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

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPL39 gene.

• Inborn genetic diseases (1 variants)

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.

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 variant						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.

Position	Type	Phenotype	Significance	ClinVar
X-119789983-C-T		Inborn genetic diseases	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