JPH4
Basic information
Region (hg38): 14:23568038-23578790
Previous symbols: [ "JPHL1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the JPH4 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 | 1 | |||||
missense | 30 | 30 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 30 | 1 | 0 |
Variants in JPH4
This is a list of pathogenic ClinVar variants found in the JPH4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
14-23570939-G-T | not specified | Uncertain significance (Jun 09, 2022) | ||
14-23570953-G-C | not specified | Uncertain significance (Mar 29, 2022) | ||
14-23570963-C-T | not specified | Uncertain significance (Mar 07, 2024) | ||
14-23570965-A-T | not specified | Uncertain significance (Apr 20, 2023) | ||
14-23570984-C-G | not specified | Uncertain significance (Mar 25, 2024) | ||
14-23570984-C-T | not specified | Uncertain significance (Jul 14, 2021) | ||
14-23570986-G-C | not specified | Uncertain significance (Dec 19, 2023) | ||
14-23570987-C-T | not specified | Uncertain significance (Jul 27, 2021) | ||
14-23571068-G-C | not specified | Uncertain significance (Jul 05, 2023) | ||
14-23571085-T-C | not specified | Uncertain significance (Feb 08, 2023) | ||
14-23571098-C-G | not specified | Uncertain significance (May 27, 2022) | ||
14-23571107-G-A | not specified | Uncertain significance (Jul 06, 2021) | ||
14-23571157-G-C | not specified | Uncertain significance (Oct 06, 2021) | ||
14-23571229-C-T | not specified | Uncertain significance (Jan 04, 2022) | ||
14-23571230-C-A | not specified | Uncertain significance (Oct 25, 2023) | ||
14-23571230-C-G | not specified | Uncertain significance (Apr 26, 2024) | ||
14-23571232-C-T | not specified | Uncertain significance (Sep 27, 2021) | ||
14-23571235-C-A | not specified | Uncertain significance (Oct 06, 2022) | ||
14-23571244-G-A | not specified | Uncertain significance (Mar 31, 2024) | ||
14-23571250-G-A | not specified | Uncertain significance (Jan 23, 2023) | ||
14-23571316-C-T | not specified | Uncertain significance (Aug 12, 2021) | ||
14-23571338-C-T | not specified | Uncertain significance (Dec 20, 2023) | ||
14-23571852-C-T | not specified | Uncertain significance (Oct 18, 2021) | ||
14-23571865-C-T | not specified | Uncertain significance (Feb 06, 2023) | ||
14-23571878-G-A | Likely benign (Feb 01, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
JPH4 | protein_coding | protein_coding | ENST00000397118 | 5 | 10766 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.999 | 0.000525 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.56 | 193 | 322 | 0.599 | 0.0000199 | 3901 |
Missense in Polyphen | 72 | 123.93 | 0.58098 | 1453 | ||
Synonymous | 1.38 | 122 | 143 | 0.854 | 0.00000943 | 1402 |
Loss of Function | 4.32 | 0 | 21.7 | 0.00 | 0.00000123 | 238 |
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) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Junctophilins contribute to the formation of junctional membrane complexes (JMCs) which link the plasma membrane with the endoplasmic or sarcoplasmic reticulum in excitable cells. Provides a structural foundation for functional cross-talk between the cell surface and intracellular calcium release channels. JPH4 is brain- specific and appears to have an active role in certain neurons involved in motor coordination and memory (By similarity). {ECO:0000250}.;
Haploinsufficiency Scores
- pHI
- 0.458
- hipred
- Y
- hipred_score
- 0.674
- ghis
- 0.544
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.666
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Jph4
- Phenotype
- hematopoietic system phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; 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); growth/size/body region phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- regulation of cytokine production;learning;regulation of synaptic plasticity;neuromuscular process controlling balance;release of sequestered calcium ion into cytosol;regulation of ryanodine-sensitive calcium-release channel activity;calcium ion transport into cytosol;regulation of store-operated calcium entry
- Cellular component
- endoplasmic reticulum;endoplasmic reticulum membrane;smooth endoplasmic reticulum;plasma membrane;junctional sarcoplasmic reticulum membrane;integral component of membrane;junctional membrane complex;dendritic shaft
- Molecular function
- calcium-release channel activity