MRPL19

mitochondrial ribosomal protein L19, the group of Large subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 2:75646782-75690851

Links

ENSG00000115364 ∙ NCBI:9801 ∙ OMIM:611832 ∙ HGNC:14052 ∙ Uniprot:P49406 ∙ 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 MRPL19 gene.

• Inborn genetic diseases (14 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPL19 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				2		2
Total	0	0	14	3	0

Variants in MRPL19

This is a list of pathogenic ClinVar variants found in the MRPL19 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-75646830-G-C		not specified	Uncertain significance (Dec 21, 2022)
2-75646844-A-G		not specified	Uncertain significance (Jul 09, 2021)
2-75646871-G-T		not specified	Uncertain significance (Dec 19, 2022)
2-75647119-G-A		not specified	Uncertain significance (Jun 03, 2022)
2-75647146-G-C		not specified	Uncertain significance (Aug 13, 2021)
2-75647192-A-G		not specified	Uncertain significance (Mar 11, 2022)
2-75647209-C-T		not specified	Uncertain significance (Jan 31, 2022)
2-75652236-C-T		not specified	Uncertain significance (Dec 03, 2021)
2-75652255-A-G		not specified	Uncertain significance (Oct 25, 2022)
2-75652257-G-A		not specified	Uncertain significance (Aug 03, 2022)
2-75652531-C-G		not specified	Uncertain significance (Jun 29, 2023)
2-75652537-G-A		not specified	Uncertain significance (Mar 24, 2023)
2-75654860-T-C			Likely benign (Oct 01, 2022)
2-75655055-C-A			Likely benign (Dec 31, 2019)
2-75655055-C-T			Likely benign (Apr 09, 2018)
2-75655161-A-T		not specified	Uncertain significance (Jan 05, 2022)
2-75655218-G-A		not specified	Uncertain significance (Sep 17, 2021)
2-75655228-T-A		not specified	Uncertain significance (Nov 17, 2022)
2-75655278-G-A		not specified	Likely benign (Nov 15, 2023)
2-75664678-A-C		not specified	Uncertain significance (Sep 20, 2023)
2-75664757-A-G		not specified	Uncertain significance (Mar 05, 2024)
2-75665954-G-A		not specified	Uncertain significance (Apr 24, 2023)
2-75670175-G-T		not specified	Uncertain significance (Mar 16, 2022)
2-75670205-T-C		not specified	Uncertain significance (Sep 27, 2021)
2-75670221-G-A			Likely benign (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPL19	protein_coding	protein_coding	ENST00000393909	6	44069

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0292	0.961	124726	0	53	124779	0.000212

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.126	153	157	0.972	0.00000810	1891
Missense in Polyphen		49	60.716	0.80703		724
Synonymous	-0.739	60	53.1	1.13	0.00000259	539
Loss of Function	2.27	5	14.3	0.351	7.67e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000642	0.000641
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000257	0.000256
Middle Eastern	0.0000556	0.0000556
South Asian	0.000197	0.000196
Other	0.000498	0.000495

dbNSFP

Source: dbNSFP

• Pathway: Ribosome - Homo sapiens (human);Cytoplasmic Ribosomal Proteins;Mitochondrial translation initiation;Translation;Metabolism of proteins;Mitochondrial translation elongation;Mitochondrial translation termination;Mitochondrial translation (Consensus)

Recessive Scores

• pRec: 0.0856

Intolerance Scores

• loftool: 0.417
• rvis_EVS: -0.29
• rvis_percentile_EVS: 32.94

Haploinsufficiency Scores

• pHI: 0.0946
• hipred: Y
• hipred_score: 0.513
• ghis: 0.614

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.877

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrpl19

Gene ontology

• Biological process: mitochondrial translational elongation;mitochondrial translational termination
• Cellular component: nucleus;mitochondrion;mitochondrial inner membrane;mitochondrial large ribosomal subunit;nuclear membrane
• Molecular function: structural constituent of ribosome