CHP1
calcineurin like EF-hand protein 1, the group of EF-hand domain containing
Basic information
Region (hg38): 15:41230839-41281887
Links
Phenotypes
GenCC
Source:
- spastic ataxia 9, autosomal recessive (Limited), mode of inheritance: Unknown
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Spastic ataxia 9, autosomal recessive | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Musculoskeletal; Neurologic | 29379881 |
ClinVar
This is a list of variants' phenotypes submitted to
- CHP1-related_disorder (2 variants)
- not_provided (1 variants)
- Spastic_ataxia_9,_autosomal_recessive (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000007236.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 0 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 0 | 1 | 1 |
Highest pathogenic variant AF is 0.000002755656
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CHP1 | protein_coding | protein_coding | ENST00000334660 | 7 | 51007 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.627 | 0.372 | 125740 | 0 | 4 | 125744 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.26 | 50 | 119 | 0.419 | 0.00000694 | 1300 |
| Missense in Polyphen | 11 | 41.018 | 0.26818 | 438 | ||
| Synonymous | 0.0391 | 40 | 40.3 | 0.992 | 0.00000197 | 353 |
| Loss of Function | 2.64 | 2 | 11.8 | 0.170 | 6.50e-7 | 128 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000264 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Calcium-binding protein involved in different processes such as regulation of vesicular trafficking, plasma membrane Na(+)/H(+) exchanger and gene transcription. Involved in the constitutive exocytic membrane traffic. Mediates the association between microtubules and membrane-bound organelles of the endoplasmic reticulum and Golgi apparatus and is also required for the targeting and fusion of transcytotic vesicles (TCV) with the plasma membrane. Functions as an integral cofactor in cell pH regulation by controlling plasma membrane-type Na(+)/H(+) exchange activity. Affects the pH sensitivity of SLC9A1/NHE1 by increasing its sensitivity at acidic pH. Required for the stabilization and localization of SLC9A1/NHE1 at the plasma membrane. Inhibits serum- and GTPase-stimulated Na(+)/H(+) exchange. Plays a role as an inhibitor of ribosomal RNA transcription by repressing the nucleolar UBF1 transcriptional activity. May sequester UBF1 in the nucleoplasm and limit its translocation to the nucleolus. Associates to the ribosomal gene promoter. Acts as a negative regulator of the calcineurin/NFAT signaling pathway. Inhibits NFAT nuclear translocation and transcriptional activity by suppressing the calcium-dependent calcineurin phosphatase activity. Also negatively regulates the kinase activity of the apoptosis-induced kinase STK17B. Inhibits both STK17B auto- and substrate- phosphorylations in a calcium-dependent manner. {ECO:0000269|PubMed:10593895, ECO:0000269|PubMed:11350981, ECO:0000269|PubMed:15035633, ECO:0000269|PubMed:8901634}.;
- Pathway
- Alzheimers Disease;T-Cell antigen Receptor (TCR) pathway during Staphylococcus aureus infection;Hyaluronan uptake and degradation;Hyaluronan metabolism;Metabolism of carbohydrates;Glycosaminoglycan metabolism;Metabolism;Role of Calcineurin-dependent NFAT signaling in lymphocytes;Calcium signaling in the CD4+ TCR pathway
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.39
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.760
- ghis
- 0.506
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- gene_indispensability_score
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Chp1
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- chp1
- Affected structure
- CaP motoneuron
- Phenotype tag
- abnormal
- Phenotype quality
- branchiness
Gene ontology
- Biological process
- microtubule bundle formation;negative regulation of protein phosphorylation;negative regulation of protein kinase activity;protein export from nucleus;potassium ion transport;small GTPase mediated signal transduction;negative regulation of phosphatase activity;calcium ion regulated exocytosis;membrane docking;hyaluronan catabolic process;cytoplasmic microtubule organization;negative regulation of protein ubiquitination;negative regulation of protein autophosphorylation;negative regulation of NF-kappaB transcription factor activity;positive regulation of sodium:proton antiporter activity;negative regulation of protein import into nucleus;protein stabilization;positive regulation of protein transport;protein complex oligomerization;regulation of intracellular pH;positive regulation of protein glycosylation;membrane organization;membrane fusion;negative regulation of calcineurin-NFAT signaling cascade;cellular response to acidic pH;positive regulation of protein targeting to membrane;regulation of neuron death
- Cellular component
- Golgi membrane;nucleus;cytoplasm;endoplasmic reticulum;endoplasmic reticulum-Golgi intermediate compartment;cytosol;plasma membrane;focal adhesion;microtubule cytoskeleton;transport vesicle;extracellular exosome
- Molecular function
- protein kinase inhibitor activity;transporter activity;calcium ion binding;protein binding;microtubule binding;potassium channel regulator activity;kinase binding;calcium-dependent protein binding