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GeneBe

RPL9

ribosomal protein L9, the group of L ribosomal proteins

Basic information

Region (hg38): 4:39452586-39458931

Links

ENSG00000163682NCBI:6133OMIM:603686HGNC:10369Uniprot:P32969AlphaFoldGenCCjaxSfariGnomADPubmed

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPL9 gene.

  • 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)link
4-39454558-C-A Inborn genetic diseases Uncertain significance (Jan 26, 2023)link
4-39454631-G-A Uncertain significance (Jun 08, 2022)link
4-39454658-G-A Likely benign (Aug 23, 2022)link
4-39454772-G-A Benign (May 14, 2021)link
4-39454922-T-G Uncertain significance (Jul 16, 2022)link
4-39454931-T-C Likely benign (Oct 18, 2022)link
4-39455015-T-C Benign (May 14, 2021)link
4-39456237-T-C Benign (May 14, 2021)link
4-39456250-T-TG Benign (May 14, 2021)link
4-39456390-G-A Likely benign (Jul 21, 2022)link
4-39456390-G-C Benign (Nov 01, 2022)link
4-39456422-C-G Uncertain significance (Jul 17, 2022)link
4-39456431-A-G Benign (Nov 03, 2022)link
4-39456462-A-G Inborn genetic diseases Uncertain significance (Jul 13, 2022)link
4-39456514-C-G Uncertain significance (Sep 30, 2022)link
4-39456532-G-A Inborn genetic diseases Uncertain significance (Oct 04, 2022)link
4-39456544-TTAAA-T Benign (Nov 02, 2022)link
4-39456552-A-G Likely benign (May 21, 2022)link
4-39457411-T-C Benign (May 15, 2021)link
4-39457534-G-A Benign (May 14, 2021)link
4-39457570-T-C Likely benign (Oct 19, 2022)link
4-39457625-A-G Likely benign (Jul 08, 2022)link
4-39457637-G-A Likely benign (Sep 09, 2022)link
4-39457677-C-T Inborn genetic diseases Uncertain significance (Mar 11, 2022)link

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPL9protein_codingprotein_codingENST00000449470 64825
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9620.038000000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.59621090.5710.000005741254
Missense in Polyphen513.320.37537199
Synonymous-1.604735.01.340.00000166358
Loss of Function2.96010.20.005.16e-7121

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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
0.107

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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