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

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• not provided (69 variants)
• Diamond-Blackfan anemia (11 variants)

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				21	1	22
missense			19	1	2	22
nonsense			2			2
start loss						0
frameshift				1		1
inframe indel				1		1
splice variant			4	7		11
non coding				12	2	14
Total	0	0	25	43	5

Variants in RPL19

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

Position	Type	Phenotype	Significance	ClinVar
17-39200346-T-G			Uncertain significance (Aug 24, 2021)
17-39200347-G-C			Uncertain significance (Jun 20, 2022)
17-39200355-G-A			Uncertain significance (Apr 01, 2022)
17-39200356-G-A			Likely benign (Jul 18, 2022)
17-39200357-C-T			Uncertain significance (Mar 26, 2022)
17-39200361-C-G			Likely benign (Aug 21, 2022)
17-39200365-TCTC-T			Likely benign (Aug 31, 2022)
17-39200366-C-G			Likely benign (Jun 14, 2022)
17-39200366-C-T			Likely benign (Jun 20, 2022)
17-39200367-T-A			Likely benign (Jul 15, 2022)
17-39200368-C-T			Likely benign (Nov 02, 2022)
17-39200369-C-G			Likely benign (Aug 31, 2022)
17-39201190-AATC-A			Likely benign (Oct 21, 2022)
17-39201196-G-C			Likely benign (Sep 25, 2021)
17-39201205-G-GT			Likely benign (Oct 05, 2022)
17-39201234-G-A			Likely benign (Aug 30, 2022)
17-39201238-G-T			Uncertain significance (Oct 04, 2022)
17-39201240-C-T			Likely benign (Sep 23, 2022)
17-39201242-C-G			Uncertain significance (Oct 21, 2022)
17-39201245-G-T			Uncertain significance (Sep 01, 2021)
17-39201246-T-C			Likely benign (Oct 20, 2022)
17-39201253-C-T			Uncertain significance (Mar 13, 2022)
17-39201253-CG-AT			Uncertain significance (Sep 01, 2021)
17-39201268-A-G			Uncertain significance (Aug 03, 2022)
17-39201297-T-C			Likely benign (Jul 13, 2021)

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