MRPL39

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

Basic information

Region (hg38): 21:25585655-25607517

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

ClinVar

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

• Inborn genetic diseases (15 variants)
• Leigh syndrome (2 variants)
• Combined oxidative phosphorylation deficiency 59 (2 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.

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			14			14
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding		1	1		1	3
Total	0	2	15	0	1

Highest pathogenic variant AF is 0.000125

Variants in MRPL39

This is a list of pathogenic ClinVar variants found in the MRPL39 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-25587768-G-C		not specified	Uncertain significance (Apr 11, 2023)
21-25592807-C-T		Leigh syndrome • Combined oxidative phosphorylation deficiency 59	Pathogenic/Likely pathogenic (Dec 05, 2023)
21-25592837-C-A		Mitochondrial disease • Combined oxidative phosphorylation deficiency 59	Likely pathogenic (Feb 04, 2021)
21-25592891-G-A		not specified	Uncertain significance (Jan 26, 2022)
21-25592951-A-G		not specified	Uncertain significance (Jun 13, 2023)
21-25593918-G-C		not specified	Uncertain significance (Nov 17, 2022)
21-25593941-A-G		not specified	Uncertain significance (Oct 25, 2023)
21-25597305-C-A		not specified	Uncertain significance (Aug 04, 2023)
21-25597366-C-T		not specified	Uncertain significance (Aug 13, 2021)
21-25597371-T-C		not specified	Uncertain significance (Jun 11, 2021)
21-25597380-G-A		not specified	Uncertain significance (Mar 27, 2023)
21-25598338-C-T		Leigh syndrome • Combined oxidative phosphorylation deficiency 59	Likely pathogenic (Jun 24, 2022)
21-25599832-C-A		not specified	Uncertain significance (Jun 09, 2022)
21-25599860-GA-G		Leigh syndrome • Combined oxidative phosphorylation deficiency 59	Likely pathogenic (Jun 24, 2022)
21-25601389-C-T		not specified	Uncertain significance (Jan 18, 2022)
21-25601445-A-G		not specified	Uncertain significance (May 17, 2023)
21-25601452-A-T		not specified	Uncertain significance (Feb 06, 2024)
21-25603803-A-G		not specified	Uncertain significance (Jan 26, 2022)
21-25603928-G-C		not specified	Uncertain significance (May 18, 2022)
21-25606461-T-A		not specified	Uncertain significance (Feb 28, 2024)
21-25606509-C-T		not specified	Uncertain significance (Apr 03, 2023)
21-25606523-T-C		not specified	Uncertain significance (Feb 09, 2023)
21-25606638-A-A			Benign (Dec 31, 2019)

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