MRPS9

mitochondrial ribosomal protein S9, the group of Mitochondrial ribosomal proteins

Basic information

Region (hg38): 2:105038069-105099960

Links

ENSG00000135972 ∙ NCBI:64965 ∙ OMIM:611975 ∙ HGNC:14501 ∙ Uniprot:P82933 ∙ 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 MRPS9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPS9 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			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	2	0

Variants in MRPS9

This is a list of pathogenic ClinVar variants found in the MRPS9 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-105038117-G-A		not specified	Uncertain significance (Jan 10, 2023)
2-105038124-C-T		not specified	Uncertain significance (Jul 09, 2021)
2-105038208-A-C		not specified	Uncertain significance (Oct 05, 2023)
2-105049236-A-C		not specified	Uncertain significance (Oct 05, 2023)
2-105049280-A-G		not specified	Uncertain significance (Sep 27, 2021)
2-105049283-T-C		not specified	Uncertain significance (Mar 23, 2023)
2-105049304-A-G		not specified	Uncertain significance (Mar 14, 2023)
2-105071462-C-G		not specified	Uncertain significance (Jun 16, 2023)
2-105080018-T-G		not specified	Uncertain significance (Nov 09, 2021)
2-105080019-A-G		not specified	Uncertain significance (Jun 29, 2023)
2-105088985-A-C		not specified	Uncertain significance (Nov 06, 2023)
2-105089047-C-T			Uncertain significance (Dec 01, 2022)
2-105089924-G-A		not specified	Uncertain significance (Jan 03, 2024)
2-105089973-T-G		not specified	Uncertain significance (May 18, 2023)
2-105092460-G-A			Likely benign (Dec 01, 2022)
2-105092470-G-T		not specified	Uncertain significance (Jan 27, 2022)
2-105092478-G-C		not specified	Uncertain significance (Apr 14, 2022)
2-105092483-G-A			Likely benign (Mar 01, 2023)
2-105092507-A-T		not specified	Uncertain significance (Dec 06, 2022)
2-105093535-A-G		not specified	Uncertain significance (May 02, 2024)
2-105093551-C-T		not specified	Uncertain significance (Aug 02, 2021)
2-105093572-A-G		not specified	Uncertain significance (May 26, 2024)
2-105093604-G-A		not specified	Uncertain significance (Feb 10, 2023)
2-105093629-C-G		not specified	Uncertain significance (May 16, 2024)
2-105097207-G-A		not specified	Uncertain significance (May 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPS9	protein_coding	protein_coding	ENST00000258455	11	61978

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.26e-9	0.791	125717	0	31	125748	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.208	206	215	0.960	0.0000116	2568
Missense in Polyphen		68	79.208	0.8585		915
Synonymous	0.631	69	76.0	0.908	0.00000417	728
Loss of Function	1.57	18	26.8	0.673	0.00000149	307

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000252	0.000246
Ashkenazi Jewish	0.00	0.00
East Asian	0.000166	0.000163
Finnish	0.0000933	0.0000924
European (Non-Finnish)	0.000135	0.000132
Middle Eastern	0.000166	0.000163
South Asian	0.000145	0.000131
Other	0.000164	0.000163

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: 0.0872

Intolerance Scores

• loftool: 0.513
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.31

Haploinsufficiency Scores

• pHI: 0.303
• hipred: Y
• hipred_score: 0.545
• ghis: 0.504

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.680

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrps9

Gene ontology

• Biological process: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);DNA damage response, detection of DNA damage;mitochondrial translational elongation;mitochondrial translational termination
• Cellular component: nucleolus;mitochondrion;mitochondrial inner membrane;mitochondrial small ribosomal subunit
• Molecular function: RNA binding;structural constituent of ribosome;protein binding