RPL13A

ribosomal protein L13a, the group of L ribosomal proteins

Basic information

Region (hg38): 19:49487510-49493057

Previous symbols: [ "TSTA1" ]

Links

ENSG00000142541 ∙ NCBI:23521 ∙ OMIM:619225 ∙ HGNC:10304 ∙ Uniprot:P40429 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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	1	3
missense			21			21
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	21	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
19-49487634-C-G		not specified	Uncertain significance (Mar 25, 2024)
19-49487637-A-G		not specified	Uncertain significance (Feb 27, 2024)
19-49490225-C-T			Benign (Jun 19, 2018)
19-49490249-G-A		not specified	Uncertain significance (Nov 08, 2024)
19-49490262-G-A		not specified	Uncertain significance (Apr 17, 2024)
19-49490270-A-G		not specified	Uncertain significance (Aug 09, 2021)
19-49490496-G-A		not specified	Uncertain significance (Jul 30, 2024)
19-49490523-G-A		not specified	Uncertain significance (Jan 02, 2024)
19-49490776-C-T			Likely benign (Jan 30, 2018)
19-49490790-C-T		not specified	Uncertain significance (Aug 02, 2022)
19-49490813-C-T			Benign (Jul 19, 2018)
19-49490837-T-G		not specified	Uncertain significance (Dec 08, 2023)
19-49491052-G-A		not specified	Uncertain significance (Oct 29, 2024)
19-49491055-G-C		not specified	Uncertain significance (Jul 19, 2022)
19-49491093-A-C			Likely benign (Mar 01, 2023)
19-49491420-C-G			Benign (Dec 31, 2019)
19-49491421-G-A			Benign (Jun 05, 2018)
19-49491432-A-G		not specified	Uncertain significance (Oct 12, 2022)
19-49491441-G-A		not specified	Uncertain significance (Nov 08, 2022)
19-49491452-G-C		not specified	Uncertain significance (Apr 12, 2023)
19-49491545-A-C		not specified	Uncertain significance (Jan 17, 2024)
19-49491545-A-G		not specified	Uncertain significance (Sep 10, 2024)
19-49491735-C-T		not specified	Uncertain significance (Jun 01, 2023)
19-49491736-G-A		not specified	Uncertain significance (Sep 08, 2024)
19-49491743-G-A			Likely benign (Jun 20, 2018)

GnomAD

Source: gnomAD

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: 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

• 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