MRPL39

mitochondrial ribosomal protein L39, the group of Large subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 21:25585656-25607517

Links

ENSG00000154719 ∙ NCBI:54148 ∙ OMIM:611845 ∙ HGNC:14027 ∙ Uniprot:Q9NYK5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• mitochondrial disease (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Combined oxidative phosphorylation deficiency 59	AR	Cardiovascular	The condition has been described as including hypertrophic cardiomyopathy, and awareness may allow early recognition and management	Biochemical; Cardiovascular; Neurologic	37133451

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MRPL39 gene.

• not_specified (43 variants)
• Combined_oxidative_phosphorylation_deficiency_59 (4 variants)
• Leigh_syndrome (3 variants)
• Mitochondrial_disease (3 variants)
• not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPL39 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017446.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense		1	39			40
nonsense		1				1
start loss			1	1		2
frameshift		1				1
splice donor/acceptor (+/-2bp)						0
Total	0	3	40	1	0

Highest pathogenic variant AF is 0.0002628525

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPL39	protein_coding	protein_coding	ENST00000307301	11	21862

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000431	0.959	125671	0	77	125748	0.000306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.373	206	191	1.08	0.00000979	2297
Missense in Polyphen		50	53.466	0.93518		711
Synonymous	-0.771	74	66.0	1.12	0.00000348	647
Loss of Function	1.90	12	21.5	0.557	0.00000118	263

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000631	0.000623
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000397	0.000396
Middle Eastern	0.0000544	0.0000544
South Asian	0.000366	0.000359
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Mitochondrial translation initiation;Translation;Metabolism of proteins;Mitochondrial translation elongation;Mitochondrial translation termination;Mitochondrial translation (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.874
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.44

Haploinsufficiency Scores

• pHI: 0.149
• hipred: N
• hipred_score: 0.196
• ghis: 0.563

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.587

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Mrpl39

Gene ontology

• Biological process: mitochondrial translational elongation;mitochondrial translational termination
• Cellular component: mitochondrion;mitochondrial inner membrane;mitochondrial ribosome;mitochondrial large ribosomal subunit
• Molecular function: nucleotide binding;RNA binding