (Apr 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAPZA1	protein_coding	protein_coding	ENST00000263168	10	52447

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.933	0.0671	125694	0	3	125697	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	113	159	0.710	0.00000840	1910
Missense in Polyphen		16	40.122	0.39879		517
Synonymous	0.806	46	53.5	0.860	0.00000274	491
Loss of Function	3.42	2	17.4	0.115	7.35e-7	219

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000632	0.0000617
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000185	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: F-actin-capping proteins bind in a Ca(2+)-independent manner to the fast growing ends of actin filaments (barbed end) thereby blocking the exchange of subunits at these ends. Unlike other capping proteins (such as gelsolin and severin), these proteins do not sever actin filaments. May play a role in the formation of epithelial cell junctions. {ECO:0000269|PubMed:22891260}.
• Pathway: Endocytosis - Homo sapiens (human);Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation;Vesicle-mediated transport;Membrane Trafficking;Factors involved in megakaryocyte development and platelet production;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Hemostasis;COPI-independent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;COPI-mediated anterograde transport;Advanced glycosylation endproduct receptor signaling;ER to Golgi Anterograde Transport;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.176

Intolerance Scores

• loftool: 0.0503
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.18

Haploinsufficiency Scores

• pHI: 0.745
• hipred: Y
• hipred_score: 0.606
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.937

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Capza1

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;blood coagulation;antigen processing and presentation of exogenous peptide antigen via MHC class II;actin cytoskeleton organization;cell junction assembly;interleukin-12-mediated signaling pathway;innate immune response;barbed-end actin filament capping;protein-containing complex assembly
• Cellular component: extracellular region;cytosol;cytoskeleton;F-actin capping protein complex;actin cytoskeleton;actin cortical patch;extracellular exosome;WASH complex
• Molecular function: actin binding;protein binding;cadherin binding;actin filament binding