MRPL53

mitochondrial ribosomal protein L53, the group of Large subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 2:74471982-74472687

Links

ENSG00000204822 ∙ NCBI:116540 ∙ OMIM:611857 ∙ HGNC:16684 ∙ Uniprot:Q96EL3 ∙ 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 MRPL53 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPL53 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in MRPL53

This is a list of pathogenic ClinVar variants found in the MRPL53 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-74472123-C-G		not specified	Uncertain significance (Sep 14, 2023)
2-74472154-T-G		not specified	Uncertain significance (Nov 07, 2022)
2-74472168-C-T		not specified	Uncertain significance (Oct 10, 2023)
2-74472214-T-C		not specified	Uncertain significance (Feb 12, 2024)
2-74472229-G-A		not specified	Uncertain significance (Jan 26, 2023)
2-74472415-A-G		not specified	Uncertain significance (Dec 02, 2022)
2-74472432-G-A		not specified	Uncertain significance (Aug 29, 2022)
2-74472436-G-C		not specified	Uncertain significance (Nov 29, 2021)
2-74472456-G-C		not specified	Uncertain significance (Oct 12, 2022)
2-74472617-T-G		not specified	Uncertain significance (May 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPL53	protein_coding	protein_coding	ENST00000258105	3	1365

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.285	0.637	125629	0	2	125631	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.643	87	71.7	1.21	0.00000323	717
Missense in Polyphen		31	27.413	1.1308		275
Synonymous	-1.34	39	29.7	1.31	0.00000140	243
Loss of Function	1.33	1	3.81	0.263	1.62e-7	42

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)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
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: 0.311
• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.48

Haploinsufficiency Scores

• pHI: 0.0940
• hipred: N
• hipred_score: 0.279

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.974

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrpl53

Gene ontology

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