MRPS5

mitochondrial ribosomal protein S5, the group of Mitochondrial ribosomal proteins

Basic information

Region (hg38): 2:95085369-95122006

Links

ENSG00000144029 ∙ NCBI:64969 ∙ OMIM:611972 ∙ HGNC:14498 ∙ Uniprot:P82675 ∙ 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 MRPS5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPS5 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				1		1
missense			26	2		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	3	0

Variants in MRPS5

This is a list of pathogenic ClinVar variants found in the MRPS5 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-95087395-G-A		not specified	Uncertain significance (Jan 03, 2024)
2-95087429-G-C		not specified	Uncertain significance (Feb 28, 2023)
2-95087433-A-C		not specified	Uncertain significance (Apr 18, 2023)
2-95087440-C-T		not specified	Likely benign (Dec 16, 2023)
2-95087493-G-A		not specified	Uncertain significance (Jun 13, 2024)
2-95087521-A-T		not specified	Uncertain significance (May 30, 2023)
2-95087531-G-T			Likely benign (Sep 01, 2022)
2-95087566-G-C		not specified	Uncertain significance (Nov 14, 2023)
2-95090414-T-C		not specified	Likely benign (May 26, 2024)
2-95090428-C-A		not specified	Uncertain significance (Jan 23, 2023)
2-95090432-T-C		not specified	Uncertain significance (Sep 26, 2023)
2-95090465-T-G		not specified	Uncertain significance (May 26, 2024)
2-95090510-C-T		not specified	Uncertain significance (Mar 16, 2022)
2-95100480-G-C		not specified	Uncertain significance (Jul 25, 2023)
2-95101690-T-A		not specified	Uncertain significance (Oct 06, 2022)
2-95101696-C-T		not specified	Uncertain significance (Aug 08, 2023)
2-95108198-G-A		not specified	Uncertain significance (Jan 20, 2023)
2-95108199-G-A		not specified	Uncertain significance (Mar 19, 2024)
2-95108242-C-A		not specified	Uncertain significance (Oct 26, 2022)
2-95108246-C-T		not specified	Uncertain significance (Feb 07, 2023)
2-95108247-G-A		not specified	Uncertain significance (Oct 14, 2021)
2-95108253-C-A		not specified	Uncertain significance (Feb 02, 2022)
2-95108279-T-C		not specified	Uncertain significance (Feb 23, 2023)
2-95108298-T-C		not specified	Uncertain significance (Aug 17, 2022)
2-95108310-C-T		not specified	Uncertain significance (Dec 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPS5	protein_coding	protein_coding	ENST00000272418	12	62228

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000363	0.998	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.327	232	246	0.941	0.0000137	2783
Missense in Polyphen		49	72.415	0.67665		888
Synonymous	-0.180	91	88.8	1.02	0.00000500	810
Loss of Function	2.71	10	24.5	0.409	0.00000130	293

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000453	0.000452
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000955	0.0000924
European (Non-Finnish)	0.0000799	0.0000791
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000674	0.0000653
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Ribosome - Homo sapiens (human);Mitochondrial translation initiation;Translation;Metabolism of proteins;Mitochondrial translation elongation;Mitochondrial translation termination;Mitochondrial translation (Consensus)

Recessive Scores

• pRec: 0.0811

Intolerance Scores

• loftool: 0.184
• rvis_EVS: -0.24
• rvis_percentile_EVS: 36.17

Haploinsufficiency Scores

• pHI: 0.0523
• hipred: N
• hipred_score: 0.387
• ghis: 0.515

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.990

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrps5
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

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