JPH1

junctophilin 1, the group of Junctophilins

Basic information

Region (hg38): 8:74234699-74321540

Links

ENSG00000104369 ∙ NCBI:56704 ∙ OMIM:605266 ∙ HGNC:14201 ∙ Uniprot:Q9HDC5 ∙ 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 JPH1 gene.

• Inborn genetic diseases (16 variants)
• not provided (5 variants)
• CHARCOT-MARIE-TOOTH DISEASE, AXONAL, AUTOSOMAL DOMINANT, TYPE 2K, MODIFIER OF (1 variants)
• Charcot-Marie-Tooth disease axonal type 2K (1 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the JPH1 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	3	4
missense			16		3	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	6

Variants in JPH1

This is a list of pathogenic ClinVar variants found in the JPH1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
8-74237237-G-A		not specified	Uncertain significance (Jan 23, 2023)
8-74244540-C-G		not specified	Uncertain significance (Jan 23, 2024)
8-74244568-G-C		not specified	Uncertain significance (Oct 05, 2023)
8-74244604-C-T			Benign (May 08, 2017)
8-74244702-A-G		not specified	Uncertain significance (May 30, 2023)
8-74244724-G-A		not specified	Likely benign (Nov 20, 2023)
8-74244788-T-C		not specified	Uncertain significance (Oct 26, 2021)
8-74244804-C-T		not specified	Uncertain significance (Jul 14, 2021)
8-74244858-C-T			Benign (Dec 31, 2019)
8-74244859-C-T			Benign (Jul 11, 2017)
8-74244884-T-C		not specified	Uncertain significance (Apr 07, 2023)
8-74244891-T-C		not specified	Uncertain significance (Mar 23, 2022)
8-74244898-C-A		not specified	Uncertain significance (Dec 14, 2021)
8-74244914-G-A		JPH1-related disorder	Benign (Jun 11, 2019)
8-74244953-A-G		not specified	Uncertain significance (Jun 07, 2023)
8-74245112-T-C			Benign (May 08, 2017)
8-74245139-A-G		not specified	Uncertain significance (Jan 23, 2023)
8-74259436-C-T		not specified	Uncertain significance (Feb 26, 2024)
8-74259447-C-T		not specified	Uncertain significance (Apr 28, 2022)
8-74259478-C-T		not specified	Uncertain significance (Jul 14, 2021)
8-74259486-G-A		not specified	Uncertain significance (Feb 28, 2024)
8-74315000-T-C		not specified	Uncertain significance (Nov 21, 2022)
8-74315057-C-T		not specified	Uncertain significance (Nov 15, 2021)
8-74315149-T-A		not specified	Uncertain significance (Nov 09, 2021)
8-74315233-G-A		not specified	Uncertain significance (Jan 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
JPH1	protein_coding	protein_coding	ENST00000342232	5	86629

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.767	0.233	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.46	340	425	0.800	0.0000269	4309
Missense in Polyphen		87	161.53	0.53861		1506
Synonymous	0.868	169	184	0.919	0.0000140	1311
Loss of Function	3.60	4	22.4	0.179	9.57e-7	284

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000267	0.0000264
Middle Eastern	0.000109	0.000109
South Asian	0.0000336	0.0000327
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. JPH1 contributes to the construction of the skeletal muscle triad by linking the t-tubule (transverse-tubule) and SR (sarcoplasmic reticulum) membranes.

Recessive Scores

• pRec: 0.140

Intolerance Scores

• loftool: 0.215
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.65

Haploinsufficiency Scores

• pHI: 0.622
• hipred: Y
• hipred_score: 0.728
• ghis: 0.504

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.789

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Jph1
• Phenotype: muscle phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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)

Gene ontology

• Biological process: muscle organ development;release of sequestered calcium ion into cytosol;regulation of ryanodine-sensitive calcium-release channel activity;calcium ion transport into cytosol
• Cellular component: nucleus;nucleoplasm;endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;junctional sarcoplasmic reticulum membrane;integral component of membrane;sarcoplasmic reticulum;Z disc;junctional membrane complex
• Molecular function: molecular_function;structural constituent of muscle;calcium-release channel activity