RPL13
ribosomal protein L13, the group of Small nucleolar RNA protein coding host genes|L ribosomal proteins
Basic information
Region (hg38): 16:89560676-89564542
Links
Phenotypes
GenCC
Source:
- spondyloepiphyseal dysplasia (Moderate), mode of inheritance: AD
- spondyloepimetaphyseal dysplasia, Isidor-Toutain type (Limited), mode of inheritance: AD
- spondyloepimetaphyseal dysplasia, Isidor-Toutain type (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Spondyloepimetaphyseal dysplasia, Isidor-Toutain type | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Musculoskeletal | 23956136; 31630789 |
ClinVar
This is a list of variants' phenotypes submitted to
- Spondyloepimetaphyseal dysplasia, Isidor-Toutain type (10 variants)
- Inborn genetic diseases (7 variants)
- Spondyloepimetaphyseal dysplasia (4 variants)
- not provided (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL13 gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 2 | ||||
| missense | 4 | 1 | 8 | 1 | 14 | |
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 3 | 3 | ||||
| non coding | 0 | |||||
| Total | 7 | 1 | 9 | 1 | 2 |
Variants in RPL13
This is a list of pathogenic ClinVar variants found in the RPL13 region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 16-89561052-T-G | Spondyloepimetaphyseal dysplasia, Isidor-Toutain type | Benign (Nov 07, 2021) | ||
| 16-89561263-C-T | Spondyloepimetaphyseal dysplasia, Isidor-Toutain type | Benign (Nov 07, 2021) | ||
| 16-89561315-C-T | Uncertain significance (Jan 12, 2023) | |||
| 16-89561363-C-T | Inborn genetic diseases | Uncertain significance (Jun 29, 2022) | ||
| 16-89561636-G-A | Inborn genetic diseases | Uncertain significance (Mar 29, 2022) | ||
| 16-89561669-A-G | Inborn genetic diseases | Uncertain significance (Jan 26, 2023) | ||
| 16-89562341-G-A | Inborn genetic diseases | Uncertain significance (Dec 13, 2021) | ||
| 16-89562344-C-G | Inborn genetic diseases | Uncertain significance (Mar 06, 2023) | ||
| 16-89562378-T-C | Inborn genetic diseases | Uncertain significance (Oct 18, 2021) | ||
| 16-89562383-G-A | Inborn genetic diseases | Likely benign (Jul 15, 2021) | ||
| 16-89562392-G-A | Spondyloepimetaphyseal dysplasia • Spondyloepimetaphyseal dysplasia, Isidor-Toutain type | Pathogenic (Jun 27, 2023) | ||
| 16-89562392-G-T | Spondyloepimetaphyseal dysplasia • Spondyloepimetaphyseal dysplasia, Isidor-Toutain type | Pathogenic (Jan 03, 2022) | ||
| 16-89562393-T-C | Spondyloepimetaphyseal dysplasia • Spondyloepimetaphyseal dysplasia, Isidor-Toutain type | Pathogenic (Jan 06, 2020) | ||
| 16-89562936-A-C | Inborn genetic diseases | Uncertain significance (Aug 26, 2022) | ||
| 16-89562939-C-A | Spondyloepimetaphyseal dysplasia, Isidor-Toutain type | Pathogenic (Dec 15, 2019) | ||
| 16-89562954-G-A | Spondyloepimetaphyseal dysplasia, Isidor-Toutain type • RPL13-related condition | Conflicting interpretations of pathogenicity (May 30, 2023) | ||
| 16-89562954-G-C | Spondyloepimetaphyseal dysplasia, Isidor-Toutain type | Pathogenic (Jan 07, 2020) | ||
| 16-89562954-G-T | Spondyloepimetaphyseal dysplasia | Pathogenic (Apr 22, 2019) | ||
| 16-89562959-G-C | Spondyloepimetaphyseal dysplasia, Isidor-Toutain type | Pathogenic (Dec 15, 2019) | ||
| 16-89562963-G-C | Uncertain significance (Jan 17, 2022) | |||
| 16-89562969-A-G | Inborn genetic diseases | Uncertain significance (Sep 06, 2022) | ||
| 16-89562975-G-T | Spondyloepimetaphyseal dysplasia, Isidor-Toutain type | Likely pathogenic (Jul 25, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RPL13 | protein_coding | protein_coding | ENST00000393099 | 5 | 3886 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.951 | 0.0492 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.322 | 141 | 131 | 1.08 | 0.00000723 | 1331 |
| Missense in Polyphen | 24 | 21.843 | 1.0987 | 298 | ||
| Synonymous | -1.36 | 67 | 54.2 | 1.24 | 0.00000296 | 425 |
| Loss of Function | 2.85 | 0 | 9.47 | 0.00 | 5.57e-7 | 102 |
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:
- Pathway
- Ribosome - Homo sapiens (human);Cytoplasmic Ribosomal Proteins;SRP-dependent cotranslational protein targeting to membrane;Eukaryotic Translation Initiation;Eukaryotic Translation Termination;Translation;Selenocysteine synthesis;Metabolism of proteins;Metabolism of amino acids and derivatives;Metabolism of RNA;Formation of a pool of free 40S subunits;Metabolism;Nonsense-Mediated Decay (NMD);Selenoamino acid metabolism;Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC);Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC);L13a-mediated translational silencing of Ceruloplasmin expression;Peptide chain elongation;Eukaryotic Translation Elongation;GTP hydrolysis and joining of the 60S ribosomal subunit;Cap-dependent Translation Initiation
(Consensus)
Recessive Scores
- pRec
- 0.195
Intolerance Scores
- loftool
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58.53
Haploinsufficiency Scores
- pHI
- 0.760
- hipred
- Y
- hipred_score
- 0.802
- ghis
- 0.587
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.989
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rpl13
- Phenotype
Zebrafish Information Network
- Gene name
- rpl13
- Affected structure
- trunk
- Phenotype tag
- abnormal
- Phenotype quality
- curved dorsal
Gene ontology
- Biological process
- nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane
- Cellular component
- nucleus;nucleolus;endoplasmic reticulum;cytosol;membrane;cytosolic large ribosomal subunit;cytosolic ribosome
- Molecular function
- RNA binding;structural constituent of ribosome;protein binding