RPL6
Basic information
Region (hg38): 12:112405188-112418838
Previous symbols: [ "TXREB1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | Noonan syndrome 1 • LEOPARD syndrome 1 • Metachondromatosis | Uncertain significance (Jan 13, 2018) | ||
12-112418795-C-T | RASopathy | Benign/Likely benign (Jun 01, 2023) | ||
12-112418821-G-A | Metachondromatosis • Noonan syndrome 1 • LEOPARD syndrome 1 | 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 • Noonan syndrome 1;Juvenile myelomonocytic leukemia;LEOPARD syndrome 1;Metachondromatosis | Benign (Jan 19, 2024) |
GnomAD
Source:
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:
- 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
- loftool
- 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_CRISPR2
- 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
- Phenotype
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