CAPS2

calcyphosine 2, the group of EF-hand domain containing

Basic information

Region (hg38): 12:75275979-75390928

Links

ENSG00000180881 ∙ NCBI:84698 ∙ OMIM:607724 ∙ HGNC:16471 ∙ Uniprot:Q9BXY5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CAPS2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAPS2 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	2
missense			33	2	1	36
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			13	1		14
Total	0	0	47	3	3

Variants in CAPS2

This is a list of pathogenic ClinVar variants found in the CAPS2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-75282301-A-G		not specified	Likely benign (Dec 03, 2021)
12-75282305-T-C		not specified	Uncertain significance (Apr 23, 2024)
12-75284965-C-T		not specified	Uncertain significance (Aug 15, 2023)
12-75285005-T-C		not specified	Uncertain significance (Aug 17, 2021)
12-75285038-C-T		not specified	Uncertain significance (Dec 28, 2022)
12-75285073-T-C		not specified	Uncertain significance (Nov 08, 2022)
12-75285077-A-C		not specified	Uncertain significance (Mar 04, 2024)
12-75289683-G-C		not specified	Uncertain significance (Jul 12, 2023)
12-75293250-T-G		not specified	Uncertain significance (Dec 13, 2022)
12-75293274-C-G		not specified	Uncertain significance (Oct 12, 2022)
12-75293337-G-T		not specified	Uncertain significance (Jan 20, 2023)
12-75293352-A-G		not specified	Uncertain significance (Oct 05, 2023)
12-75298689-C-A		not specified	Uncertain significance (Apr 01, 2024)
12-75298704-G-A		not specified	Uncertain significance (Jul 09, 2021)
12-75298755-T-G		not specified	Uncertain significance (Jun 10, 2024)
12-75298779-T-C		not specified	Uncertain significance (Jul 12, 2022)
12-75298874-T-C		not specified	Uncertain significance (May 31, 2023)
12-75298901-A-C		not specified	Uncertain significance (Mar 16, 2023)
12-75298908-G-A		not specified	Uncertain significance (Jan 30, 2024)
12-75298917-C-A		not specified	Uncertain significance (Jul 09, 2021)
12-75298922-G-A		not specified	Uncertain significance (Dec 03, 2021)
12-75299853-C-T		not specified	Uncertain significance (Nov 07, 2022)
12-75299870-T-C		not specified	Uncertain significance (Dec 19, 2022)
12-75299876-A-C		not specified	Uncertain significance (Mar 06, 2023)
12-75304766-T-G		not specified	Uncertain significance (Apr 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAPS2	protein_coding	protein_coding	ENST00000409445	18	114950

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.07e-24	0.000734	125625	0	110	125735	0.000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0866	271	267	1.01	0.0000127	3675
Missense in Polyphen		66	64.39	1.025		861
Synonymous	1.09	75	88.0	0.852	0.00000401	971
Loss of Function	0.0994	36	36.6	0.982	0.00000210	445

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00128	0.00128
Ashkenazi Jewish	0.00184	0.00169
East Asian	0.000224	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000333	0.000325
Middle Eastern	0.000224	0.000217
South Asian	0.000370	0.000359
Other	0.000671	0.000652

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0922

Intolerance Scores

• loftool: 0.570
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.3

Haploinsufficiency Scores

• pHI: 0.0790
• hipred: N
• hipred_score: 0.170
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.410

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Caps2

Gene ontology

• Molecular function: calcium ion binding