MRPL9

mitochondrial ribosomal protein L9, the group of Mitochondrial ribosomal proteins

Basic information

Region (hg38): 1:151759647-151763496

Links

ENSG00000143436 ∙ NCBI:65005 ∙ OMIM:611824 ∙ HGNC:14277 ∙ Uniprot:Q9BYD2 ∙ 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 MRPL9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPL9 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		1
missense			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	19	2	1

Variants in MRPL9

This is a list of pathogenic ClinVar variants found in the MRPL9 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-151760061-G-A		not specified	Likely benign (Aug 22, 2023)
1-151760142-C-A		not specified	Uncertain significance (May 31, 2023)
1-151760142-C-T		not specified	Uncertain significance (Jan 16, 2024)
1-151760163-C-G		not specified	Uncertain significance (Nov 03, 2023)
1-151760181-C-G		not specified	Uncertain significance (Jan 27, 2022)
1-151760884-C-T		not specified	Uncertain significance (Oct 12, 2021)
1-151760891-A-C			Likely benign (Jun 01, 2022)
1-151760903-C-CAA		not specified	Benign (Mar 29, 2016)
1-151761460-G-T		not specified	Uncertain significance (Dec 27, 2023)
1-151761468-G-A		not specified	Uncertain significance (Apr 17, 2023)
1-151761503-T-C		not specified	Uncertain significance (May 14, 2024)
1-151762121-G-A		not specified	Uncertain significance (Jan 23, 2023)
1-151762509-T-C			Benign (Jul 16, 2018)
1-151763029-T-C		not specified	Uncertain significance (Mar 01, 2023)
1-151763035-G-A		not specified	Uncertain significance (Sep 27, 2021)
1-151763039-C-G		not specified	Uncertain significance (Aug 19, 2023)
1-151763053-C-G		not specified	Uncertain significance (Mar 31, 2024)
1-151763067-C-G		not specified	Uncertain significance (Oct 12, 2021)
1-151763077-G-A		not specified	Uncertain significance (Feb 27, 2023)
1-151763086-G-A		not specified	Uncertain significance (Dec 09, 2023)
1-151763118-T-A		not specified	Uncertain significance (May 13, 2024)
1-151763341-G-A		not specified	Uncertain significance (May 27, 2022)
1-151763343-C-T		not specified	Uncertain significance (Apr 04, 2023)
1-151763403-A-C		not specified	Uncertain significance (Dec 18, 2023)
1-151763412-C-T		not specified	Uncertain significance (Jun 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPL9	protein_coding	protein_coding	ENST00000368830	7	3922

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000156	0.884	125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.263	141	150	0.939	0.00000747	1659
Missense in Polyphen		26	32.896	0.79038		359
Synonymous	-0.753	70	62.4	1.12	0.00000289	557
Loss of Function	1.43	8	13.7	0.583	6.44e-7	162

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000204	0.000204
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000117	0.000114
Middle Eastern	0.000109	0.000109
South Asian	0.000330	0.000327
Other	0.000723	0.000652

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: 0.0910

Intolerance Scores

• loftool: 0.729
• rvis_EVS: 1.02
• rvis_percentile_EVS: 90.86

Haploinsufficiency Scores

• pHI: 0.364
• hipred: N
• hipred_score: 0.312
• ghis: 0.421

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.522

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrpl9

Gene ontology

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