JSRP1

junctional sarcoplasmic reticulum protein 1

Basic information

Region (hg38): 19:2252251-2269759

Links

ENSG00000167476 ∙ NCBI:126306 ∙ OMIM:608743 ∙ HGNC:24963 ∙ Uniprot:Q96MG2 ∙ 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 JSRP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the JSRP1 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						0
missense			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in JSRP1

This is a list of pathogenic ClinVar variants found in the JSRP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-2252334-C-G		not specified	Uncertain significance (Jun 24, 2022)
19-2252337-G-A		not specified	Uncertain significance (Oct 25, 2023)
19-2252364-G-C		not specified	Uncertain significance (Mar 17, 2023)
19-2252370-C-T		not specified	Uncertain significance (May 15, 2024)
19-2252448-G-C		not specified	Uncertain significance (May 24, 2023)
19-2252456-G-C		not specified	Uncertain significance (Sep 29, 2023)
19-2252522-C-T		not specified	Uncertain significance (Feb 27, 2024)
19-2252533-C-G		not specified	Uncertain significance (Apr 18, 2023)
19-2252543-G-T		not specified	Uncertain significance (Jun 11, 2024)
19-2252558-G-C		not specified	Uncertain significance (Sep 28, 2022)
19-2252576-G-A		not specified	Uncertain significance (Jul 05, 2023)
19-2252660-G-C		not specified	Uncertain significance (Apr 25, 2022)
19-2252789-A-G		not specified	Uncertain significance (Sep 27, 2021)
19-2252977-G-C		not specified	Uncertain significance (Jul 20, 2021)
19-2253656-C-T		not specified	Uncertain significance (Jun 17, 2024)
19-2253697-C-T		not specified	Uncertain significance (May 24, 2023)
19-2253721-G-A		not specified	Uncertain significance (May 18, 2022)
19-2253731-G-A		not specified	Uncertain significance (Jun 21, 2022)
19-2253772-C-A		not specified	Uncertain significance (Nov 18, 2023)
19-2254193-C-T		not specified	Uncertain significance (Jan 24, 2023)
19-2254208-C-T		not specified	Uncertain significance (Oct 16, 2023)
19-2254211-T-C		not specified	Uncertain significance (May 07, 2024)
19-2255226-G-T		not specified	Uncertain significance (Dec 17, 2023)
19-2255230-C-T		not specified	Uncertain significance (Oct 12, 2021)
19-2255241-G-C		not specified	Uncertain significance (Dec 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
JSRP1	protein_coding	protein_coding	ENST00000300961	6	17508

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.10e-10	0.0190	125540	0	116	125656	0.000462

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.152	190	196	0.969	0.0000124	2043
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000582	0.000576
Ashkenazi Jewish	0.00195	0.00189
East Asian	0.000109	0.000109
Finnish	0.0000497	0.0000462
European (Non-Finnish)	0.000665	0.000634
Middle Eastern	0.000109	0.000109
South Asian	0.000133	0.000131
Other	0.000855	0.000815

dbNSFP

Source: dbNSFP

• 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

Haploinsufficiency Scores

• pHI: 0.0789
• hipred: N
• hipred_score: 0.220
• ghis: 0.458

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0336

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Jsrp1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; muscle phenotype

Gene ontology

• Biological process: skeletal muscle contraction;regulation of ryanodine-sensitive calcium-release channel activity
• Cellular component: sarcoplasmic reticulum;sarcoplasmic reticulum membrane