MRPL12

mitochondrial ribosomal protein L12, the group of Large subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 17:81703366-81707517

Previous symbols: [ "RPML12" ]

Links

ENSG00000262814 ∙ NCBI:6182 ∙ OMIM:602375 ∙ HGNC:10378 ∙ Uniprot:P52815 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• combined oxidative phosphorylation deficiency 45 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Combined oxidative phosphorylation deficiency 45	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Biochemical; Craniofacial; Neurologic	23603806

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MRPL12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPL12 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				20		20
missense			33	2	2	37
nonsense						0
start loss						0
frameshift			1			1
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			2	5		7
non coding				14	9	23
Total	0	0	35	36	11

Variants in MRPL12

This is a list of pathogenic ClinVar variants found in the MRPL12 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-81703456-C-T		not specified	Likely benign (Jan 22, 2018)
17-81703472-A-C		not specified	Likely benign (Oct 07, 2016)
17-81703508-C-T			Likely benign (Aug 10, 2023)
17-81703536-C-G		not specified	Uncertain significance (Sep 09, 2023)
17-81703539-G-A		not specified	Uncertain significance (May 28, 2024)
17-81703545-G-A			Benign (Dec 25, 2023)
17-81703561-G-A			Likely benign (Nov 01, 2023)
17-81703574-A-G			Uncertain significance (Jul 22, 2022)
17-81703587-C-A			Likely benign (Sep 03, 2023)
17-81703612-G-A			Benign (Jun 16, 2018)
17-81703666-G-A			Benign (Jun 28, 2018)
17-81704124-G-A			Likely benign (Jul 17, 2018)
17-81704178-T-C			Benign (Jun 16, 2018)
17-81704228-TGGG-T			Benign (Jan 24, 2024)
17-81704238-G-A		not specified	Likely benign (Mar 25, 2016)
17-81704245-C-A			Likely benign (Sep 09, 2021)
17-81704246-G-A		not specified	Conflicting classifications of pathogenicity (Mar 21, 2023)
17-81704250-G-C			Uncertain significance (May 21, 2022)
17-81704254-C-T		not specified	Uncertain significance (Sep 20, 2023)
17-81704256-A-G		not specified	Likely benign (May 22, 2017)
17-81704257-T-C			Uncertain significance (Jul 22, 2022)
17-81704266-G-A			Uncertain significance (Aug 23, 2022)
17-81704268-C-T		not specified	Benign/Likely benign (Jan 22, 2024)
17-81704272-C-G		not specified	Uncertain significance (Dec 07, 2021)
17-81704274-A-G			Likely benign (Oct 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPL12	protein_coding	protein_coding	ENST00000333676	5	4170

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00322	0.838	125719	0	8	125727	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.279	111	120	0.928	0.00000732	1255
Missense in Polyphen		47	50.699	0.92704		566
Synonymous	-0.555	62	56.7	1.09	0.00000409	423
Loss of Function	1.17	5	8.73	0.573	4.91e-7	97

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000618	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000337	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Associates with mitochondrial RNA polymerase to activate transcription. {ECO:0000269|PubMed:22003127}.
• Pathway: Ribosome - Homo sapiens (human);Mitochondrial translation initiation;Translation;Metabolism of proteins;Mitochondrial translation elongation;Mitochondrial translation termination;Mitochondrial translation (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.465
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.92

Haploinsufficiency Scores

• pHI: 0.795
• hipred: N
• hipred_score: 0.396
• ghis: 0.450

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: Mrpl12

Gene ontology

• Biological process: mitochondrial transcription;positive regulation of transcription, DNA-templated;mitochondrial translational elongation;mitochondrial translational termination
• Cellular component: mitochondrion;mitochondrial inner membrane;mitochondrial large ribosomal subunit
• Molecular function: RNA binding;structural constituent of ribosome;protein binding