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GeneBe

RPL3L

ribosomal protein L3 like, the group of L ribosomal proteins

Basic information

Region (hg38): 16:1943973-1957606

Links

ENSG00000140986NCBI:6123OMIM:617416HGNC:10351Uniprot:Q92901AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • dilated cardiomyopathy (Limited), mode of inheritance: AR
  • cardiomyopathy, dilated, 2D (Limited), mode of inheritance: AR
  • cardiomyopathy, dilated, 2D (Strong), mode of inheritance: AR
  • cardiomyopathy, dilated, 2D (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Cardiomyopathy, dilated, 2DARCardiovascularThe condition involves severe, early onset dilated cardiomyopathy, and awareness may enable early interventions related to cardiac disease; Cardiac transplant has been describedCardiovascular32514796; 32870709

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPL3L gene.

  • Inborn genetic diseases (36 variants)
  • not provided (10 variants)
  • Cardiomyopathy, dilated, 2D (4 variants)
  • not specified (1 variants)
  • Cardiomyopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL3L 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
2
clinvar
2
missense
1
clinvar
41
clinvar
2
clinvar
2
clinvar
46
nonsense
0
start loss
0
frameshift
1
clinvar
1
inframe indel
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
0
non coding
0
Total 0 1 43 4 2

Variants in RPL3L

This is a list of pathogenic ClinVar variants found in the RPL3L region.

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

Position Type Phenotype Significance ClinVar
16-1944859-G-A Cardiomyopathy, dilated, 2D Uncertain significance (Feb 20, 2024)3062007
16-1945498-C-T Uncertain significance (Jan 28, 2023)2413034
16-1945539-T-C Inborn genetic diseases Uncertain significance (Mar 20, 2023)2527187
16-1945585-CCACGG-C Cardiomyopathy, dilated, 2D Uncertain significance (Jun 23, 2021)1199411
16-1945588-C-T Likely benign (Jan 19, 2018)784692
16-1945597-G-A Inborn genetic diseases Uncertain significance (May 04, 2022)2226178
16-1945606-G-A Inborn genetic diseases Uncertain significance (Dec 20, 2021)2341216
16-1945855-G-A Cardiomyopathy, dilated, 2D Pathogenic (Jun 06, 2021)1162249
16-1945869-G-C Likely benign (Aug 01, 2023)2498637
16-1945880-C-G Inborn genetic diseases Uncertain significance (Dec 21, 2022)2371291
16-1945897-C-T Inborn genetic diseases Uncertain significance (May 30, 2023)2553107
16-1946653-T-A Cardiomyopathy, dilated, 2D Pathogenic (Jun 06, 2021)1162248
16-1946654-C-T Cardiomyopathy, dilated, 2D • not specified Uncertain significance (Jun 09, 2023)1162251
16-1946658-G-T Inborn genetic diseases Uncertain significance (Sep 06, 2022)2310413
16-1946671-T-C Inborn genetic diseases Uncertain significance (Nov 12, 2021)2210969
16-1946677-T-C Inborn genetic diseases Uncertain significance (May 04, 2023)2543481
16-1946719-C-T Inborn genetic diseases Uncertain significance (May 30, 2023)2527778
16-1946958-G-A Cardiomyopathy, dilated, 2D Uncertain significance (Apr 11, 2023)2498271
16-1946979-C-T Cardiomyopathy, dilated, 2D Uncertain significance (Mar 27, 2023)3066154
16-1947005-C-T Inborn genetic diseases Uncertain significance (Aug 13, 2021)2396071
16-1947009-C-G Uncertain significance (Dec 01, 2023)3026160
16-1947009-C-T Inborn genetic diseases Uncertain significance (May 04, 2022)2352897
16-1947021-C-T Inborn genetic diseases Uncertain significance (Nov 07, 2022)2382973
16-1947035-ACCT-A Cardiomyopathy, dilated, 2D Uncertain significance (Mar 26, 2024)3065369
16-1947041-C-T Inborn genetic diseases Uncertain significance (Apr 12, 2023)2561064

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPL3Lprotein_codingprotein_codingENST00000268661 1013633
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
4.95e-160.0034712535513901257460.00156
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.6863012691.120.00001812642
Missense in Polyphen7475.2280.98368752
Synonymous-2.581501151.310.00000825811
Loss of Function-0.5312219.51.130.00000102219

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.002740.00271
Ashkenazi Jewish0.000.00
East Asian0.0007080.000707
Finnish0.0005180.000508
European (Non-Finnish)0.002420.00233
Middle Eastern0.0007080.000707
South Asian0.0006870.000653
Other0.001500.00147

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
0.152

Intolerance Scores

loftool
rvis_EVS
0.76
rvis_percentile_EVS
86.85

Haploinsufficiency Scores

pHI
0.846
hipred
Y
hipred_score
0.675
ghis
0.488

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.839

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rpl3l
Phenotype

Gene ontology

Biological process
ribosomal large subunit assembly;translation
Cellular component
ribosome;membrane;cytosolic large ribosomal subunit
Molecular function
RNA binding;structural constituent of ribosome