RPL6

ribosomal protein L6, the group of L ribosomal proteins

Basic information

Region (hg38): 12:112405189-112418838

Previous symbols: [ "TXREB1" ]

Links

ENSG00000089009 ∙ NCBI:6128 ∙ OMIM:603703 ∙ HGNC:10362 ∙ Uniprot:Q02878 ∙ 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 RPL6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL6 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						0
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in RPL6

This is a list of pathogenic ClinVar variants found in the RPL6 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-112405258-G-A		not specified	Uncertain significance (Jun 11, 2024)
12-112405306-T-G		not specified	Uncertain significance (Aug 04, 2023)
12-112405354-C-T		not specified	Uncertain significance (May 20, 2024)
12-112405899-C-T		not specified	Uncertain significance (Dec 13, 2023)
12-112405902-A-T		not specified	Uncertain significance (Dec 13, 2022)
12-112405916-G-T		not specified	Uncertain significance (Jul 06, 2021)
12-112406317-G-A		not specified	Uncertain significance (Sep 20, 2023)
12-112406761-G-A		not specified	Uncertain significance (Oct 20, 2023)
12-112406862-G-A		not specified	Uncertain significance (Dec 13, 2023)
12-112406878-G-A		not specified	Uncertain significance (Aug 12, 2021)
12-112408298-G-C		not specified	Uncertain significance (Dec 13, 2022)
12-112408597-C-G		not specified	Uncertain significance (Feb 06, 2023)
12-112408610-G-C		not specified	Uncertain significance (Apr 08, 2024)
12-112408625-G-A		not specified	Uncertain significance (Feb 13, 2024)
12-112418795-C-G		LEOPARD syndrome 1 • Noonan syndrome 1 • Metachondromatosis	Uncertain significance (Jan 13, 2018)
12-112418795-C-T		RASopathy	Benign/Likely benign (Jun 01, 2023)
12-112418821-G-A		Noonan syndrome 1 • LEOPARD syndrome 1 • Metachondromatosis	Uncertain significance (Jan 13, 2018)
12-112418825-G-C		Metachondromatosis • LEOPARD syndrome 1 • Noonan syndrome 1	Benign/Likely benign (Jan 12, 2018)
12-112418839-G-A		Noonan syndrome 1 • Metachondromatosis • LEOPARD syndrome 1 • RASopathy • LEOPARD syndrome 1;Noonan syndrome 1;Metachondromatosis;Juvenile myelomonocytic leukemia	Benign (Jan 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPL6	protein_coding	protein_coding	ENST00000424576	6	13649

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00674	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	129	166	0.775	0.00000940	1854
Missense in Polyphen		26	39.472	0.65869		542
Synonymous	-0.391	67	63.1	1.06	0.00000373	575
Loss of Function	3.58	0	14.9	0.00	9.92e-7	177

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

• Function: FUNCTION: Component of the large ribosomal subunit. {ECO:0000269|PubMed:23636399, ECO:0000269|PubMed:25901680, ECO:0000269|PubMed:25957688, ECO:0000305|PubMed:12962325}.
• 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;TNFalpha;Peptide chain elongation;Eukaryotic Translation Elongation;GTP hydrolysis and joining of the 60S ribosomal subunit;Cap-dependent Translation Initiation (Consensus)

Recessive Scores

• pRec: 0.212

Intolerance Scores

• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.650
• hipred: Y
• hipred_score: 0.756
• ghis: 0.593

Essentials

• essential_gene_CRISPR: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rpl6

Zebrafish Information Network

• Gene name: rpl6
• Affected structure: anatomical system
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: ribosomal large subunit assembly;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;cytoplasmic translation;regulation of transcription, DNA-templated;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane
• Cellular component: nucleus;rough endoplasmic reticulum;cytosol;focal adhesion;postsynaptic density;membrane;cytosolic large ribosomal subunit;cytoplasmic ribonucleoprotein granule;polysomal ribosome
• Molecular function: DNA binding;RNA binding;structural constituent of ribosome;cadherin binding