RPL3L

ribosomal protein L3 like, the group of L ribosomal proteins

Basic information

Region (hg38): 16:1943973-1957606

Links

ENSG00000140986

∙ NCBI:6123 ∙ OMIM:617416 ∙ HGNC:10351 ∙ Uniprot:Q92901 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed

Phenotypes

GenCC

Source: genCC

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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cardiomyopathy, dilated, 2D	AR	Cardiovascular	The condition involves severe, early onset dilated cardiomyopathy, and awareness may enable early interventions related to cardiac disease; Cardiac transplant has been described	Cardiovascular	32514796; 32870709

ClinVar

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

Inborn genetic diseases (25 variants)
Cardiomyopathy, dilated, 2D (8 variants)
not provided (7 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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense	5	1	29	1	2	38
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice variant			1			1
non coding						0
Total	5	1	31	1	2

Highest pathogenic variant AF is 0.0000854

Variants in RPL3L

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

Position	Phenotype	Significance	ClinVar
16-1945498-C-T		Uncertain significance (Jan 28, 2023)	link
16-1945539-T-C	Inborn genetic diseases	Uncertain significance (Mar 20, 2023)	link
16-1945585-CCACGG-C	Cardiomyopathy, dilated, 2D	Uncertain significance (Jun 23, 2021)	link
16-1945588-C-T		Likely benign (Jan 19, 2018)	link
16-1945597-G-A	Inborn genetic diseases	Uncertain significance (May 04, 2022)	link
16-1945606-G-A	Inborn genetic diseases	Uncertain significance (Dec 20, 2021)	link
16-1945855-G-A	Cardiomyopathy, dilated, 2D	Pathogenic (Jun 06, 2021)	link
16-1945869-G-C		Likely benign (Aug 01, 2023)	link
16-1945880-C-G	Inborn genetic diseases	Uncertain significance (Dec 21, 2022)	link
16-1945897-C-T	Inborn genetic diseases	Uncertain significance (May 30, 2023)	link
16-1946653-T-A	Cardiomyopathy, dilated, 2D	Pathogenic (Jun 06, 2021)	link
16-1946654-C-T	Cardiomyopathy, dilated, 2D • not specified	Uncertain significance (Jun 09, 2023)	link
16-1946658-G-T	Inborn genetic diseases	Uncertain significance (Sep 06, 2022)	link
16-1946671-T-C	Inborn genetic diseases	Uncertain significance (Nov 12, 2021)	link
16-1946677-T-C	Inborn genetic diseases	Uncertain significance (May 04, 2023)	link
16-1946719-C-T	Inborn genetic diseases	Uncertain significance (May 30, 2023)	link
16-1946958-G-A	Cardiomyopathy, dilated, 2D	Uncertain significance (Apr 11, 2023)	link
16-1947005-C-T	Inborn genetic diseases	Uncertain significance (Aug 13, 2021)	link
16-1947009-C-T	Inborn genetic diseases	Uncertain significance (May 04, 2022)	link
16-1947021-C-T	Inborn genetic diseases	Uncertain significance (Nov 07, 2022)	link
16-1947041-C-T	Inborn genetic diseases	Uncertain significance (Apr 12, 2023)	link
16-1947063-G-A		Benign (Jan 19, 2018)	link
16-1947065-G-A	Cardiomyopathy	Uncertain significance (May 06, 2021)	link
16-1947086-C-A	Inborn genetic diseases	Uncertain significance (May 31, 2023)	link
16-1947096-C-A		Uncertain significance (Jun 04, 2022)	link

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPL3L	protein_coding	protein_coding	ENST00000268661	10	13633

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.95e-16	0.00347	125355	1	390	125746	0.00156

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.686	301	269	1.12	0.0000181	2642
Missense in Polyphen		74	75.228	0.98368		752
Synonymous	-2.58	150	115	1.31	0.00000825	811
Loss of Function	-0.531	22	19.5	1.13	0.00000102	219

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00274	0.00271
Ashkenazi Jewish	0.00	0.00
East Asian	0.000708	0.000707
Finnish	0.000518	0.000508
European (Non-Finnish)	0.00242	0.00233
Middle Eastern	0.000708	0.000707
South Asian	0.000687	0.000653
Other	0.00150	0.00147

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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