RPL39

ribosomal protein L39, the group of L ribosomal proteins|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): X:119786503-119791630

Previous symbols: [ "RPL39P42" ]

Links

ENSG00000198918 ∙ NCBI:6170 ∙ OMIM:300899 ∙ HGNC:10350 ∙ Uniprot:P62891 ∙ 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 RPL39 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL39 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						0
missense			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in RPL39

This is a list of pathogenic ClinVar variants found in the RPL39 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-119789983-C-T		not specified	Uncertain significance (Aug 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPL39	protein_coding	protein_coding	ENST00000361575	3	5140

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.576	0.383	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.33	2	17.8	0.112	0.00000129	329
Missense in Polyphen		0	3.0716	0		69
Synonymous	0.184	5	5.55	0.901	3.54e-7	87
Loss of Function	1.51	0	2.64	0.00	2.04e-7	38

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: 0.130

Intolerance Scores

• rvis_EVS: 0.15
• rvis_percentile_EVS: 63.81

Haploinsufficiency Scores

• pHI: 0.588
• hipred: Y
• hipred_score: 0.601
• ghis: 0.541

Essentials

• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.222

Mouse Genome Informatics

• Gene name: Rpl39

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;cytoplasmic translation;innate immune response in mucosa;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;antibacterial humoral response;defense response to Gram-positive bacterium;antimicrobial humoral immune response mediated by antimicrobial peptide
• Cellular component: extracellular space;cytosol;cytosolic large ribosomal subunit;polysomal ribosome
• Molecular function: RNA binding;structural constituent of ribosome