MRPS12

mitochondrial ribosomal protein S12, the group of Small subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 19:38930943-38933168

Previous symbols: [ "RPMS12" ]

Links

ENSG00000128626 ∙ NCBI:6183 ∙ OMIM:603021 ∙ HGNC:10380 ∙ Uniprot:O15235 ∙ 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 MRPS12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPS12 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in MRPS12

This is a list of pathogenic ClinVar variants found in the MRPS12 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-38932339-C-T		not specified	Uncertain significance (Apr 28, 2023)
19-38932407-C-T		not specified	Uncertain significance (May 31, 2023)
19-38932418-G-A			Likely benign (Mar 01, 2023)
19-38932422-C-T		not specified	Uncertain significance (Sep 06, 2022)
19-38932427-G-T		not specified	Uncertain significance (Nov 17, 2022)
19-38932476-A-G		not specified	Uncertain significance (Apr 07, 2022)
19-38932548-C-T		not specified	Uncertain significance (Jul 16, 2021)
19-38932549-G-A		not specified	Uncertain significance (Nov 09, 2023)
19-38932618-G-A		not specified	Uncertain significance (Oct 02, 2023)
19-38932695-A-G		not specified	Uncertain significance (Mar 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPS12	protein_coding	protein_coding	ENST00000407800	2	2615

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000204	0.302	125712	0	14	125726	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.420	86	97.7	0.880	0.00000715	862
Missense in Polyphen		26	39.684	0.65517		408
Synonymous	-0.850	48	41.1	1.17	0.00000264	313
Loss of Function	-0.423	5	4.08	1.23	2.39e-7	42

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000155	0.000150
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000444	0.0000440
Middle Eastern	0.000110	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

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: 0.175

Intolerance Scores

• loftool: 0.734
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.319
• hipred: Y
• hipred_score: 0.612
• ghis: 0.594

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.994

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrps12

Gene ontology

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