CAPS

calcyphosine, the group of EF-hand domain containing

Basic information

Region (hg38): 19:5912339-5916211

Links

ENSG00000105519 ∙ NCBI:828 ∙ OMIM:114212 ∙ HGNC:1487 ∙ Uniprot:Q13938 ∙ 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 CAPS gene.

• not_specified (46 variants)
• not_provided (2 variants)
• CAPS-related_disorder (2 variants)

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. These statistics are base on transcript: NM_000004058.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			43	2	3	48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	43	3	3

GnomAD

Source: gnomAD

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: 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

	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