CAPZB
capping actin protein of muscle Z-line subunit beta, the group of Dynactin subunits
Basic information
Region (hg38): 1:19338775-19485539
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
| missense | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 4 | |||||
| Total | 0 | 0 | 7 | 2 | 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) | ||
| 1-19342853-G-A | not specified | Likely benign (Oct 04, 2024) | ||
| 1-19342862-G-C | not specified | Uncertain significance (Jun 23, 2023) | ||
| 1-19345197-C-T | not specified | Uncertain significance (Jan 16, 2025) | ||
| 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) | ||
| 1-19357454-A-T | not specified | Uncertain significance (Sep 03, 2024) | ||
| 1-19378549-T-C | not specified | Uncertain significance (Dec 15, 2022) | ||
| 1-19419657-G-A | Likely benign (Jan 01, 2023) |
GnomAD
Source:
| 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:
- 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