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GeneBe

RPLP1

ribosomal protein lateral stalk subunit P1, the group of L ribosomal proteins

Basic information

Region (hg38): 15:69452813-69456205

Links

ENSG00000137818NCBI:6176OMIM:180520HGNC:10372Uniprot:P05386AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPLP1 gene.

  • Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPLP1 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
5
clinvar
5
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 5 0 0

Variants in RPLP1

This is a list of pathogenic ClinVar variants found in the RPLP1 region.

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

Position Type Phenotype Significance ClinVar
15-69455180-A-G not specified Uncertain significance (Feb 09, 2022)2230239
15-69455181-C-A not specified Uncertain significance (Jan 27, 2022)2274231
15-69455182-G-A not specified Uncertain significance (Oct 03, 2022)2315427
15-69455218-G-A not specified Uncertain significance (Dec 21, 2023)3156122
15-69455270-C-T not specified Uncertain significance (Jun 16, 2023)2602739
15-69455284-C-T not specified Uncertain significance (Dec 18, 2023)3156123
15-69455478-G-A not specified Uncertain significance (Aug 22, 2023)2621503

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPLP1protein_codingprotein_codingENST00000260379 43133
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.3700.586125744021257460.00000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1095860.40.9600.00000277724
Missense in Polyphen16.09820.16398100
Synonymous-0.6582723.01.170.00000119229
Loss of Function1.5914.730.2111.99e-760

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004650.0000462
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.00003270.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Plays an important role in the elongation step of protein synthesis.;
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
0.212

Intolerance Scores

loftool
rvis_EVS
-0.05
rvis_percentile_EVS
49.39

Haploinsufficiency Scores

pHI
0.310
hipred
Y
hipred_score
0.821
ghis
0.607

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
S
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.908

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rplp1
Phenotype
immune system phenotype; limbs/digits/tail phenotype; digestive/alimentary 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); reproductive system phenotype; hematopoietic system phenotype; liver/biliary system phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype;

Zebrafish Information Network

Gene name
rplp1
Affected structure
nucleate erythrocyte
Phenotype tag
abnormal
Phenotype quality
decreased amount

Gene ontology

Biological process
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;cytoplasmic translation;translation;translational initiation;translational elongation;SRP-dependent cotranslational protein targeting to membrane;activation of protein kinase activity
Cellular component
cytosol;focal adhesion;cytosolic large ribosomal subunit
Molecular function
structural constituent of ribosome;protein binding;protein kinase activator activity;ribonucleoprotein complex binding