CAPNS1
calpain small subunit 1, the group of EF-hand domain containing
Basic information
Region (hg38): 19:36139953-36150353
Previous symbols: [ "CAPN4" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Pulmonary hypertension, primary, 6 | AR | Cardiovascular; Pulmonary | The condition can involve severe, early-onset pulmonary hypertension, with related cardiovascular sequelae, and awareness may allow early identification and management | Cardiovascular; Pulmonary | 38230350 |
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 CAPNS1 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 | 2 | |||||
| missense | 16 | 16 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 16 | 2 | 0 |
Variants in CAPNS1
This is a list of pathogenic ClinVar variants found in the CAPNS1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-36141058-G-C | not specified | Uncertain significance (Jul 05, 2023) | ||
| 19-36141076-G-T | not specified | Uncertain significance (Aug 17, 2022) | ||
| 19-36141100-G-A | not specified | Uncertain significance (Aug 16, 2021) | ||
| 19-36141146-C-A | Likely benign (Jun 01, 2022) | |||
| 19-36141171-G-T | not specified | Uncertain significance (Jan 19, 2022) | ||
| 19-36141175-G-A | not specified | Uncertain significance (Dec 19, 2022) | ||
| 19-36141210-A-G | not specified | Uncertain significance (Feb 13, 2023) | ||
| 19-36142298-A-G | Pulmonary hypertension, primary, 6 | Pathogenic (Apr 02, 2024) | ||
| 19-36142712-C-T | not specified | Uncertain significance (Nov 08, 2022) | ||
| 19-36142713-G-A | not specified | Uncertain significance (Jan 10, 2022) | ||
| 19-36142737-G-C | not specified | Uncertain significance (Jan 07, 2022) | ||
| 19-36143105-C-T | not specified | Uncertain significance (Aug 16, 2021) | ||
| 19-36145993-C-A | not specified | Uncertain significance (Sep 20, 2023) | ||
| 19-36146015-A-T | not specified | Uncertain significance (Mar 08, 2024) | ||
| 19-36146216-C-T | not specified | Uncertain significance (Jul 12, 2023) | ||
| 19-36146220-A-G | not specified | Uncertain significance (Jun 29, 2023) | ||
| 19-36146302-C-T | Likely benign (Feb 01, 2024) | |||
| 19-36146303-G-A | not specified | Uncertain significance (Dec 13, 2022) | ||
| 19-36146313-G-A | Pulmonary hypertension, primary, 6 | Pathogenic (Apr 03, 2024) | ||
| 19-36149599-A-G | not specified | Uncertain significance (Feb 17, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CAPNS1 | protein_coding | protein_coding | ENST00000246533 | 10 | 10779 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 7.11e-7 | 0.724 | 125699 | 0 | 49 | 125748 | 0.000195 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.592 | 124 | 144 | 0.861 | 0.00000834 | 1745 |
| Missense in Polyphen | 37 | 54.776 | 0.67548 | 697 | ||
| Synonymous | -1.13 | 62 | 51.6 | 1.20 | 0.00000280 | 504 |
| Loss of Function | 1.21 | 12 | 17.5 | 0.687 | 0.00000124 | 177 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000867 | 0.0000867 |
| Ashkenazi Jewish | 0.000298 | 0.000298 |
| East Asian | 0.0000589 | 0.0000544 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000302 | 0.000299 |
| Middle Eastern | 0.0000589 | 0.0000544 |
| South Asian | 0.000196 | 0.000196 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Regulatory subunit of the calcium-regulated non- lysosomal thiol-protease which catalyzes limited proteolysis of substrates involved in cytoskeletal remodeling and signal transduction.;
- Pathway
- Apoptosis Modulation and Signaling;Integrin-mediated Cell Adhesion;Keratinization;Developmental Biology;Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer,s disease models;Neurodegenerative Diseases;Disease;ucalpain and friends in cell spread;role of mef2d in t-cell apoptosis;mcalpain and friends in cell motility;Extracellular matrix organization;Degradation of the extracellular matrix;Formation of the cornified envelope
(Consensus)
Recessive Scores
- pRec
- 0.341
Intolerance Scores
- loftool
- 0.656
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 33.97
Haploinsufficiency Scores
- pHI
- 0.0837
- hipred
- N
- hipred_score
- 0.489
- ghis
- 0.550
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.828
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Capns1
- Phenotype
- respiratory system phenotype; embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- proteolysis;positive regulation of cell population proliferation;regulation of macroautophagy;cornification
- Cellular component
- cytosol;plasma membrane;membrane;extracellular exosome
- Molecular function
- endopeptidase activity;calcium-dependent cysteine-type endopeptidase activity;calcium ion binding;protein binding