MRPL46

mitochondrial ribosomal protein L46, the group of Large subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 15:88459476-88467390

Previous symbols: [ "C15orf4" ]

Links

ENSG00000259494 ∙ NCBI:26589 ∙ OMIM:611851 ∙ HGNC:1192 ∙ Uniprot:Q9H2W6 ∙ 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 MRPL46 gene.

• Inborn genetic diseases (22 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPL46 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						0
missense			20	2		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	2	0

Variants in MRPL46

This is a list of pathogenic ClinVar variants found in the MRPL46 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-88459663-A-T		not specified	Uncertain significance (Jan 31, 2024)
15-88459713-C-T		not specified	Uncertain significance (Jan 23, 2024)
15-88459792-T-C		not specified	Likely benign (Nov 22, 2021)
15-88459803-A-T		not specified	Uncertain significance (Jun 22, 2021)
15-88459816-A-G		not specified	Uncertain significance (Jun 02, 2023)
15-88459860-T-G		not specified	Uncertain significance (Dec 19, 2023)
15-88464742-G-A		not specified	Uncertain significance (Jan 23, 2023)
15-88464753-G-A		not specified	Uncertain significance (Aug 08, 2023)
15-88464760-A-G		not specified	Uncertain significance (Mar 20, 2023)
15-88464835-G-C		not specified	Uncertain significance (Oct 27, 2022)
15-88464855-C-A		not specified	Uncertain significance (Aug 12, 2022)
15-88464855-C-T		not specified	Uncertain significance (Jun 12, 2023)
15-88464864-T-C		not specified	Uncertain significance (Feb 27, 2023)
15-88465593-T-C		not specified	Likely benign (Apr 22, 2022)
15-88465596-G-A		not specified	Uncertain significance (Aug 11, 2021)
15-88465612-C-A		not specified	Uncertain significance (Feb 14, 2023)
15-88465689-G-A		not specified	Uncertain significance (Oct 05, 2021)
15-88465691-T-C		not specified	Uncertain significance (Dec 07, 2021)
15-88465713-G-A		Malignant tumor of prostate	Uncertain significance (-)
15-88467169-A-G		not specified	Uncertain significance (Nov 01, 2022)
15-88467171-C-G		not specified	Uncertain significance (May 11, 2022)
15-88467215-G-A		not specified	Uncertain significance (Jul 08, 2022)
15-88467221-G-C		not specified	Uncertain significance (Nov 22, 2021)
15-88467247-G-A		not specified	Uncertain significance (Jan 05, 2022)
15-88467253-C-G		not specified	Uncertain significance (Jun 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPL46	protein_coding	protein_coding	ENST00000312475	4	7944

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.36e-7	0.381	125689	0	59	125748	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.656	175	152	1.15	0.00000747	1791
Missense in Polyphen		30	35.05	0.85591		387
Synonymous	-0.825	73	64.6	1.13	0.00000311	569
Loss of Function	0.668	12	14.8	0.812	9.68e-7	139

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000472	0.000454
Ashkenazi Jewish	0.00	0.00
East Asian	0.000490	0.000489
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000260	0.000255
Middle Eastern	0.000490	0.000489
South Asian	0.000167	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Mitochondrial translation initiation;Translation;Metabolism of proteins;Mitochondrial translation elongation;Mitochondrial translation termination;Mitochondrial translation (Consensus)

Recessive Scores

• pRec: 0.0905

Intolerance Scores

• loftool: 0.813
• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.44

Haploinsufficiency Scores

• pHI: 0.0593
• hipred: N
• hipred_score: 0.442
• ghis: 0.457

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.982

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrpl46

Gene ontology

• Biological process: biological_process;mitochondrial translational elongation;mitochondrial translational termination
• Cellular component: nucleoplasm;mitochondrion;mitochondrial inner membrane;mitochondrial large ribosomal subunit;cell junction
• Molecular function: molecular_function;structural constituent of ribosome;hydrolase activity