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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:P40429AlphaFoldGenCCjaxSfariGnomADPubmed

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 (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)link
19-49490270-A-G Inborn genetic diseases Uncertain significance (Aug 09, 2021)link
19-49490776-C-T Likely benign (Jan 30, 2018)link
19-49490790-C-T Inborn genetic diseases Uncertain significance (Aug 02, 2022)link
19-49490813-C-T Benign (Jul 19, 2018)link
19-49491055-G-C Inborn genetic diseases Uncertain significance (Jul 19, 2022)link
19-49491420-C-G Benign (Dec 31, 2019)link
19-49491421-G-A Benign (Jun 05, 2018)link
19-49491432-A-G Inborn genetic diseases Uncertain significance (Oct 12, 2022)link
19-49491441-G-A Inborn genetic diseases Uncertain significance (Nov 08, 2022)link
19-49491452-G-C Inborn genetic diseases Uncertain significance (Apr 12, 2023)link
19-49491735-C-T Inborn genetic diseases Uncertain significance (Jun 01, 2023)link
19-49491743-G-A Likely benign (Jun 20, 2018)link

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