SLN
sarcolipin
Basic information
Region (hg38): 11:107707378-107719693
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLN 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 | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 0 |
Variants in SLN
This is a list of pathogenic ClinVar variants found in the SLN region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 11-107707858-G-T | not specified | Uncertain significance (Jan 10, 2023) | ||
| 11-107707866-A-G | not specified | Uncertain significance (Aug 28, 2023) | ||
| 11-107707878-G-A | not specified | Uncertain significance (Sep 22, 2023) | ||
| 11-107707893-G-A | not specified | Uncertain significance (Jun 28, 2024) | ||
| 11-107707914-C-T | not specified | Uncertain significance (Dec 11, 2024) | ||
| 11-107707923-A-G | not specified | Uncertain significance (Jul 12, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLN | protein_coding | protein_coding | ENST00000531293 | 1 | 12316 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.287 | 0.501 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.189 | 15 | 17.2 | 0.872 | 9.44e-7 | 197 |
| Missense in Polyphen | 2 | 2.4486 | 0.81678 | 23 | ||
| Synonymous | 0.300 | 6 | 7.01 | 0.856 | 3.86e-7 | 64 |
| Loss of Function | 0.233 | 0 | 0.0634 | 0.00 | 2.60e-9 | 1 |
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:
- Function
- FUNCTION: Reversibly inhibits the activity of ATP2A1 in sarcoplasmic reticulum by decreasing the apparent affinity of the ATPase for Ca(2+). Modulates calcium re-uptake during muscle relaxation and plays an important role in calcium homeostasis in muscle. Required for muscle-based, non-shivering thermogenesis (By similarity). {ECO:0000250|UniProtKB:Q9CQD6, ECO:0000269|PubMed:11781085, ECO:0000269|PubMed:9575189}.;
- Pathway
- Ion channel transport;Ion homeostasis;Transport of small molecules;Cardiac conduction;Muscle contraction;Ion transport by P-type ATPases
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- 0.08
- rvis_percentile_EVS
- 59.43
Haploinsufficiency Scores
- pHI
- 0.332
- hipred
- N
- hipred_score
- 0.279
- ghis
- 0.527
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Sln
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system 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); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); muscle phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- calcium ion transport;negative regulation of catalytic activity;negative regulation of protein complex disassembly;regulation of calcium ion transport;sarcoplasmic reticulum calcium ion transport;negative regulation of calcium ion import;positive regulation of cold-induced thermogenesis;negative regulation of calcium ion transmembrane transporter activity;regulation of relaxation of muscle;negative regulation of calcium ion binding;positive regulation of protein depolymerization;regulation of calcium-transporting ATPase activity
- Cellular component
- integral component of membrane;sarcoplasmic reticulum;sarcoplasmic reticulum membrane
- Molecular function
- enzyme inhibitor activity;protein binding;ATPase binding