MRPS2

mitochondrial ribosomal protein S2, the group of Small subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 9:135499983-135504673

Links

ENSG00000122140 ∙ NCBI:51116 ∙ OMIM:611971 ∙ HGNC:14495 ∙ Uniprot:Q9Y399 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• combined oxidative phosphorylation deficiency 36 (Limited), mode of inheritance: AR
• combined oxidative phosphorylation deficiency 36 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Combined oxidative phosphorylation deficiency 36	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Audiologic/Otolaryngologic; Biochemical; Neurologic	29576219

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MRPS2 gene.

• not provided (43 variants)
• Inborn genetic diseases (17 variants)
• Combined oxidative phosphorylation deficiency 36 (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPS2 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				10	2	12
missense	2		35	1	7	45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region				1		1
non coding			2	2		4
Total	2	1	37	13	9

Highest pathogenic variant AF is 0.0000329

Variants in MRPS2

This is a list of pathogenic ClinVar variants found in the MRPS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-135500724-C-T		Combined oxidative phosphorylation deficiency 36	Uncertain significance (Aug 14, 2023)
9-135500735-C-A		not specified	Uncertain significance (Aug 02, 2021)
9-135500735-C-T		not specified	Uncertain significance (Jul 11, 2022)
9-135500755-TGAGC-T			Uncertain significance (Dec 11, 2023)
9-135500987-C-G			Uncertain significance (Jun 14, 2023)
9-135500990-C-A			Likely benign (Dec 07, 2023)
9-135501000-G-A			Uncertain significance (Nov 04, 2023)
9-135501019-G-A			Uncertain significance (Jun 06, 2023)
9-135501025-G-A		not specified	Uncertain significance (Oct 23, 2023)
9-135501026-C-G			Likely benign (Jun 12, 2023)
9-135501043-C-A		MRPS2-related disorder	Benign (Jan 29, 2024)
9-135501047-C-T			Likely benign (Nov 10, 2023)
9-135501050-G-A			Likely benign (Jul 14, 2023)
9-135501058-G-T		not specified	Uncertain significance (Feb 13, 2023)
9-135501066-C-G		not specified	Likely benign (Sep 12, 2023)
9-135501094-T-A		MRPS2-related disorder • not specified	Conflicting classifications of pathogenicity (Jan 26, 2023)
9-135501109-C-T			Benign (Jun 22, 2023)
9-135501132-G-A		MRPS2-related disorder	Likely benign (Jan 13, 2020)
9-135501840-G-A		MRPS2-related disorder	Likely benign (Jan 06, 2020)
9-135501877-A-G			Uncertain significance (Aug 30, 2022)
9-135501878-G-A		MRPS2-related disorder	Likely benign (Apr 03, 2019)
9-135501897-G-A		Combined oxidative phosphorylation deficiency 36	Uncertain significance (Feb 14, 2023)
9-135501910-T-A		not specified	Conflicting classifications of pathogenicity (Apr 01, 2024)
9-135501980-G-A		MRPS2-related disorder	Likely benign (Mar 09, 2021)
9-135501989-A-C			Likely benign (Aug 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPS2	protein_coding	protein_coding	ENST00000371785	4	4690

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.13e-7	0.101	125717	0	23	125740	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0738	197	200	0.985	0.0000129	1925
Missense in Polyphen		61	73.6	0.82881		650
Synonymous	-0.805	99	89.3	1.11	0.00000610	618
Loss of Function	-0.579	9	7.31	1.23	3.95e-7	82

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000584	0.0000584
Ashkenazi Jewish	0.00	0.00
East Asian	0.000385	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.0000989	0.0000967
Middle Eastern	0.000385	0.000381
South Asian	0.0000994	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for mitoribosome formation and stability, and mitochondrial translation. {ECO:0000269|PubMed:29576219}.
• Disease: DISEASE: Combined oxidative phosphorylation deficiency 36 (COXPD36) [MIM:617950]: An autosomal recessive, multisystem disease resulting from deficiencies of mitochondrial respiratory enzyme complexes and mitochondrial dysfunction. Clinical manifestations include sensorineural hearing impairment, mild developmental delay, hypoglycemia, and intellectual disability. {ECO:0000269|PubMed:29576219}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Ribosome - Homo sapiens (human);Mitochondrial translation initiation;Translation;Metabolism of proteins;Mitochondrial translation elongation;Mitochondrial translation termination;Mitochondrial translation (Consensus)

Recessive Scores

• pRec: 0.158

Intolerance Scores

• loftool: 0.588
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.74

Haploinsufficiency Scores

• pHI: 0.163
• hipred: N
• hipred_score: 0.472
• ghis: 0.481

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.849

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrps2

Gene ontology

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