RPL13A
ribosomal protein L13a, the group of L ribosomal proteins
Basic information
Region (hg38): 19:49487509-49493057
Previous symbols: [ "TSTA1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (6 variants)
- Inborn genetic diseases (5 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL13A gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 5 | 1 | 6 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 1 | 3 | 4 | |||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 2 | 4 |
Variants in RPL13A
This is a list of pathogenic ClinVar variants found in the RPL13A region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-49490225-C-T | Benign (Jun 19, 2018) | |||
| 19-49490270-A-G | Inborn genetic diseases | Uncertain significance (Aug 09, 2021) | ||
| 19-49490776-C-T | Likely benign (Jan 30, 2018) | |||
| 19-49490790-C-T | Inborn genetic diseases | Uncertain significance (Aug 02, 2022) | ||
| 19-49490813-C-T | Benign (Jul 19, 2018) | |||
| 19-49491055-G-C | Inborn genetic diseases | Uncertain significance (Jul 19, 2022) | ||
| 19-49491420-C-G | Benign (Dec 31, 2019) | |||
| 19-49491421-G-A | Benign (Jun 05, 2018) | |||
| 19-49491432-A-G | Inborn genetic diseases | Uncertain significance (Oct 12, 2022) | ||
| 19-49491441-G-A | Inborn genetic diseases | Uncertain significance (Nov 08, 2022) | ||
| 19-49491452-G-C | Inborn genetic diseases | Uncertain significance (Apr 12, 2023) | ||
| 19-49491735-C-T | Inborn genetic diseases | Uncertain significance (Jun 01, 2023) | ||
| 19-49491743-G-A | Likely benign (Jun 20, 2018) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RPL13A | protein_coding | protein_coding | ENST00000391857 | 8 | 4755 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.833 | 0.167 | 125737 | 0 | 1 | 125738 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.321 | 121 | 131 | 0.921 | 0.00000942 | 1284 |
| Missense in Polyphen | 7 | 14.929 | 0.4689 | 236 | ||
| Synonymous | -0.962 | 59 | 50.3 | 1.17 | 0.00000327 | 412 |
| Loss of Function | 3.07 | 2 | 14.7 | 0.136 | 9.51e-7 | 143 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| 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: Associated with ribosomes but is not required for canonical ribosome function and has extra-ribosomal functions. Component of the GAIT (gamma interferon-activated inhibitor of translation) complex which mediates interferon-gamma-induced transcript-selective translation inhibition in inflammation processes. Upon interferon-gamma activation and subsequent phosphorylation dissociates from the ribosome and assembles into the GAIT complex which binds to stem loop-containing GAIT elements in the 3'-UTR of diverse inflammatory mRNAs (such as ceruplasmin) and suppresses their translation. In the GAIT complex interacts with m7G cap-bound eIF4G at or near the eIF3-binding site and blocks the recruitment of the 43S ribosomal complex. Involved in methylation of rRNA. {ECO:0000269|PubMed:14567916, ECO:0000269|PubMed:17218275, ECO:0000269|PubMed:17921318, ECO:0000269|PubMed:23071094}.;
- 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
- 0.265
Intolerance Scores
- loftool
- rvis_EVS
- -0.43
- rvis_percentile_EVS
- 25.15
Haploinsufficiency Scores
- pHI
- 0.752
- hipred
- Y
- hipred_score
- 0.809
- ghis
- 0.572
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.988
Mouse Genome Informatics
- Gene name
- Rpl13a
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; hematopoietic system phenotype; 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);
Gene ontology
- Biological process
- nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;negative regulation of translation;cellular response to interferon-gamma;negative regulation of formation of translation preinitiation complex
- Cellular component
- nucleus;nucleolus;cytoplasm;cytosol;ribosome;focal adhesion;large ribosomal subunit;membrane;cytosolic large ribosomal subunit;GAIT complex;ribonucleoprotein complex
- Molecular function
- RNA binding;mRNA binding;structural constituent of ribosome