MRPL16

mitochondrial ribosomal protein L16, the group of Large subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 11:59806139-59810778

Links

ENSG00000166902 ∙ NCBI:54948 ∙ OMIM:611829 ∙ HGNC:14476 ∙ Uniprot:Q9NX20 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MRPL16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPL16 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						0
missense			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in MRPL16

This is a list of pathogenic ClinVar variants found in the MRPL16 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-59806483-C-G		not specified	Uncertain significance (Aug 15, 2023)
11-59806483-C-T		not specified	Uncertain significance (Jun 17, 2022)
11-59806484-G-A			Likely benign (Aug 15, 2017)
11-59806510-A-G		not specified	Uncertain significance (Nov 17, 2023)
11-59806516-T-C		not specified	Uncertain significance (Apr 23, 2024)
11-59806554-C-G		not specified	Uncertain significance (Aug 12, 2021)
11-59806561-T-C		not specified	Uncertain significance (Dec 03, 2021)
11-59806589-C-T		not specified	Uncertain significance (Feb 22, 2023)
11-59806696-A-G		not specified	Uncertain significance (Apr 13, 2023)
11-59806717-T-C		not specified	Uncertain significance (Mar 20, 2023)
11-59806739-A-G		not specified	Uncertain significance (Mar 07, 2024)
11-59806765-A-G		not specified	Uncertain significance (Apr 26, 2024)
11-59806786-C-T		not specified	Uncertain significance (Feb 26, 2024)
11-59806805-C-T		not specified	Uncertain significance (Oct 29, 2021)
11-59807775-G-A		not specified	Uncertain significance (Jan 09, 2024)
11-59807776-T-A		not specified	Uncertain significance (May 03, 2023)
11-59807830-T-A		not specified	Uncertain significance (Dec 28, 2022)
11-59809903-G-A		not specified	Uncertain significance (Apr 08, 2024)
11-59810640-G-A		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPL16	protein_coding	protein_coding	ENST00000300151	4	4738

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000247	0.530	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.199	158	151	1.05	0.00000893	1638
Missense in Polyphen		61	62.719	0.97259		672
Synonymous	0.725	45	51.6	0.872	0.00000269	512
Loss of Function	0.628	8	10.2	0.787	7.00e-7	104

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000363	0.000362
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000265	0.000264
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.766
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.66

Haploinsufficiency Scores

• pHI: 0.0738
• hipred: Y
• hipred_score: 0.501
• ghis: 0.493

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.961

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrpl16

Gene ontology

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