MRPL58

mitochondrial ribosomal protein L58, the group of Large subunit mitochondrial ribosomal proteins| Mitochondrial translation release factor family

Basic information

Region (hg38): 17:75012670-75021261

Previous symbols: [ "ICT1" ]

Links

ENSG00000167862 ∙ NCBI:3396 ∙ OMIM:603000 ∙ HGNC:5359 ∙ Uniprot:Q14197 ∙ 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 MRPL58 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPL58 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 MRPL58

This is a list of pathogenic ClinVar variants found in the MRPL58 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-75020542-C-A		not specified	Uncertain significance (Aug 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPL58	protein_coding	protein_coding	ENST00000301585	6	8592

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000562	0.454	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0269	121	120	1.01	0.00000667	1341
Missense in Polyphen		46	43.191	1.065		476
Synonymous	0.0882	44	44.8	0.983	0.00000251	386
Loss of Function	0.565	9	11.0	0.816	5.38e-7	123

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000190	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.00137	0.00136
Finnish	0.00	0.00
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.00137	0.00136
South Asian	0.000133	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential peptidyl-tRNA hydrolase component of the mitochondrial large ribosomal subunit. Acts as a codon-independent translation release factor that has lost all stop codon specificity and directs the termination of translation in mitochondrion, possibly in case of abortive elongation. May be involved in the hydrolysis of peptidyl-tRNAs that have been prematurely terminated and thus in the recycling of stalled mitochondrial ribosomes. {ECO:0000269|PubMed:20186120}.
• Pathway: Mitochondrial translation initiation;Translation;Metabolism of proteins;Mitochondrial translation elongation;Mitochondrial translation termination;Mitochondrial translation (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.78

Haploinsufficiency Scores

• pHI: 0.108
• hipred: N
• hipred_score: 0.255
• ghis: 0.404

Essentials

• essential_gene_gene_trap: H

Mouse Genome Informatics

• Gene name: Mrpl58

Gene ontology

• Biological process: mitochondrial translational elongation;mitochondrial translational termination
• Cellular component: mitochondrion;mitochondrial inner membrane;mitochondrial matrix;mitochondrial large ribosomal subunit
• Molecular function: aminoacyl-tRNA hydrolase activity;translation release factor activity, codon nonspecific