CAPS
Basic information
Region (hg38): 19:5912339-5916211
Links
Phenotypes
GenCC
Source:
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 CAPS 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 | 23 | 28 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 1 | |||||
Total | 0 | 0 | 23 | 3 | 3 |
Variants in CAPS
This is a list of pathogenic ClinVar variants found in the CAPS region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
19-5914067-G-A | CAPS-related disorder | Likely benign (May 07, 2019) | ||
19-5914127-G-A | CAPS-related disorder | Likely benign (Jul 12, 2019) | ||
19-5914416-G-A | not specified | Uncertain significance (Jan 31, 2024) | ||
19-5914440-C-T | not specified | Uncertain significance (Mar 25, 2024) | ||
19-5914456-C-A | not specified | Uncertain significance (Mar 23, 2022) | ||
19-5914459-G-A | CAPS-related disorder | Benign (Jul 26, 2018) | ||
19-5914461-G-C | not specified | Uncertain significance (Sep 25, 2023) | ||
19-5914468-C-T | not specified | Uncertain significance (Sep 28, 2022) | ||
19-5914474-T-C | not specified | Uncertain significance (Apr 18, 2024) | ||
19-5914580-A-G | not specified | Uncertain significance (Oct 04, 2022) | ||
19-5914606-G-A | not specified | Uncertain significance (Sep 06, 2022) | ||
19-5914619-G-A | not specified | Likely benign (Jun 16, 2022) | ||
19-5914639-G-A | CAPS-related disorder | Benign (Feb 17, 2020) | ||
19-5914687-G-A | not specified | Uncertain significance (Oct 25, 2023) | ||
19-5914690-C-G | not specified | Uncertain significance (Jun 01, 2023) | ||
19-5914690-C-T | not specified | Uncertain significance (Jul 09, 2021) | ||
19-5914697-G-A | not specified | Uncertain significance (Nov 10, 2023) | ||
19-5914706-C-T | not specified | Uncertain significance (Sep 14, 2023) | ||
19-5914713-T-A | not specified | Uncertain significance (Dec 19, 2023) | ||
19-5914738-C-T | not specified | Uncertain significance (Aug 08, 2022) | ||
19-5914940-C-A | Benign (Jul 26, 2018) | |||
19-5914958-C-G | not specified | Uncertain significance (Feb 27, 2023) | ||
19-5914971-T-A | not specified | Uncertain significance (Feb 17, 2023) | ||
19-5914998-G-A | not specified | Uncertain significance (Nov 17, 2022) | ||
19-5915019-C-T | not specified | Uncertain significance (Apr 25, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CAPS | protein_coding | protein_coding | ENST00000222125 | 4 | 4171 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0000172 | 0.267 | 125642 | 0 | 41 | 125683 | 0.000163 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.491 | 161 | 144 | 1.11 | 0.0000107 | 1223 |
Missense in Polyphen | 53 | 52.646 | 1.0067 | 480 | ||
Synonymous | 0.782 | 55 | 62.9 | 0.875 | 0.00000495 | 384 |
Loss of Function | -0.137 | 7 | 6.62 | 1.06 | 2.82e-7 | 72 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000856 | 0.000851 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000109 | 0.000109 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000160 | 0.000158 |
Middle Eastern | 0.000109 | 0.000109 |
South Asian | 0.0000984 | 0.0000980 |
Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Calcium-binding protein. May play a role in cellular signaling events (Potential). {ECO:0000305}.;
Intolerance Scores
- loftool
- 0.889
- rvis_EVS
- 0.46
- rvis_percentile_EVS
- 78.69
Haploinsufficiency Scores
- pHI
- 0.133
- hipred
- N
- hipred_score
- 0.146
- ghis
- 0.537
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.273
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- intracellular signal transduction
- Cellular component
- cytoplasm;vesicle
- Molecular function
- calcium ion binding