MRPS23

mitochondrial ribosomal protein S23, the group of Small subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 17:57834780-57850056

Links

ENSG00000181610 ∙ NCBI:51649 ∙ OMIM:611985 ∙ HGNC:14509 ∙ Uniprot:Q9Y3D9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• combined oxidative phosphorylation deficiency 46 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Combined oxidative phosphorylation deficiency 46	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	Biochemical; Gastrointestinal	26741492

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MRPS23 gene.

• not provided (28 variants)
• Inborn genetic diseases (9 variants)
• Combined oxidative phosphorylation deficiency 46 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPS23 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			14	2	1	17
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			1	2	1	4
Total	0	0	16	14	4

Variants in MRPS23

This is a list of pathogenic ClinVar variants found in the MRPS23 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-57839816-A-G		MRPS23-related disorder	Likely benign (Apr 25, 2022)
17-57839816-AG-CC			Uncertain significance (Jan 22, 2024)
17-57839817-G-C		not specified	Uncertain significance (Sep 06, 2022)
17-57839857-T-C		not specified	Uncertain significance (Jan 08, 2024)
17-57839870-C-A		not specified	Uncertain significance (May 17, 2023)
17-57839876-A-G		MRPS23-related disorder	Likely benign (Jul 19, 2023)
17-57839903-G-A			Likely benign (Nov 28, 2023)
17-57839911-G-A		not specified	Likely benign (Apr 12, 2022)
17-57839918-G-A			Likely benign (Apr 07, 2023)
17-57839918-G-C			Uncertain significance (Nov 19, 2022)
17-57839930-G-A			Benign/Likely benign (Feb 01, 2024)
17-57839943-G-T			Likely benign (Aug 18, 2022)
17-57840906-T-C			Uncertain significance (Dec 22, 2021)
17-57840911-CAATG-C			Likely benign (Jun 28, 2023)
17-57840930-C-T		not specified	Uncertain significance (Feb 12, 2024)
17-57840934-C-T			Uncertain significance (Sep 24, 2021)
17-57840938-G-A			Benign (Jan 04, 2024)
17-57840946-G-A			Uncertain significance (Nov 28, 2022)
17-57840978-T-C		not specified	Uncertain significance (Jan 20, 2023)
17-57841001-C-A		not specified	Uncertain significance (Mar 07, 2024)
17-57841009-C-A			Uncertain significance (Sep 05, 2023)
17-57841031-C-T		MRPS23-related disorder	Likely benign (Dec 21, 2022)
17-57841184-G-A		not specified	Uncertain significance (Feb 02, 2024)
17-57841191-G-A			Likely benign (Nov 22, 2022)
17-57841258-T-C		not specified	Uncertain significance (Apr 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPS23	protein_coding	protein_coding	ENST00000313608	5	10576

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.128	0.852	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.169	107	112	0.955	0.00000638	1217
Missense in Polyphen		38	33.459	1.1357		371
Synonymous	0.166	43	44.4	0.968	0.00000268	373
Loss of Function	1.99	3	9.71	0.309	5.71e-7	99

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000363	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.000134	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Note=Defects in MRPS23 may play a role in mitochondrial disorders characterized by combined respiratory chain complex deficiencies. {ECO:0000269|PubMed:26741492}.
• Pathway: Mitochondrial translation initiation;Translation;Metabolism of proteins;Mitochondrial translation elongation;Mitochondrial translation termination;Mitochondrial translation (Consensus)

Recessive Scores

• pRec: 0.0793

Intolerance Scores

• loftool: 0.299
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.115
• hipred: N
• hipred_score: 0.233
• ghis: 0.610

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.987

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrps23

Gene ontology

• Biological process: mitochondrial translational elongation;mitochondrial translational termination
• Cellular component: mitochondrion;mitochondrial inner membrane;ribosome;nuclear membrane;intermediate filament cytoskeleton
• Molecular function: RNA binding;structural constituent of ribosome;protein binding