MRPS25

mitochondrial ribosomal protein S25, the group of Small subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 3:15009610-15065339

Links

ENSG00000131368 ∙ NCBI:64432 ∙ OMIM:611987 ∙ HGNC:14511 ∙ Uniprot:P82663 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• mitochondrial encephalomyopathy (Limited), mode of inheritance: AR
• combined oxidative phosphorylation deficiency 50 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Combined oxidative phosphorylation deficiency 50	AR	Endocrine	In addition to other features, an individual has been described as involving adrenal insufficiency requiring hydrocortisone replacement, and awareness may allow early diagnosis and medical management	Biochemical; Endocrine; Neurologic	31039582

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MRPS25 gene.

• Inborn genetic diseases (10 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPS25 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		1	2
Total	0	0	10	1	1

Variants in MRPS25

This is a list of pathogenic ClinVar variants found in the MRPS25 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-15013691-G-A		not specified	Uncertain significance (Nov 22, 2023)
3-15016180-G-A		not specified	Uncertain significance (Dec 21, 2023)
3-15023315-T-A			Benign (May 08, 2018)
3-15030298-C-T		not specified	Uncertain significance (Mar 22, 2023)
3-15030397-C-T		not specified	Uncertain significance (Oct 05, 2023)
3-15052467-C-T		not specified	Uncertain significance (Oct 26, 2022)
3-15053465-A-G		not specified	Uncertain significance (Jun 17, 2022)
3-15059374-T-C		not specified	Uncertain significance (Nov 15, 2021)
3-15059395-G-A		Combined oxidative phosphorylation deficiency 50	Pathogenic (Sep 23, 2020)
3-15059458-T-C		not specified	Uncertain significance (Nov 21, 2023)
3-15065067-C-A		not specified	Uncertain significance (Aug 30, 2022)
3-15065068-C-T		not specified	Uncertain significance (Feb 28, 2024)
3-15065074-C-A		not specified	Uncertain significance (Jun 13, 2023)
3-15065088-G-T		not specified	Uncertain significance (Aug 12, 2021)
3-15065090-G-A			Likely benign (Jan 01, 2023)
3-15065131-C-T		not specified	Uncertain significance (Mar 31, 2023)
3-15065139-C-T		not specified	Uncertain significance (May 17, 2023)
3-15065169-A-T		not specified	Uncertain significance (Jan 30, 2024)
3-15065191-G-A		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPS25	protein_coding	protein_coding	ENST00000253686	4	22876

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000479	0.690	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.809	73	95.2	0.767	0.00000478	1138
Missense in Polyphen		16	24.074	0.66462		287
Synonymous	0.207	36	37.6	0.957	0.00000198	308
Loss of Function	0.811	6	8.56	0.701	5.11e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000320	0.0000320
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000629	0.0000615
Middle Eastern	0.000109	0.0000544
South Asian	0.0000654	0.0000653
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)

Recessive Scores

• pRec: 0.0978

Intolerance Scores

• loftool: 0.458
• rvis_EVS: 0.13
• rvis_percentile_EVS: 62.74

Haploinsufficiency Scores

• pHI: 0.119
• hipred: N
• hipred_score: 0.332
• ghis: 0.487

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.988

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrps25
• Phenotype: 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); embryo phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

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