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RPL13A

ribosomal protein L13a, the group of L ribosomal proteins

Basic information

Region (hg38): 19:49487509-49493057

Previous symbols: [ "TSTA1" ]

Links

ENSG00000142541NCBI:23521OMIM:619225HGNC:10304Uniprot:P40429AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPL13A gene.

  • not provided (7 variants)
  • Inborn genetic diseases (7 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.

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
2
clinvar
1
clinvar
3
missense
7
clinvar
7
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
3
4
non coding
0
Total 0 0 7 2 1

Variants in RPL13A

This is a list of pathogenic ClinVar variants found in the RPL13A region.

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

Position Type Phenotype Significance ClinVar
19-49490225-C-T Benign (Jun 19, 2018)769031
19-49490270-A-G Inborn genetic diseases Uncertain significance (Aug 09, 2021)2211331
19-49490776-C-T Likely benign (Jan 30, 2018)715747
19-49490790-C-T Inborn genetic diseases Uncertain significance (Aug 02, 2022)2304721
19-49490813-C-T Benign (Jul 19, 2018)723856
19-49491055-G-C Inborn genetic diseases Uncertain significance (Jul 19, 2022)2302044
19-49491093-A-C Likely benign (Mar 01, 2023)2650247
19-49491420-C-G Benign (Dec 31, 2019)770467
19-49491421-G-A Benign (Jun 05, 2018)775419
19-49491432-A-G Inborn genetic diseases Uncertain significance (Oct 12, 2022)2373335
19-49491441-G-A Inborn genetic diseases Uncertain significance (Nov 08, 2022)2324184
19-49491452-G-C Inborn genetic diseases Uncertain significance (Apr 12, 2023)2536488
19-49491735-C-T Inborn genetic diseases Uncertain significance (Jun 01, 2023)2558141
19-49491743-G-A Likely benign (Jun 20, 2018)750491

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPL13Aprotein_codingprotein_codingENST00000391857 84755
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8330.167125737011257380.00000398
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3211211310.9210.000009421284
Missense in Polyphen714.9290.4689236
Synonymous-0.9625950.31.170.00000327412
Loss of Function3.07214.70.1369.51e-7143

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006150.0000615
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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