CHP2

calcineurin like EF-hand protein 2, the group of EF-hand domain containing

Basic information

Region (hg38): 16:23755026-23758935

Links

ENSG00000166869NCBI:63928HGNC:24927Uniprot:O43745AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CHP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHP2 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
28
clinvar
1
clinvar
29
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 28 1 0

Variants in CHP2

This is a list of pathogenic ClinVar variants found in the CHP2 region.

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

Position Type Phenotype Significance ClinVar
16-23755060-G-A not specified Uncertain significance (Sep 22, 2022)2313100
16-23755063-G-C not specified Uncertain significance (Nov 09, 2023)3144495
16-23755682-G-A not specified Uncertain significance (Sep 27, 2024)3492423
16-23755688-A-G not specified Uncertain significance (May 21, 2024)3267085
16-23755690-C-T not specified Uncertain significance (Jul 05, 2024)3492422
16-23755699-C-T not specified Uncertain significance (Aug 02, 2022)2341768
16-23755702-G-A not specified Uncertain significance (Sep 20, 2023)3144493
16-23755718-A-C not specified Uncertain significance (Jan 26, 2023)2479419
16-23755730-T-C not specified Uncertain significance (May 20, 2024)3267084
16-23755900-G-A not specified Uncertain significance (May 31, 2023)2553658
16-23755906-T-C not specified Uncertain significance (Apr 24, 2023)2539740
16-23756070-C-G not specified Uncertain significance (Aug 14, 2023)2618058
16-23756106-C-T not specified Uncertain significance (Sep 29, 2023)3144496
16-23756112-C-T not specified Uncertain significance (Mar 31, 2023)2532210
16-23756130-G-A not specified Uncertain significance (Dec 19, 2022)2402596
16-23756138-A-C not specified Uncertain significance (May 07, 2024)3267083
16-23756187-C-T not specified Uncertain significance (Apr 11, 2023)2519397
16-23756415-G-A not specified Uncertain significance (Apr 25, 2024)2343227
16-23756417-G-A not specified Uncertain significance (Jun 11, 2021)2232166
16-23756420-G-A not specified Uncertain significance (Aug 04, 2023)2615847
16-23757216-G-A not specified Uncertain significance (Sep 01, 2021)2401981
16-23757262-G-A not specified Uncertain significance (Jun 11, 2024)3267086
16-23757308-C-G not specified Uncertain significance (Mar 22, 2023)2528151
16-23757315-T-G not specified Uncertain significance (Mar 07, 2023)2473755
16-23757548-G-A not specified Likely benign (Jul 05, 2023)2588851

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CHP2protein_codingprotein_codingENST00000300113 74325
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
9.63e-70.3351256530951257480.000378
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.6771451241.170.000007481292
Missense in Polyphen5549.1671.1186522
Synonymous0.4684448.10.9140.00000286375
Loss of Function0.4171011.50.8676.59e-7113

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001140.00114
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.0005630.000563
Middle Eastern0.00005440.0000544
South Asian0.00006530.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Functions as an integral cofactor in cell pH regulation by controlling plasma membrane-type Na(+)/H(+) exchange activity. Binds to and activates SLC9A1/NHE1 in a serum-independent manner, thus increasing pH and protecting cells from serum deprivation- induced death. Also plays a role in the regulation of cell proliferation and tumor growth by increasing the phosphatase activity of PPP3CA in a calcium-dependent manner. Activator of the calcineurin/NFAT signaling pathway. Involved in the cytoplasmic translocation of the transcription factor NFATC3 to the nucleus. {ECO:0000269|PubMed:12226101, ECO:0000269|PubMed:18815128}.;
Pathway
Alzheimers Disease (Consensus)

Intolerance Scores

loftool
0.813
rvis_EVS
0.39
rvis_percentile_EVS
76.05

Haploinsufficiency Scores

pHI
hipred
N
hipred_score
0.490
ghis
0.480

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.539

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Chp2
Phenotype
behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process
positive regulation of cell population proliferation;positive regulation of phosphatase activity;protein transport;positive regulation of protein import into nucleus;positive regulation of transcription by RNA polymerase II;positive regulation of calcineurin-NFAT signaling cascade;cellular response to calcium ion
Cellular component
nucleus;cytoplasm;plasma membrane
Molecular function
calcium ion binding;protein binding