JPH4

junctophilin 4, the group of Junctophilins

Basic information

Region (hg38): 14:23568038-23578790

Previous symbols: [ "JPHL1" ]

Links

ENSG00000092051NCBI:84502OMIM:619863HGNC:20156Uniprot:Q96JJ6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the JPH4 gene.

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
clinvar
1
missense
30
clinvar
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)3112510
14-23570953-G-C not specified Uncertain significance (Mar 29, 2022)2205008
14-23570963-C-T not specified Uncertain significance (Mar 07, 2024)3112508
14-23570965-A-T not specified Uncertain significance (Apr 20, 2023)2539594
14-23570984-C-G not specified Uncertain significance (Mar 25, 2024)3287254
14-23570984-C-T not specified Uncertain significance (Jul 14, 2021)2343809
14-23570986-G-C not specified Uncertain significance (Dec 19, 2023)3112507
14-23570987-C-T not specified Uncertain significance (Jul 27, 2021)2394136
14-23571068-G-C not specified Uncertain significance (Jul 05, 2023)2591572
14-23571085-T-C not specified Uncertain significance (Feb 08, 2023)2470294
14-23571098-C-G not specified Uncertain significance (May 27, 2022)2391333
14-23571107-G-A not specified Uncertain significance (Jul 06, 2021)2407335
14-23571157-G-C not specified Uncertain significance (Oct 06, 2021)2410036
14-23571229-C-T not specified Uncertain significance (Jan 04, 2022)2269108
14-23571230-C-A not specified Uncertain significance (Oct 25, 2023)3112505
14-23571230-C-G not specified Uncertain significance (Apr 26, 2024)3287252
14-23571232-C-T not specified Uncertain significance (Sep 27, 2021)2252255
14-23571235-C-A not specified Uncertain significance (Oct 06, 2022)2397491
14-23571244-G-A not specified Uncertain significance (Mar 31, 2024)2393403
14-23571250-G-A not specified Uncertain significance (Jan 23, 2023)2472898
14-23571316-C-T not specified Uncertain significance (Aug 12, 2021)2243563
14-23571338-C-T not specified Uncertain significance (Dec 20, 2023)3112504
14-23571852-C-T not specified Uncertain significance (Oct 18, 2021)2266066
14-23571865-C-T not specified Uncertain significance (Feb 06, 2023)2460996
14-23571878-G-A Likely benign (Feb 01, 2024)2644125

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
JPH4protein_codingprotein_codingENST00000397118 510766
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9990.00052500000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.561933220.5990.00001993901
Missense in Polyphen72123.930.580981453
Synonymous1.381221430.8540.000009431402
Loss of Function4.32021.70.000.00000123238

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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