MRPS14

mitochondrial ribosomal protein S14, the group of Small subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 1:175010789-175023425

Links

ENSG00000120333 ∙ NCBI:63931 ∙ OMIM:611978 ∙ HGNC:14049 ∙ Uniprot:O60783 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• combined oxidative phosphorylation deficiency 38 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Combined oxidative phosphorylation deficiency 38	AR	Cardiovascular	The condition has been described as including features such as hypertrophic cardiomyopathy and arrhythmia, and awareness may allow prompt management of these features	Biochemical; Cardiovascular; Craniofacial; Neurologic	30358850

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MRPS14 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPS14 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				8	1	9
missense		1	21	1		23
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	1	22	10	1

Variants in MRPS14

This is a list of pathogenic ClinVar variants found in the MRPS14 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-175014678-C-T			Likely benign (Sep 12, 2023)
1-175014705-A-G		MRPS14-related disorder	Benign/Likely benign (Jun 01, 2024)
1-175014721-C-T			Uncertain significance (Aug 28, 2023)
1-175014725-A-G			Uncertain significance (Dec 31, 2023)
1-175014726-G-T			Likely benign (Aug 30, 2022)
1-175014731-T-C		not specified	Uncertain significance (Apr 20, 2024)
1-175014734-G-A		Combined oxidative phosphorylation deficiency 38	Likely pathogenic (Aug 01, 2023)
1-175014748-C-T		not specified	Uncertain significance (Nov 08, 2022)
1-175014759-A-G			Likely benign (Sep 13, 2022)
1-175014763-C-T			Uncertain significance (Oct 30, 2023)
1-175014764-G-A		not specified	Uncertain significance (Apr 25, 2023)
1-175014774-C-T		MRPS14-related disorder	Likely benign (Jan 22, 2024)
1-175014778-A-G			Likely benign (Sep 27, 2022)
1-175014811-C-T		not specified	Uncertain significance (Mar 11, 2024)
1-175014817-C-A			Uncertain significance (Mar 04, 2022)
1-175018437-A-G		not specified	Uncertain significance (Aug 15, 2023)
1-175018444-T-C		not specified	Uncertain significance (Jun 09, 2022)
1-175018464-C-T			Uncertain significance (Nov 01, 2022)
1-175018477-C-T			Uncertain significance (Oct 20, 2023)
1-175018498-T-C		not specified	Uncertain significance (Dec 27, 2023)
1-175018506-T-C			Uncertain significance (Nov 13, 2023)
1-175018511-A-G			Likely benign (Sep 30, 2023)
1-175018513-C-A		not specified	Uncertain significance (Jun 22, 2024)
1-175018514-G-A		MRPS14-related disorder	Benign (Oct 23, 2023)
1-175018516-G-A			Uncertain significance (Aug 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPS14	protein_coding	protein_coding	ENST00000476371	3	12637

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000165	0.462	125719	0	27	125746	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.349	78	87.2	0.895	0.00000595	817
Missense in Polyphen		26	40.168	0.64728		354
Synonymous	0.684	25	29.7	0.841	0.00000172	266
Loss of Function	0.279	6	6.78	0.884	4.49e-7	67

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.000596	0.000595
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• loftool: 0.424
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.109
• hipred: Y
• hipred_score: 0.769
• ghis: 0.680

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.940

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrps14

Gene ontology

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