CRACR2A

calcium release activated channel regulator 2A, the group of EF-hand domain containing

Basic information

Region (hg38): 12:3606632-3764819

Previous symbols: [ "EFCAB4B" ]

Links

ENSG00000130038 ∙ NCBI:84766 ∙ OMIM:614178 ∙ HGNC:28657 ∙ Uniprot:Q9BSW2 ∙ 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 CRACR2A gene.

• Inborn genetic diseases (44 variants)
• not specified (19 variants)
• not provided (2 variants)
• - (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRACR2A 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			44	1	5	50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					12	12
Total	0	0	44	1	19

Variants in CRACR2A

This is a list of pathogenic ClinVar variants found in the CRACR2A region.

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

Position	Type	Phenotype	Significance	ClinVar
12-3615390-C-T		not specified	Uncertain significance (Jan 19, 2024)
12-3615432-T-G		not specified	Uncertain significance (Jun 24, 2022)
12-3619279-G-T		not specified	Uncertain significance (May 04, 2023)
12-3619288-C-T		not specified	Uncertain significance (Dec 15, 2023)
12-3619297-G-A		not specified	Uncertain significance (Sep 30, 2021)
12-3619304-T-G		not specified	Uncertain significance (Nov 17, 2022)
12-3619308-C-T		not specified	Uncertain significance (Dec 18, 2023)
12-3619369-C-A		not specified	Uncertain significance (Aug 23, 2021)
12-3627497-A-G		not specified	Uncertain significance (Oct 10, 2023)
12-3627568-C-T		not specified	Benign (Jan 24, 2024)
12-3627579-T-C		not specified	Benign (Jan 24, 2024)
12-3627631-T-C		not specified	Uncertain significance (Mar 31, 2023)
12-3627658-G-A		not specified	Uncertain significance (Mar 20, 2023)
12-3627671-T-C		not specified	Likely benign (Jul 27, 2023)
12-3627674-C-A		not specified	Uncertain significance (Jan 31, 2022)
12-3627694-C-T		not specified	Uncertain significance (Feb 03, 2022)
12-3627774-C-T		not specified	Benign (Jan 24, 2024)
12-3633630-A-T		not specified	Uncertain significance (Jul 05, 2023)
12-3633631-A-G		not specified	Uncertain significance (Apr 08, 2022)
12-3633675-G-A		not specified	Uncertain significance (Jul 09, 2021)
12-3638118-C-T			Likely benign (Jun 01, 2023)
12-3638158-C-T		not specified	Uncertain significance (Aug 22, 2023)
12-3638174-T-C		not specified	Uncertain significance (May 05, 2023)
12-3638197-G-A		not specified	Uncertain significance (Nov 18, 2022)
12-3638213-C-A		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRACR2A	protein_coding	protein_coding	ENST00000440314	17	158187

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.43e-12	0.963	125622	0	126	125748	0.000501

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.928	357	410	0.871	0.0000235	4784
Missense in Polyphen		117	136.27	0.8586		1742
Synonymous	0.873	155	169	0.915	0.00000975	1387
Loss of Function	2.22	24	39.0	0.616	0.00000174	468

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000597	0.000597
Ashkenazi Jewish	0.00576	0.00577
East Asian	0.0000548	0.0000544
Finnish	0.000278	0.000277
European (Non-Finnish)	0.000249	0.000246
Middle Eastern	0.0000548	0.0000544
South Asian	0.000393	0.000392
Other	0.000656	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ca(2+)-binding protein that plays a key role in store- operated Ca(2+) entry (SOCE) in T-cells by regulating CRAC channel activation. Acts as a cytoplasmic calcium-sensor that facilitates the clustering of ORAI1 and STIM1 at the junctional regions between the plasma membrane and the endoplasmic reticulum upon low Ca(2+) concentration. It thereby regulates CRAC channel activation, including translocation and clustering of ORAI1 and STIM1. Upon increase of cytoplasmic Ca(2+) resulting from opening of CRAC channels, dissociates from ORAI1 and STIM1, thereby destabilizing the ORAI1-STIM1 complex. {ECO:0000269|PubMed:20418871}.
• Pathway: Vitamin D Receptor Pathway;Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.100

Intolerance Scores

• rvis_EVS: 1.85
• rvis_percentile_EVS: 97.12

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.281
• ghis: 0.411

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Cracr2a

Gene ontology

• Biological process: store-operated calcium entry;adaptive immune response;activation of store-operated calcium channel activity;neutrophil degranulation;positive regulation of calcium ion transport
• Cellular component: extracellular region;cytoplasm;membrane;specific granule lumen
• Molecular function: calcium ion binding;protein binding