MRPS15

mitochondrial ribosomal protein S15, the group of Small subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 1:36455717-36464384

Links

ENSG00000116898 ∙ NCBI:64960 ∙ OMIM:611979 ∙ HGNC:14504 ∙ Uniprot:P82914 ∙ 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 MRPS15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPS15 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			16	3		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	4	0

Variants in MRPS15

This is a list of pathogenic ClinVar variants found in the MRPS15 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-36455801-T-G		not specified	Uncertain significance (Oct 12, 2021)
1-36455846-C-T		not specified	Likely benign (Dec 14, 2023)
1-36455877-C-A		not specified	Uncertain significance (Jan 26, 2023)
1-36455921-A-G		not specified	Uncertain significance (Aug 17, 2022)
1-36456188-C-T		not specified	Likely benign (Feb 05, 2024)
1-36456211-C-T			Likely benign (Sep 01, 2022)
1-36456218-C-T		not specified	Uncertain significance (Feb 15, 2023)
1-36456222-G-A		not specified	Uncertain significance (Mar 19, 2024)
1-36456245-G-A		not specified	Uncertain significance (Dec 09, 2023)
1-36456246-G-A		not specified	Uncertain significance (Jun 07, 2023)
1-36456251-A-G		not specified	Uncertain significance (Nov 09, 2021)
1-36456267-C-G		not specified	Uncertain significance (Oct 18, 2021)
1-36460709-C-G		not specified	Uncertain significance (Jun 24, 2022)
1-36461267-G-T		not specified	Uncertain significance (Oct 27, 2022)
1-36461295-T-G		not specified	Uncertain significance (Oct 26, 2022)
1-36461299-C-T		not specified	Uncertain significance (Oct 06, 2021)
1-36461311-C-T		not specified	Uncertain significance (Apr 24, 2023)
1-36462090-C-G		not specified	Uncertain significance (Apr 20, 2024)
1-36462149-C-T		not specified	Likely benign (Sep 16, 2021)
1-36463832-G-C		not specified	Uncertain significance (May 07, 2024)
1-36463844-A-T		not specified	Uncertain significance (Mar 29, 2022)
1-36464152-G-A		not specified	Uncertain significance (Aug 04, 2023)
1-36464245-A-C		not specified	Uncertain significance (Apr 09, 2024)
1-36464263-C-A		not specified	Uncertain significance (Aug 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPS15	protein_coding	protein_coding	ENST00000373116	8	8720

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.00e-10	0.116	125587	0	159	125746	0.000632

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.351	136	148	0.919	0.00000798	1664
Missense in Polyphen		30	39.479	0.7599		497
Synonymous	0.764	48	55.2	0.869	0.00000263	500
Loss of Function	0.275	15	16.2	0.926	9.92e-7	164

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000855	0.000855
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000163	0.000163
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000960	0.000941
Middle Eastern	0.000163	0.000163
South Asian	0.000523	0.000523
Other	0.000326	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)

Recessive Scores

• pRec: 0.0660

Intolerance Scores

• loftool: 0.398
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.74

Haploinsufficiency Scores

• pHI: 0.103
• hipred: Y
• hipred_score: 0.539
• ghis: 0.587

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.928

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrps15

Gene ontology

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