RPL19

ribosomal protein L19, the group of L ribosomal proteins

Basic information

Region (hg38): 17:39200282-39204840

Links

ENSG00000108298 ∙ NCBI:6143 ∙ OMIM:180466 ∙ HGNC:10312 ∙ Uniprot:P84098 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPL19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL19 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				31	1	32
missense			29	2		31
nonsense						0
start loss			3			3
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			4	8		12
non coding			1	27	2	30
Total	0	0	34	60	3

Variants in RPL19

This is a list of pathogenic ClinVar variants found in the RPL19 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-39200345-A-T			Uncertain significance (Mar 17, 2023)
17-39200346-T-G			Uncertain significance (Dec 04, 2023)
17-39200347-G-C			Uncertain significance (Jun 20, 2022)
17-39200355-G-A			Uncertain significance (Nov 08, 2023)
17-39200356-G-A			Likely benign (Jul 18, 2022)
17-39200357-C-T			Uncertain significance (Jul 27, 2023)
17-39200358-G-A			Likely benign (Nov 19, 2023)
17-39200359-A-T			Likely benign (Mar 14, 2023)
17-39200361-C-G			Likely benign (Aug 21, 2022)
17-39200365-TCTC-T			Likely benign (Feb 03, 2023)
17-39200366-C-G			Likely benign (Nov 15, 2023)
17-39200366-C-T			Likely benign (Jun 20, 2022)
17-39200367-T-A			Likely benign (Jul 15, 2022)
17-39200368-C-T			Likely benign (Dec 19, 2023)
17-39200369-C-G			Likely benign (Feb 03, 2023)
17-39201190-AATC-A			Likely benign (Jan 23, 2024)
17-39201196-G-C			Likely benign (Sep 25, 2021)
17-39201201-C-T			Likely benign (Mar 29, 2023)
17-39201203-G-C			Likely benign (Jan 11, 2024)
17-39201205-G-GT			Likely benign (May 17, 2023)
17-39201209-C-T			Likely benign (Nov 04, 2022)
17-39201218-T-C			Uncertain significance (Feb 27, 2023)
17-39201234-G-A			Likely benign (Jan 02, 2024)
17-39201238-G-T			Uncertain significance (Jan 26, 2024)
17-39201240-C-T			Likely benign (May 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPL19	protein_coding	protein_coding	ENST00000225430	6	4445

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.982	0.0180	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.39	58	137	0.425	0.00000967	1279
Missense in Polyphen		7	16.075	0.43545		256
Synonymous	-0.607	47	42.0	1.12	0.00000211	364
Loss of Function	3.24	0	12.2	0.00	8.40e-7	125

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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: 0.221

Intolerance Scores

• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

• pHI: 0.254
• hipred: Y
• hipred_score: 0.783
• ghis: 0.645

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

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Rpl19

Zebrafish Information Network

• Gene name: rpl19
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: atrophied

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;cytoplasmic translation;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;liver regeneration
• Cellular component: cytosol;focal adhesion;membrane;cytosolic large ribosomal subunit;polysomal ribosome;synapse
• Molecular function: RNA binding;structural constituent of ribosome;protein binding;large ribosomal subunit rRNA binding;5.8S rRNA binding