RPL9
ribosomal protein L9, the group of L ribosomal proteins
Basic information
Region (hg38): 4:39452586-39458931
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (32 variants)
- Inborn genetic diseases (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL9 gene is commonly pathogenic or not.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 3 | 1 | 4 | |||
missense | 10 | 10 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice variant | 2 | 1 | 3 | |||
non coding | 6 | 12 | 18 | |||
Total | 0 | 0 | 10 | 11 | 14 |
Variants in RPL9
This is a list of pathogenic ClinVar variants found in the RPL9 region.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
4-39454554-C-A | Inborn genetic diseases | Uncertain significance (Mar 02, 2023) | ||
4-39454558-C-A | Inborn genetic diseases | Uncertain significance (Jan 26, 2023) | ||
4-39454631-G-A | Uncertain significance (Jun 08, 2022) | |||
4-39454658-G-A | Likely benign (Aug 23, 2022) | |||
4-39454772-G-A | Benign (May 14, 2021) | |||
4-39454922-T-G | Uncertain significance (Jul 16, 2022) | |||
4-39454931-T-C | Likely benign (Oct 18, 2022) | |||
4-39455015-T-C | Benign (May 14, 2021) | |||
4-39456237-T-C | Benign (May 14, 2021) | |||
4-39456250-T-TG | Benign (May 14, 2021) | |||
4-39456390-G-A | Likely benign (Jul 21, 2022) | |||
4-39456390-G-C | Benign (Nov 01, 2022) | |||
4-39456422-C-G | Uncertain significance (Jul 17, 2022) | |||
4-39456431-A-G | Benign (Nov 03, 2022) | |||
4-39456462-A-G | Inborn genetic diseases | Uncertain significance (Jul 13, 2022) | ||
4-39456514-C-G | Uncertain significance (Sep 30, 2022) | |||
4-39456532-G-A | Inborn genetic diseases | Uncertain significance (Oct 04, 2022) | ||
4-39456544-TTAAA-T | Benign (Nov 02, 2022) | |||
4-39456552-A-G | Likely benign (May 21, 2022) | |||
4-39457411-T-C | Benign (May 15, 2021) | |||
4-39457534-G-A | Benign (May 14, 2021) | |||
4-39457570-T-C | Likely benign (Oct 19, 2022) | |||
4-39457625-A-G | Likely benign (Jul 08, 2022) | |||
4-39457637-G-A | Likely benign (Sep 09, 2022) | |||
4-39457677-C-T | Inborn genetic diseases | Uncertain significance (Mar 11, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RPL9 | protein_coding | protein_coding | ENST00000449470 | 6 | 4825 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.962 | 0.0380 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.59 | 62 | 109 | 0.571 | 0.00000574 | 1254 |
Missense in Polyphen | 5 | 13.32 | 0.37537 | 199 | ||
Synonymous | -1.60 | 47 | 35.0 | 1.34 | 0.00000166 | 358 |
Loss of Function | 2.96 | 0 | 10.2 | 0.00 | 5.16e-7 | 121 |
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:
- 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
- 0.107
Intolerance Scores
- loftool
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.25
Haploinsufficiency Scores
- pHI
- 0.993
- hipred
- Y
- hipred_score
- 0.802
- ghis
- 0.473
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.897
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rpl9
- Phenotype
Zebrafish Information Network
- Gene name
- rpl9
- Affected structure
- head
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- Biological process
- nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;cytoplasmic translation;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane
- Cellular component
- nucleus;cytosol;ribosome;focal adhesion;membrane;cytosolic large ribosomal subunit
- Molecular function
- RNA binding;structural constituent of ribosome;protein binding;rRNA binding