CAPZB

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

Basic information

Region (hg38): 1:19338774-19485539

Links

ENSG00000077549 ∙ NCBI:832 ∙ OMIM:601572 ∙ HGNC:1491 ∙ Uniprot:P47756 ∙ 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 CAPZB gene.

• Inborn genetic diseases (3 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAPZB 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			1			1
Total	0	0	3	1	0

Variants in CAPZB

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

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

Position	Type	Phenotype	Significance	ClinVar
1-19342790-C-T		not specified	Uncertain significance (Dec 11, 2023)
1-19342838-T-C		not specified	Uncertain significance (Sep 20, 2023)
1-19342862-G-C		not specified	Uncertain significance (Jun 23, 2023)
1-19356731-G-A			Likely benign (Jan 01, 2023)
1-19356732-G-A		not specified	Uncertain significance (Oct 31, 2023)
1-19357433-C-T		not specified	Uncertain significance (May 03, 2023)
1-19378549-T-C		not specified	Uncertain significance (Dec 15, 2022)
1-19419657-G-A			Likely benign (Jan 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAPZB	protein_coding	protein_coding	ENST00000375142	9	146800

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.912	0.0883	120783	0	3	120786	0.0000124

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.83	58	158	0.367	0.00000861	1823
Missense in Polyphen		17	72.329	0.23504		842
Synonymous	0.641	55	61.4	0.896	0.00000356	508
Loss of Function	3.32	2	16.6	0.120	7.67e-7	204

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000700	0.0000700
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000933	0.00000933
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000167	0.000167

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. Plays a role in the regulation of cell morphology and cytoskeletal organization. {ECO:0000269|PubMed:21834987}.
• Pathway: Endocytosis - Homo sapiens (human);Vesicle-mediated transport;Membrane Trafficking;Factors involved in megakaryocyte development and platelet production;Post-translational protein modification;Metabolism of proteins;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;ER to Golgi Anterograde Transport;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.287
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.209
• hipred: Y
• hipred_score: 0.688
• ghis: 0.603

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.789

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Capzb
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); hearing/vestibular/ear phenotype

Zebrafish Information Network

• Gene name: capzb
• Affected structure: epidermal cell
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: cell morphogenesis;endoplasmic reticulum to Golgi vesicle-mediated transport;cytoskeleton organization;blood coagulation;regulation of lamellipodium assembly;antigen processing and presentation of exogenous peptide antigen via MHC class II;regulation of cell morphogenesis;actin cytoskeleton organization;barbed-end actin filament capping;negative regulation of filopodium assembly
• Cellular component: cytosol;cytoskeleton;F-actin capping protein complex;actin cytoskeleton;sarcomere;extracellular exosome;WASH complex
• Molecular function: actin binding;protein binding;cadherin binding;actin filament binding