MRPL50

mitochondrial ribosomal protein L50, the group of Large subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 9:101387633-101398618

Links

ENSG00000136897 ∙ NCBI:54534 ∙ OMIM:611854 ∙ HGNC:16654 ∙ Uniprot:Q8N5N7 ∙ 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 MRPL50 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPL50 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	8	2		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	8	2	0

Variants in MRPL50

This is a list of pathogenic ClinVar variants found in the MRPL50 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-101390485-T-G		not specified	Uncertain significance (Dec 20, 2021)
9-101390500-A-G		not specified	Uncertain significance (Jul 13, 2021)
9-101390533-C-T		not specified	Uncertain significance (Sep 14, 2023)
9-101390581-C-T		not specified	Uncertain significance (Jun 29, 2023)
9-101390608-A-T		See cases	Likely pathogenic (Dec 20, 2022)
9-101390636-G-A		not specified	Uncertain significance (Mar 31, 2024)
9-101390647-T-C		not specified	Likely benign (Mar 15, 2024)
9-101390659-C-G		not specified	Uncertain significance (Dec 21, 2023)
9-101390659-C-T		not specified	Likely benign (Oct 13, 2021)
9-101390680-T-A		not specified	Uncertain significance (May 08, 2024)
9-101390714-C-T		not specified	Likely benign (Jan 08, 2024)
9-101390725-T-G		not specified	Uncertain significance (Mar 18, 2024)
9-101390731-T-A		not specified	Uncertain significance (Jan 06, 2023)
9-101390735-A-C		not specified	Uncertain significance (Aug 13, 2021)
9-101390737-C-T		not specified	Uncertain significance (Mar 02, 2023)
9-101398544-T-C		not specified	Uncertain significance (May 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPL50	protein_coding	protein_coding	ENST00000374865	2	10982

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000381	0.394	125725	0	21	125746	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.732	104	85.0	1.22	0.00000410	1026
Missense in Polyphen		21	20.667	1.0161		291
Synonymous	-0.0530	31	30.6	1.01	0.00000142	313
Loss of Function	0.234	7	7.70	0.909	5.13e-7	71

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000177	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.0000887	0.0000879
Middle Eastern	0.000326	0.000326
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• loftool: 0.690
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.49

Haploinsufficiency Scores

• pHI: 0.185
• hipred: N
• hipred_score: 0.144
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.820

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrpl50

Gene ontology

• Biological process: mitochondrial translational elongation;mitochondrial translational termination
• Cellular component: mitochondrion;mitochondrial inner membrane;mitochondrial large ribosomal subunit