CHP2

Chr 16

calcineurin like EF-hand protein 2

NCBI Gene: 63928ENSG00000166869UniProt: O43745

This gene product is a small calcium-binding protein that regulates cell pH by controlling plasma membrane-type Na+/H+ exchange activity. This protein shares sequence similarity with calcineurin B and can bind to and stimulate the protein phosphatase activity of calcineurin A (CnA) and functions in the calcineurin/NFAT (nuclear factor of activated T cells) signaling pathway. Another member of the CHP subfamily, Calcineurin B homologous protein 1, is located on Chromosome 15 and is an inhibitor of calcineurin activity and has a genetic phenotype associated with Parkinson's Disease (OMIM:606988). This gene was initially identified as a tumor-associated antigen and was previously referred to as Hepatocellular carcinoma-associated antigen 520. [provided by RefSeq, Jul 2013]

76
ClinVar variants
30
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— CHP2
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
30 Pathogenic / Likely Pathogenic· 45 VUS of 76 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.47LOEUF
pLI 0.000
Z-score 0.42
OE 0.87 (0.53–1.47)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.68Z-score
OE missense 1.17 (1.02–1.34)
145 obs / 123.8 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.87 (0.53–1.47)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.17 (1.02–1.34)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.91
0≤1.21.6
LoF obs/exp: 10 / 11.5Missense obs/exp: 145 / 123.8Syn Z: 0.47

ClinVar Variant Classifications

76 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic27
Likely Pathogenic3
VUS45
Likely Benign1
27
Pathogenic
3
Likely Pathogenic
45
VUS
1
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
27
0
27
Likely Pathogenic
0
0
3
0
3
VUS
0
40
5
0
45
Likely Benign
0
1
0
0
1
Benign
0
0
0
0
0
Total04135076

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

CHP2 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype

OMIM

No OMIM entries found.

Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Chlamydia bacteriophages.
Śliwa-Dominiak J et al.·Arch Microbiol
2013Review
CHP2 Promotes Cell Proliferation in Breast Cancer via Suppression of FOXO3a.
Zhao X et al.·Mol Cancer Res
2018
Involvement of CHP2 in the Development of Non-Small Cell Lung Cancer and Patients' Poor Prognosis.
Xu L et al.·Appl Immunohistochem Mol Morphol
2020Cohort
[The malignant phenotype of calcineurin B homologous protein 2 in gastric cancer and its clinical significance].
Lu B et al.·Zhonghua Yi Xue Za Zhi
2020
CHP2 Modifies Chronic Pseudomonas aeruginosa Airway Infection Risk in Cystic Fibrosis.
Faino AV et al.·Ann Am Thorac Soc
2025
Analysis and validation of diagnostic biomarkers and immune cell infiltration characteristics in Crohn's disease by integrating bioinformatics and machine learning.
Ren XJ et al.·Autoimmunity
2024
Quality control material for the detection of somatic mutations in fixed clinical specimens by next-generation sequencing.
Dumur CI et al.·Diagn Pathol
2015
Gene-Expression Profiles in Generalized Aggressive Periodontitis: A Gene Network-Based Microarray Analysis.
Guzeldemir-Akcakanat E et al.·J Periodontol
2016
Artificial Neural Network Analysis-Based Immune-Related Signatures of Primary Non-Response to Infliximab in Patients With Ulcerative Colitis.
Chen X et al.·Front Immunol
2021Cohort
Assessment of total antioxidant capacity and the use of vitamin C in the treatment of non-smokers with chronic periodontitis.
Abou Sulaiman AE et al.·J Periodontol
2010
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools