OBSCN
Basic information
Region (hg38): 1:228208044-228378876
Links
Phenotypes
GenCC
Source:
- rhabdomyolysis, susceptibility to, 1 (Strong), mode of inheritance: AR
- hypertrophic cardiomyopathy (Limited), mode of inheritance: AD
- dilated cardiomyopathy (Limited), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Rhabdomyolysis, susceptibility to, 1 | AR | Musculoskeletal; Renal | The condition can include increased risk of rhabdomyolysis, due both to risk factors such as exercise and heat, as well as spontaneously, with risk of renal damage and compartment syndrome, and awareness may allow preventative measures and prompt treatment of episodes | Musculoskeletal; Renal | 34957489 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (4961 variants)
- not_provided (577 variants)
- OBSCN-related_disorder (294 variants)
- Rhabdomyolysis,_susceptibility_to,_1 (23 variants)
- Short_stature (3 variants)
- Inborn_genetic_diseases (2 variants)
- Arrhythmogenic_right_ventricular_dysplasia_9 (1 variants)
- Hearing_loss,_autosomal_recessive_120 (1 variants)
- Hypertrophic_cardiomyopathy_1 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the OBSCN gene is commonly pathogenic or not. These statistics are base on transcript: NM_001386125.1. 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 | 1482 | 43 | 1527 | |||
missense | 2689 | 645 | 71 | 3408 | ||
nonsense | 12 | 23 | ||||
start loss | 0 | |||||
frameshift | 18 | 33 | ||||
splice donor/acceptor (+/-2bp) | 11 | |||||
Total | 33 | 15 | 2707 | 2132 | 115 |
Highest pathogenic variant AF is 0.00032663564
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
OBSCN | protein_coding | protein_coding | ENST00000570156 | 115 | 170747 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.86e-164 | 2.46e-12 | 116020 | 886 | 8154 | 125060 | 0.0368 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -1.14 | 5536 | 5.30e+3 | 1.04 | 0.000363 | 56590 |
Missense in Polyphen | 2514 | 2487.2 | 1.0108 | 28018 | ||
Synonymous | -1.99 | 2490 | 2.37e+3 | 1.05 | 0.000175 | 18677 |
Loss of Function | 3.71 | 297 | 375 | 0.793 | 0.0000190 | 4191 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0339 | 0.0327 |
Ashkenazi Jewish | 0.00966 | 0.00958 |
East Asian | 0.317 | 0.311 |
Finnish | 0.0403 | 0.0396 |
European (Non-Finnish) | 0.00873 | 0.00828 |
Middle Eastern | 0.317 | 0.311 |
South Asian | 0.0524 | 0.0512 |
Other | 0.0290 | 0.0279 |
dbNSFP
Source:
- Function
- FUNCTION: Structural component of striated muscles which plays a role in myofibrillogenesis. Probably involved in the assembly of myosin into sarcomeric A bands in striated muscle (PubMed:11448995, PubMed:16205939). Has serine/threonine protein kinase activity and phosphorylates N-cadherin CDH2 and sodium/potassium-transporting ATPase subunit ATP1B1 (By similarity). {ECO:0000250|UniProtKB:A2AAJ9, ECO:0000269|PubMed:11448995, ECO:0000269|PubMed:16205939}.;
- Disease
- DISEASE: Note=A chromosomal aberration involving OBSCN has been found in Wilms tumor. Translocation t(1;7)(q42;p15) with PTHB1. {ECO:0000269|PubMed:12618763}.;
- Pathway
- Signaling by GPCR;Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases;NRAGE signals death through JNK;Death Receptor Signalling;p75 NTR receptor-mediated signalling;G alpha (12/13) signalling events;GPCR downstream signalling;Cell death signalling via NRAGE, NRIF and NADE;Regulation of RhoA activity
(Consensus)
Recessive Scores
- pRec
- 0.128
Haploinsufficiency Scores
- pHI
- 0.180
- hipred
- N
- hipred_score
- 0.270
- ghis
- 0.514
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.528
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | High | High | High |
Primary Immunodeficiency | High | High | High |
Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Obscn
- Phenotype
- muscle phenotype;
Zebrafish Information Network
- Gene name
- obscnb
- Affected structure
- cardiac muscle cell
- Phenotype tag
- abnormal
- Phenotype quality
- structure
Gene ontology
- Biological process
- protein phosphorylation;G protein-coupled receptor signaling pathway;multicellular organism development;regulation of Rho protein signal transduction;protein localization to M-band;positive regulation of apoptotic process;sarcomere organization;regulation of small GTPase mediated signal transduction
- Cellular component
- cytosol;plasma membrane;nuclear body;myofibril;Z disc;M band;sarcolemma
- Molecular function
- protein serine/threonine kinase activity;guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;protein binding;calmodulin binding;ATP binding;structural constituent of muscle;ankyrin binding;titin binding;metal ion binding