MRPL54

mitochondrial ribosomal protein L54, the group of Large subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 19:3762682-3768575

Links

ENSG00000183617 ∙ NCBI:116541 ∙ OMIM:611858 ∙ HGNC:16685 ∙ Uniprot:Q6P161 ∙ 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 MRPL54 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPL54 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	1		11
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	1	0

Variants in MRPL54

This is a list of pathogenic ClinVar variants found in the MRPL54 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-3762749-G-A		not specified	Likely benign (Dec 13, 2023)
19-3765177-G-A		not specified	Uncertain significance (Oct 13, 2023)
19-3765205-G-T		not specified	Uncertain significance (Apr 25, 2023)
19-3765295-A-G		not specified	Uncertain significance (Jun 17, 2024)
19-3765297-G-A		not specified	Uncertain significance (Mar 19, 2024)
19-3765300-C-T		not specified	Uncertain significance (Mar 21, 2024)
19-3765310-C-T		not specified	Uncertain significance (Jun 06, 2023)
19-3765319-A-C		not specified	Uncertain significance (Jan 31, 2024)
19-3767281-G-C		not specified	Uncertain significance (Dec 21, 2022)
19-3767313-G-A		not specified	Uncertain significance (Jun 13, 2024)
19-3767320-G-A		not specified	Uncertain significance (Sep 26, 2023)
19-3767320-G-C		not specified	Uncertain significance (Apr 27, 2022)
19-3767328-T-C		not specified	Uncertain significance (Jan 17, 2024)
19-3767340-C-T		not specified	Uncertain significance (Feb 07, 2023)
19-3767341-G-A		not specified	Uncertain significance (Aug 12, 2022)
19-3767378-G-C		not specified	Uncertain significance (Mar 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPL54	protein_coding	protein_coding	ENST00000330133	3	5912

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0221	0.776	125653	0	39	125692	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0640	86	87.7	0.981	0.00000543	880
Missense in Polyphen		31	30.412	1.0193		304
Synonymous	0.151	35	36.2	0.968	0.00000212	279
Loss of Function	0.917	3	5.27	0.569	2.23e-7	64

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000146	0.000146
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000297	0.000290
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• loftool: 0.244
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.49

Haploinsufficiency Scores

• pHI: 0.0823
• hipred: N
• hipred_score: 0.171
• ghis: 0.549

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.970

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrpl54

Gene ontology

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