MRPL52

mitochondrial ribosomal protein L52, the group of Large subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 14:22829879-22835037

Links

ENSG00000172590 ∙ NCBI:122704 ∙ OMIM:611856 ∙ HGNC:16655 ∙ Uniprot:Q86TS9 ∙ 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 MRPL52 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPL52 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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in MRPL52

This is a list of pathogenic ClinVar variants found in the MRPL52 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-22829931-G-T		not specified	Uncertain significance (Mar 06, 2023)
14-22830224-C-T		not specified	Uncertain significance (Sep 25, 2023)
14-22833454-G-A		not specified	Uncertain significance (Mar 26, 2024)
14-22833478-T-C		not specified	Uncertain significance (May 24, 2024)
14-22834220-T-C		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPL52	protein_coding	protein_coding	ENST00000355151	5	5159

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.16e-7	0.153	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.260	62	68.0	0.911	0.00000343	767
Missense in Polyphen		1	6.2608	0.15972		59
Synonymous	-0.622	31	26.9	1.15	0.00000139	246
Loss of Function	-0.113	10	9.62	1.04	5.76e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000247	0.000246
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.000163	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: 0.0439

Intolerance Scores

• loftool: 0.874
• rvis_EVS: 0.57
• rvis_percentile_EVS: 81.89

Haploinsufficiency Scores

• pHI: 0.0283
• hipred: N
• hipred_score: 0.170
• ghis: 0.404

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.404

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrpl52

Gene ontology

• Biological process: translation;mitochondrial translational elongation;mitochondrial translational termination
• Cellular component: mitochondrion;mitochondrial inner membrane;mitochondrial large ribosomal subunit
• Molecular function: structural constituent of ribosome