RPL13

ribosomal protein L13, the group of Small nucleolar RNA protein coding host genes|L ribosomal proteins

Basic information

Region (hg38): 16:89560677-89567834

Links

ENSG00000167526NCBI:6137OMIM:113703HGNC:10303Uniprot:P26373AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Spondyloepimetaphyseal dysplasia, Isidor-Toutain typeADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingMusculoskeletal23956136; 31630789

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPL13 gene.

  • Spondyloepimetaphyseal dysplasia, Isidor-Toutain type (3 variants)
  • Spondyloepimetaphyseal dysplasia (2 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.

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
2
missense
1
clinvar
15
clinvar
1
clinvar
17
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
3
clinvar
3
splice region
0
non coding
1
clinvar
1
Total 3 1 15 2 2

Variants in RPL13

This is a list of pathogenic ClinVar variants found in the RPL13 region.

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

Position Type Phenotype Significance ClinVar
16-89560953-G-A RPL13-related disorder Likely benign (Dec 15, 2023)3056569
16-89561052-T-G Spondyloepimetaphyseal dysplasia, Isidor-Toutain type Benign (Nov 07, 2021)1327970
16-89561249-G-A Inborn genetic diseases Uncertain significance (Oct 17, 2023)3156026
16-89561263-C-T Spondyloepimetaphyseal dysplasia, Isidor-Toutain type Benign (Nov 07, 2021)1327971
16-89561300-C-T Inborn genetic diseases Uncertain significance (Dec 08, 2023)3156027
16-89561315-C-T Uncertain significance (Jan 12, 2023)1878976
16-89561352-G-A Inborn genetic diseases Uncertain significance (Apr 26, 2024)3315173
16-89561363-C-T Inborn genetic diseases Uncertain significance (Jun 29, 2022)2220535
16-89561636-G-A Inborn genetic diseases Uncertain significance (Mar 29, 2022)2280284
16-89561669-A-G Inborn genetic diseases Uncertain significance (Jan 26, 2023)2468878
16-89562341-G-A Inborn genetic diseases Uncertain significance (Dec 13, 2021)2356618
16-89562344-C-G Inborn genetic diseases Uncertain significance (Mar 06, 2023)2494681
16-89562378-T-C Inborn genetic diseases Uncertain significance (Oct 18, 2021)2222805
16-89562383-G-A Inborn genetic diseases Likely benign (Jul 15, 2021)2237917
16-89562386-C-T Inborn genetic diseases Uncertain significance (Dec 15, 2023)3156028
16-89562387-G-A Inborn genetic diseases Uncertain significance (Feb 06, 2024)3156029
16-89562392-G-A Spondyloepimetaphyseal dysplasia • Spondyloepimetaphyseal dysplasia, Isidor-Toutain type Pathogenic (Jun 27, 2023)689802
16-89562392-G-T Spondyloepimetaphyseal dysplasia • Spondyloepimetaphyseal dysplasia, Isidor-Toutain type Pathogenic (Jan 03, 2022)689800
16-89562393-T-C Spondyloepimetaphyseal dysplasia • Spondyloepimetaphyseal dysplasia, Isidor-Toutain type Pathogenic (Jan 06, 2020)689801
16-89562883-G-T Spondyloepimetaphyseal dysplasia, Isidor-Toutain type Pathogenic (Dec 14, 2023)2671824
16-89562903-C-T Inborn genetic diseases Uncertain significance (May 06, 2024)3156030
16-89562920-G-GA Spondyloepimetaphyseal dysplasia, Isidor-Toutain type Likely pathogenic (Sep 22, 2024)3362462
16-89562936-A-C Inborn genetic diseases Uncertain significance (Aug 26, 2022)2308847
16-89562939-C-A Spondyloepimetaphyseal dysplasia, Isidor-Toutain type Pathogenic (Dec 15, 2019)813853
16-89562954-G-A Spondyloepimetaphyseal dysplasia, Isidor-Toutain type • RPL13-related disorder Conflicting classifications of pathogenicity (Jan 25, 2024)1030926

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPL13protein_codingprotein_codingENST00000393099 53886
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9510.049200000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.3221411311.080.000007231331
Missense in Polyphen2421.8431.0987298
Synonymous-1.366754.21.240.00000296425
Loss of Function2.8509.470.005.57e-7102

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
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

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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