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 ∙ ClinVar

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

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.

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		2
missense		1	58	4	2	65
nonsense						0
start loss						0
frameshift			1			1
inframe indel			1			1
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	1	61	6	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)
16-1945498-C-T			Uncertain significance (Jan 28, 2023)
16-1945539-T-C		not specified	Uncertain significance (Mar 20, 2023)
16-1945585-CCACGG-C		Cardiomyopathy, dilated, 2D	Uncertain significance (Jun 23, 2021)
16-1945588-C-T			Likely benign (Jan 19, 2018)
16-1945596-C-T		not specified	Uncertain significance (Jan 03, 2024)
16-1945597-G-A		not specified	Uncertain significance (May 04, 2022)
16-1945606-G-A		not specified	Uncertain significance (Dec 20, 2021)
16-1945855-G-A		Cardiomyopathy, dilated, 2D	Pathogenic (Jun 06, 2021)
16-1945869-G-C			Likely benign (Aug 01, 2023)
16-1945880-C-G		not specified	Uncertain significance (Dec 21, 2022)
16-1945897-C-T		not specified	Uncertain significance (May 30, 2023)
16-1946653-T-A		Cardiomyopathy, dilated, 2D	Pathogenic (Jun 06, 2021)
16-1946654-C-T		Cardiomyopathy, dilated, 2D • not specified	Uncertain significance (Jun 09, 2023)
16-1946658-G-T		not specified	Uncertain significance (Sep 06, 2022)
16-1946671-T-C		not specified	Uncertain significance (Nov 12, 2021)
16-1946677-T-C		not specified	Uncertain significance (May 04, 2023)
16-1946719-C-T		not specified	Uncertain significance (May 30, 2023)
16-1946958-G-A		Cardiomyopathy, dilated, 2D • not specified	Uncertain significance (Apr 11, 2023)
16-1946966-T-C		not specified	Uncertain significance (Mar 07, 2024)
16-1946979-C-T		Cardiomyopathy, dilated, 2D	Uncertain significance (Mar 27, 2023)
16-1947002-A-G		not specified	Uncertain significance (Aug 06, 2021)
16-1947005-C-T		not specified	Uncertain significance (Aug 13, 2021)
16-1947009-C-G			Uncertain significance (Dec 01, 2023)
16-1947009-C-T		not specified	Uncertain significance (May 04, 2022)

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

• 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

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