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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

ENSG00000262814NCBI:6182OMIM:602375HGNC:10378Uniprot:P52815AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

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

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Combined oxidative phosphorylation deficiency 45ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingBiochemical; Craniofacial; Neurologic23603806

ClinVar

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

  • not provided (57 variants)
  • not specified (12 variants)
  • Inborn genetic diseases (9 variants)

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
14
clinvar
14
missense
22
clinvar
2
clinvar
2
clinvar
26
nonsense
0
start loss
0
frameshift
1
clinvar
1
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
splice region
1
5
6
non coding
12
clinvar
9
clinvar
21
Total 0 0 24 28 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)385422
17-81703472-A-C not specified Likely benign (Oct 07, 2016)380556
17-81703508-C-T Likely benign (Aug 10, 2023)2042837
17-81703536-C-G not specified Uncertain significance (Sep 09, 2023)2052142
17-81703545-G-A Benign (Dec 25, 2023)1599574
17-81703561-G-A Likely benign (Nov 01, 2023)2672713
17-81703574-A-G Uncertain significance (Jul 22, 2022)1938901
17-81703587-C-A Likely benign (Sep 03, 2023)2972936
17-81703612-G-A Benign (Jun 16, 2018)676742
17-81703666-G-A Benign (Jun 28, 2018)1298037
17-81704124-G-A Likely benign (Jul 17, 2018)1317977
17-81704178-T-C Benign (Jun 16, 2018)676743
17-81704228-TGGG-T Benign (Jan 24, 2024)1298149
17-81704238-G-A not specified Likely benign (Mar 25, 2016)384219
17-81704245-C-A Likely benign (Sep 09, 2021)1552003
17-81704246-G-A not specified Conflicting classifications of pathogenicity (Mar 21, 2023)1923794
17-81704250-G-C Uncertain significance (May 21, 2022)1997264
17-81704254-C-T not specified Uncertain significance (Sep 20, 2023)3206737
17-81704256-A-G not specified Likely benign (May 22, 2017)506652
17-81704257-T-C Uncertain significance (Jul 22, 2022)1985685
17-81704266-G-A Uncertain significance (Aug 23, 2022)1979263
17-81704268-C-T not specified Benign/Likely benign (Jan 22, 2024)381440
17-81704272-C-G not specified Uncertain significance (Dec 07, 2021)2404102
17-81704274-A-G Likely benign (Oct 19, 2023)2792113
17-81704289-C-T Likely benign (Feb 21, 2023)2789671

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
MRPL12protein_codingprotein_codingENST00000333676 54170
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.003220.838125719081257270.0000318
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2791111200.9280.000007321255
Missense in Polyphen4750.6990.92704566
Synonymous-0.5556256.71.090.00000409423
Loss of Function1.1758.730.5734.91e-797

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00006180.0000615
Middle Eastern0.000.00
South Asian0.00003370.0000327
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Mrpl12
Phenotype

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