CHP2

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

Basic information

Region (hg38): 16:23755026-23758935

Links

ENSG00000166869 ∙ NCBI:63928 ∙ ∙ HGNC:24927 ∙ Uniprot:O43745 ∙ 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 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	1		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)
16-23755063-G-C		not specified	Uncertain significance (Nov 09, 2023)
16-23755682-G-A		not specified	Uncertain significance (Sep 27, 2024)
16-23755688-A-G		not specified	Uncertain significance (May 21, 2024)
16-23755690-C-T		not specified	Uncertain significance (Jul 05, 2024)
16-23755699-C-T		not specified	Uncertain significance (Aug 02, 2022)
16-23755702-G-A		not specified	Uncertain significance (Sep 20, 2023)
16-23755718-A-C		not specified	Uncertain significance (Jan 26, 2023)
16-23755730-T-C		not specified	Uncertain significance (May 20, 2024)
16-23755900-G-A		not specified	Uncertain significance (May 31, 2023)
16-23755906-T-C		not specified	Uncertain significance (Apr 24, 2023)
16-23756070-C-G		not specified	Uncertain significance (Aug 14, 2023)
16-23756076-G-T		not specified	Uncertain significance (Feb 24, 2025)
16-23756106-C-T		not specified	Uncertain significance (Sep 29, 2023)
16-23756112-C-T		not specified	Uncertain significance (Mar 31, 2023)
16-23756124-G-A		not specified	Uncertain significance (Feb 11, 2025)
16-23756130-G-A		not specified	Uncertain significance (Dec 19, 2022)
16-23756138-A-C		not specified	Uncertain significance (May 07, 2024)
16-23756187-C-T		not specified	Uncertain significance (Apr 11, 2023)
16-23756411-G-T		not specified	Uncertain significance (Feb 06, 2025)
16-23756415-G-A		not specified	Uncertain significance (Apr 25, 2024)
16-23756417-G-A		not specified	Uncertain significance (Jun 11, 2021)
16-23756420-G-A		not specified	Uncertain significance (Aug 04, 2023)
16-23757216-G-A		not specified	Uncertain significance (Sep 01, 2021)
16-23757262-G-A		not specified	Uncertain significance (Jun 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHP2	protein_coding	protein_coding	ENST00000300113	7	4325

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.63e-7	0.335	125653	0	95	125748	0.000378

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.677	145	124	1.17	0.00000748	1292
Missense in Polyphen		55	49.167	1.1186		522
Synonymous	0.468	44	48.1	0.914	0.00000286	375
Loss of Function	0.417	10	11.5	0.867	6.59e-7	113

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00114	0.00114
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000563	0.000563
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

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

• 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

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

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