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GeneBe

RPL28

ribosomal protein L28, the group of L ribosomal proteins|MicroRNA protein coding host genes

Basic information

Region (hg38): 19:55385931-55403250

Links

ENSG00000108107NCBI:6158OMIM:603638HGNC:10330Uniprot:P46779AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPL28 gene.

  • Inborn genetic diseases (6 variants)
  • not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL28 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
4
clinvar
4
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
1
clinvar
1
clinvar
1
clinvar
3
Total 0 0 5 1 1

Variants in RPL28

This is a list of pathogenic ClinVar variants found in the RPL28 region.

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

Position Type Phenotype Significance ClinVar
19-55386389-G-A not specified Uncertain significance (Jan 26, 2022)2273078
19-55386595-A-G not specified Uncertain significance (Dec 19, 2022)2347951
19-55386622-A-G not specified Uncertain significance (Mar 31, 2023)2531768
19-55388016-C-T not specified Uncertain significance (Aug 28, 2023)2601736
19-55391581-C-T not specified Uncertain significance (Aug 17, 2021)2385361
19-55391634-T-C Benign (Apr 10, 2018)775430
19-55391665-G-A not specified Likely benign (Nov 15, 2021)2261599
19-55391735-C-A not specified Uncertain significance (Sep 26, 2023)3156062
19-55401446-C-T not specified Uncertain significance (Jan 26, 2022)2401117
19-55401453-C-A not specified Uncertain significance (Jun 03, 2022)2386142
19-55401481-C-T not specified Likely benign (Jan 04, 2024)2672791
19-55401541-C-T Benign (Jul 20, 2018)783852
19-55401545-C-A not specified Uncertain significance (Jun 03, 2022)2294064
19-55401545-C-T not specified Uncertain significance (Mar 01, 2024)3185573
19-55401564-C-T not specified Uncertain significance (May 03, 2023)2513073
19-55401578-T-G Benign (Dec 31, 2019)770812
19-55401601-A-C Likely benign (Jul 02, 2018)781884
19-55401603-C-T not specified Uncertain significance (Apr 25, 2022)2392509
19-55401610-G-A Benign (Jun 14, 2018)716611
19-55401618-C-T not specified Uncertain significance (Apr 07, 2023)2513959
19-55401633-C-T not specified Uncertain significance (Dec 14, 2023)3185572
19-55401660-G-T not specified Uncertain significance (Jul 05, 2023)2609783
19-55401729-C-T not specified Uncertain significance (Dec 28, 2023)3185571

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPL28protein_codingprotein_codingENST00000558815 417900
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.7690.22400000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.06771011030.9810.000006091086
Missense in Polyphen2322.2221.035321
Synonymous-1.194939.51.240.00000204343
Loss of Function2.0404.850.002.04e-761

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

Function
FUNCTION: Component of the large ribosomal subunit. {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;Peptide chain elongation;Eukaryotic Translation Elongation;GTP hydrolysis and joining of the 60S ribosomal subunit;Cap-dependent Translation Initiation (Consensus)

Recessive Scores

pRec
0.221

Intolerance Scores

loftool
rvis_EVS
0.08
rvis_percentile_EVS
60.31

Haploinsufficiency Scores

pHI
0.618
hipred
N
hipred_score
0.281
ghis
0.609

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.747

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rpl28
Phenotype

Zebrafish Information Network

Gene name
rpl28
Affected structure
anatomical system
Phenotype tag
abnormal
Phenotype quality
quality

Gene ontology

Biological process
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane
Cellular component
cytosol;membrane;cytosolic large ribosomal subunit;dendrite;cytoplasmic ribonucleoprotein granule;cell body;extracellular exosome
Molecular function
RNA binding;structural constituent of ribosome;protein binding