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RPL31

ribosomal protein L31, the group of L ribosomal proteins

Basic information

Region (hg38): 2:101002228-101024032

Links

ENSG00000071082NCBI:6160OMIM:617415HGNC:10334Uniprot:P62899AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPL31 gene.

  • not provided (24 variants)
  • Inborn genetic diseases (2 variants)
  • not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL31 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
5
clinvar
1
clinvar
6
missense
7
clinvar
1
clinvar
8
nonsense
0
start loss
0
frameshift
0
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
1
clinvar
1
clinvar
8
clinvar
10
Total 0 0 9 7 9

Variants in RPL31

This is a list of pathogenic ClinVar variants found in the RPL31 region.

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

Position Type Phenotype Significance ClinVar
2-101002740-C-G Likely benign (Jan 21, 2024)1978098
2-101002740-C-T Likely benign (Sep 05, 2022)1973807
2-101002749-C-T Benign (Oct 27, 2023)1971968
2-101002753-A-G Uncertain significance (Sep 03, 2023)2757524
2-101002780-A-G Uncertain significance (Oct 11, 2023)2784148
2-101002804-G-A Uncertain significance (Aug 04, 2023)1974635
2-101002815-A-G Likely benign (May 03, 2022)2132755
2-101002817-C-T Likely benign (Nov 25, 2023)2860864
2-101002821-C-G Benign (Jan 31, 2024)1269137
2-101002825-C-T Likely benign (Sep 27, 2022)1973823
2-101002859-T-C Benign (May 14, 2021)1246390
2-101002870-G-A Benign (May 24, 2021)1251780
2-101002915-C-T Benign (May 17, 2021)1291849
2-101004140-C-T Likely benign (Sep 15, 2023)2870654
2-101004144-T-C Likely benign (Sep 24, 2023)2864615
2-101004153-C-T Likely benign (Jul 03, 2023)2786194
2-101004181-G-A Uncertain significance (Sep 07, 2022)2106535
2-101004187-T-G Uncertain significance (Nov 22, 2023)2694899
2-101004190-A-G Inborn genetic diseases Uncertain significance (Apr 17, 2023)2287297
2-101004198-C-T Inborn genetic diseases Uncertain significance (Jun 29, 2023)2603586
2-101004199-G-A Uncertain significance (Sep 22, 2023)2827489
2-101004213-AAGG-A Uncertain significance (May 25, 2022)1999045
2-101004238-G-A Uncertain significance (Jul 24, 2023)2780082
2-101004242-T-C Likely benign (Mar 04, 2023)2867356
2-101004263-T-C Likely benign (Nov 07, 2023)1972003

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPL31protein_codingprotein_codingENST00000409028 422318
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8500.148122014041220180.0000164
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.643980.40.4850.00000487820
Missense in Polyphen44.34610.9203768
Synonymous-0.1982826.71.050.00000123261
Loss of Function2.3106.220.003.53e-771

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)0.00003620.0000362
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
0.202

Intolerance Scores

loftool
rvis_EVS
0.24
rvis_percentile_EVS
68.72

Haploinsufficiency Scores

pHI
0.233
hipred
Y
hipred_score
0.669
ghis
0.413

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.824

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumLowLow
Primary ImmunodeficiencyMediumLowMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rpl31
Phenotype
endocrine/exocrine gland phenotype; reproductive system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype;

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
cytosol;focal adhesion;membrane;cytosolic large ribosomal subunit;polysomal ribosome;extracellular exosome
Molecular function
RNA binding;structural constituent of ribosome;protein binding