CAPS

calcyphosine, the group of EF-hand domain containing

Basic information

Region (hg38): 19:5912339-5916211

Links

ENSG00000105519NCBI:828OMIM:114212HGNC:1487Uniprot:Q13938AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CAPS gene.

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
clinvar
2
clinvar
3
clinvar
28
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
1
clinvar
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)3042361
19-5914127-G-A CAPS-related disorder Likely benign (Jul 12, 2019)3043112
19-5914416-G-A not specified Uncertain significance (Jan 31, 2024)3137241
19-5914440-C-T not specified Uncertain significance (Mar 25, 2024)3263266
19-5914456-C-A not specified Uncertain significance (Mar 23, 2022)2405819
19-5914459-G-A CAPS-related disorder Benign (Jul 26, 2018)781743
19-5914461-G-C not specified Uncertain significance (Sep 25, 2023)3137247
19-5914468-C-T not specified Uncertain significance (Sep 28, 2022)2342223
19-5914474-T-C not specified Uncertain significance (Apr 18, 2024)3263267
19-5914580-A-G not specified Uncertain significance (Oct 04, 2022)2358060
19-5914606-G-A not specified Uncertain significance (Sep 06, 2022)2382169
19-5914619-G-A not specified Likely benign (Jun 16, 2022)2379335
19-5914639-G-A CAPS-related disorder Benign (Feb 17, 2020)3043545
19-5914687-G-A not specified Uncertain significance (Oct 25, 2023)3137242
19-5914690-C-G not specified Uncertain significance (Jun 01, 2023)2515121
19-5914690-C-T not specified Uncertain significance (Jul 09, 2021)2234407
19-5914697-G-A not specified Uncertain significance (Nov 10, 2023)3137243
19-5914706-C-T not specified Uncertain significance (Sep 14, 2023)2597173
19-5914713-T-A not specified Uncertain significance (Dec 19, 2023)3137245
19-5914738-C-T not specified Uncertain significance (Aug 08, 2022)2305787
19-5914940-C-A Benign (Jul 26, 2018)769950
19-5914958-C-G not specified Uncertain significance (Feb 27, 2023)2489615
19-5914971-T-A not specified Uncertain significance (Feb 17, 2023)2486677
19-5914998-G-A not specified Uncertain significance (Nov 17, 2022)2231570
19-5915019-C-T not specified Uncertain significance (Apr 25, 2022)2368072

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CAPSprotein_codingprotein_codingENST00000222125 44171
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00001720.2671256420411256830.000163
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.4911611441.110.00001071223
Missense in Polyphen5352.6461.0067480
Synonymous0.7825562.90.8750.00000495384
Loss of Function-0.13776.621.062.82e-772

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0008560.000851
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.000.00
European (Non-Finnish)0.0001600.000158
Middle Eastern0.0001090.000109
South Asian0.00009840.0000980
Other0.0001640.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Gene ontology

Biological process
intracellular signal transduction
Cellular component
cytoplasm;vesicle
Molecular function
calcium ion binding