MRPS34

mitochondrial ribosomal protein S34, the group of Small subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 16:1771889-1773150

Links

ENSG00000074071 ∙ NCBI:65993 ∙ OMIM:611994 ∙ HGNC:16618 ∙ Uniprot:P82930 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• combined oxidative phosphorylation deficiency 32 (Strong), mode of inheritance: AR
• Leigh syndrome (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Combined oxidative phosphorylation deficiency 32	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; Neurologic	28777931

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MRPS34 gene.

• not provided (66 variants)
• Inborn genetic diseases (18 variants)
• Combined oxidative phosphorylation deficiency 32 (7 variants)
• Leigh syndrome (1 variants)
• MRPS34-related condition (1 variants)
• Mitochondrial disease (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPS34 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	16	4	21
missense		2	43	2	3	50
nonsense		2				2
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding	1		1	1	4	7
Total	1	5	45	19	12

Highest pathogenic variant AF is 0.000151

Variants in MRPS34

This is a list of pathogenic ClinVar variants found in the MRPS34 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-1772158-T-C			Benign (May 14, 2021)
16-1772223-A-T			Uncertain significance (Dec 07, 2021)
16-1772224-G-C			Likely benign (Nov 22, 2023)
16-1772236-C-G		Inborn genetic diseases	Uncertain significance (Apr 26, 2023)
16-1772237-T-G		Inborn genetic diseases	Uncertain significance (Dec 30, 2023)
16-1772241-C-T			Uncertain significance (Sep 27, 2022)
16-1772243-C-G			Uncertain significance (Aug 22, 2022)
16-1772250-T-C		Inborn genetic diseases	Uncertain significance (Feb 28, 2023)
16-1772253-C-G		Inborn genetic diseases	Uncertain significance (Jan 17, 2023)
16-1772258-T-A		Inborn genetic diseases	Uncertain significance (Feb 22, 2023)
16-1772280-G-A		Inborn genetic diseases	Uncertain significance (May 02, 2023)
16-1772291-A-T			Uncertain significance (Sep 27, 2022)
16-1772293-C-T			Benign/Likely benign (Dec 22, 2023)
16-1772300-A-G		Inborn genetic diseases	Uncertain significance (Jan 24, 2023)
16-1772302-A-T			Likely benign (Jul 10, 2023)
16-1772307-G-A			Likely benign (May 22, 2023)
16-1772314-C-T			Likely benign (Jun 27, 2022)
16-1772316-C-T		Combined oxidative phosphorylation deficiency 32	Likely pathogenic (Jan 04, 2022)
16-1772346-G-A		Combined oxidative phosphorylation deficiency 32	Likely pathogenic (Feb 18, 2022)
16-1772353-G-A			Likely benign (May 16, 2023)
16-1772359-C-G			Uncertain significance (May 08, 2023)
16-1772362-G-A			Likely benign (May 08, 2023)
16-1772364-C-T		Inborn genetic diseases	Uncertain significance (Aug 09, 2021)
16-1772365-C-T		MRPS34-related disorder	Likely benign (Dec 28, 2023)
16-1772371-G-A			Benign/Likely benign (Dec 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPS34	protein_coding	protein_coding	ENST00000397375	3	1266

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00264	0.576	124955	0	7	124962	0.0000280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.43	135	95.7	1.41	0.00000463	1345
Missense in Polyphen		49	37.535	1.3054		545
Synonymous	-1.76	55	40.7	1.35	0.00000210	446
Loss of Function	0.333	4	4.79	0.836	2.06e-7	68

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000549	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000358	0.0000355
Middle Eastern	0.0000549	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for mitochondrial translation, plays a role in maintaining the stability of the small ribosomal subunit and the 12S rRNA that are required for mitoribosome formation. {ECO:0000269|PubMed:28777931}.
• Disease: DISEASE: Combined oxidative phosphorylation deficiency 32 (COXPD32) [MIM:617664]: An autosomal recessive disorder due to deficiency of mitochondrial respiratory chain complexes, I, III and IV, and characterized by delayed psychomotor development and neurodevelopmental regression. Additional variable symptoms include poor or absent speech, inability to walk, and abnormal movements. {ECO:0000269|PubMed:28777931}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Mitochondrial translation initiation;Translation;Metabolism of proteins;Mitochondrial translation elongation;Mitochondrial translation termination;Mitochondrial translation (Consensus)

Recessive Scores

• pRec: 0.245

Haploinsufficiency Scores

• pHI: 0.163
• hipred: Y
• hipred_score: 0.562

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.905

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Mrps34
• Phenotype: liver/biliary system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

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