MRPS16

mitochondrial ribosomal protein S16, the group of Small subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 10:73248842-73252693

Links

ENSG00000182180 ∙ NCBI:51021 ∙ OMIM:609204 ∙ HGNC:14048 ∙ Uniprot:Q9Y3D3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• combined oxidative phosphorylation defect type 2 (Supportive), mode of inheritance: AR
• combined oxidative phosphorylation defect type 2 (Limited), mode of inheritance: AR
• mitochondrial disease (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Combined oxidative phosphorylation deficiency 2	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; Neurologic	15505824
The described dysmorphic features may have been coincident (the patient was born to consanguineous parents) as relates to the mitochondrial disorder

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MRPS16 gene.

• not provided (54 variants)
• not specified (11 variants)
• Inborn genetic diseases (10 variants)
• Combined oxidative phosphorylation deficiency (8 variants)
• Combined oxidative phosphorylation defect type 2 (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPS16 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				11		11
missense			24	4	1	29
nonsense			1			1
start loss			1			1
frameshift	1		2			3
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			3	2		5
non coding			7	8	9	24
Total	1	0	35	23	10

Highest pathogenic variant AF is 0.0000131

Variants in MRPS16

This is a list of pathogenic ClinVar variants found in the MRPS16 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-73249349-T-C		Combined oxidative phosphorylation deficiency	Uncertain significance (Jun 14, 2016)
10-73249558-CAAG-C		Combined oxidative phosphorylation deficiency	Uncertain significance (Jun 14, 2016)
10-73249995-CAGG-C		Combined oxidative phosphorylation deficiency	Uncertain significance (Jun 14, 2016)
10-73250218-C-CA		Combined oxidative phosphorylation deficiency	Uncertain significance (Jun 14, 2016)
10-73250401-AG-A		Combined oxidative phosphorylation deficiency	Uncertain significance (Jun 14, 2016)
10-73250839-A-G			Benign (Mar 03, 2015)
10-73250862-G-A			Uncertain significance (Jul 19, 2022)
10-73250877-G-A		not specified	Uncertain significance (Sep 27, 2022)
10-73250877-G-C		MRPS16-related disorder	Likely benign (Jan 22, 2024)
10-73250878-T-C		not specified	Uncertain significance (Apr 18, 2023)
10-73250886-G-A		not specified	Conflicting classifications of pathogenicity (Jul 04, 2023)
10-73250919-C-A		not specified	Uncertain significance (Sep 30, 2021)
10-73250922-G-A		not specified	Conflicting classifications of pathogenicity (Aug 17, 2022)
10-73250925-C-T			Uncertain significance (Sep 13, 2022)
10-73250926-G-A		not specified	Uncertain significance (Oct 04, 2022)
10-73250934-C-G			Uncertain significance (Aug 19, 2022)
10-73250934-C-T			Uncertain significance (Oct 31, 2022)
10-73250935-G-A		Combined oxidative phosphorylation defect type 2	Uncertain significance (Apr 07, 2022)
10-73250938-GTC-G			Uncertain significance (Mar 13, 2023)
10-73250954-G-A			Likely benign (Jan 18, 2024)
10-73250962-T-C		not specified	Uncertain significance (Dec 20, 2023)
10-73250966-A-T			Uncertain significance (Dec 06, 2023)
10-73250975-G-GA			Uncertain significance (Dec 02, 2021)
10-73250981-G-C			Likely benign (Jul 26, 2021)
10-73250990-AC-A			Pathogenic (Mar 19, 2014)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPS16	protein_coding	protein_coding	ENST00000372945	3	5942

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0583	0.728	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.550	94	80.1	1.17	0.00000490	879
Missense in Polyphen		26	24.295	1.0702		314
Synonymous	-1.82	42	29.4	1.43	0.00000158	289
Loss of Function	0.788	2	3.62	0.553	1.54e-7	47

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000467	0.000466
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.000327	0.000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Combined oxidative phosphorylation deficiency 2 (COXPD2) [MIM:610498]: A mitochondrial disease resulting in fatal neonatal metabolic acidosis with agenesis of the corpus callosum. {ECO:0000269|PubMed:15505824}. 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: 0.0794

Intolerance Scores

• loftool: 0.689
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.82

Haploinsufficiency Scores

• pHI: 0.0524
• hipred: Y
• hipred_score: 0.683
• ghis: 0.534

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrps16

Gene ontology

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