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

ENSG00000167526 ∙ NCBI:6137 ∙ OMIM:113703 ∙ HGNC:10303 ∙ Uniprot:P26373 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

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 ClinVar and linked to the RPL13 gene.

• Spondyloepimetaphyseal dysplasia, Isidor-Toutain type (2 variants)
• Spondyloepimetaphyseal dysplasia (1 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	2
missense		1	20	1		22
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)	2	1				3
splice region						0
non coding						0
Total	2	3	20	1	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)
16-89561008-G-T		Inborn genetic diseases	Uncertain significance (Oct 28, 2024)
16-89561052-T-G		Spondyloepimetaphyseal dysplasia, Isidor-Toutain type	Benign (Nov 07, 2021)
16-89561249-G-A		Inborn genetic diseases	Uncertain significance (Oct 17, 2023)
16-89561263-C-T		Spondyloepimetaphyseal dysplasia, Isidor-Toutain type	Benign (Nov 07, 2021)
16-89561277-C-G		Inborn genetic diseases	Uncertain significance (Jan 26, 2025)
16-89561300-C-T		Inborn genetic diseases	Uncertain significance (Dec 08, 2023)
16-89561315-C-T			Uncertain significance (Jan 12, 2023)
16-89561352-G-A		Inborn genetic diseases	Uncertain significance (Apr 26, 2024)
16-89561363-C-T		Inborn genetic diseases	Uncertain significance (Jun 29, 2022)
16-89561617-A-G		Inborn genetic diseases	Uncertain significance (Aug 14, 2024)
16-89561636-G-A		Inborn genetic diseases	Uncertain significance (Sep 10, 2024)
16-89561669-A-G		Inborn genetic diseases	Uncertain significance (Jan 26, 2023)
16-89562335-G-A		Inborn genetic diseases	Uncertain significance (Aug 06, 2024)
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)
16-89562386-C-T		Inborn genetic diseases	Uncertain significance (Dec 15, 2023)
16-89562387-G-A		Inborn genetic diseases	Uncertain significance (Feb 06, 2024)
16-89562392-G-A		Spondyloepimetaphyseal dysplasia • Spondyloepimetaphyseal dysplasia, Isidor-Toutain type	Pathogenic/Likely pathogenic (Sep 04, 2024)
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)
16-89562883-G-T		Spondyloepimetaphyseal dysplasia, Isidor-Toutain type	Pathogenic (Dec 14, 2023)
16-89562903-C-T		Inborn genetic diseases	Uncertain significance (May 06, 2024)

GnomAD

Source: gnomAD

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: 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

• 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

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