JSRP1
protein-codingjunctional sarcoplasmic reticulum protein 1
Gene summary
The protein encoded by this gene is involved in excitation-contraction coupling at the sarcoplasmic reticulum. The encoded protein can interact with CACNA1S, CACNB1, and calsequestrin to help regulate calcium influx and efflux in skeletal muscle. [provided by RefSeq, Jul 2012]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~17.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to JSRP1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_144616.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 53 | 3 | 56 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 53 | 4 | 0 | 57 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_653217.1 | 6 | MANE Select | |
| Ensembl | ENSP00000300961.4 | 6 | MANE Select | |
| Ensembl | ENSP00000532867.1 | 6 | Standard | |
| Ensembl | ENSP00000532867.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- skeletal muscle contraction
- regulation of ryanodine-sensitive calcium-release channel activity
Cellular Component
- sarcoplasmic reticulum
- sarcoplasmic reticulum membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000300961
- Coding exons
- 6
- Length
- 17508
- Individuals with no LoFs
- 125540
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 116
- Defined
- 125656
- p
- 0.000462
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.152 | 190 | 196 | 0.969 | 0.0000124 | 2043 |
| Missense (PolyPhen) | 62 | 61.489 | 1.0083 | 600 | ||
| Synonymous | -0.122 | 91 | 89.5 | 1.02 | 0.00000606 | 716 |
| Loss of Function | -1.18 | 12 | 8.33 | 1.44 | 4.54e-7 | 102 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00038 | 0.00037 | rare |
| Latino/Admixed American | 0.00021 | 0.00020 | rare |
| Ashkenazi Jewish | 0.0019 | 0.0019 | notable |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.000050 | 0.000046 | rare |
| European (Non-Finnish) | 0.00066 | 0.00063 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0.00085 | 0.00081 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in skeletal muscle excitation/contraction coupling (EC), probably acting as a regulator of the voltage- sensitive calcium channel CACNA1S. EC is a physiological process whereby an electrical signal (depolarization of the plasma membrane) is converted into a chemical signal, a calcium gradient, by the opening of ryanodine receptor calcium release channels. May regulate CACNA1S membrane targeting and activity. {ECO:0000269|PubMed:22927026}.;
Recessive Scores
- pRec
- 0.0749
Intolerance Scores
- LoFtool
- 0.779
- RVIS EVS
- 0.64
- RVIS percentile EVS
- 83.9
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0336
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |