JPH4

junctophilin 4, the group of Junctophilins

Basic information

Region (hg38): 14:23568038-23578790

Previous symbols: [ "JPHL1" ]

Links

ENSG00000092051

∙ NCBI:84502 ∙ OMIM:619863 ∙ HGNC:20156 ∙ Uniprot:Q96JJ6 ∙ 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 JPH4 gene.

not_specified (63 variants)
not_provided (1 variants)

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. These statistics are base on transcript: NM_001146028.2. 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				1 clinvar		1
missense			64 clinvar			64
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	64	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

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: 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

	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