MRPL1

mitochondrial ribosomal protein L1, the group of Large subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 4:77862830-77952785

Links

ENSG00000169288 ∙ NCBI:65008 ∙ OMIM:611821 ∙ HGNC:14275 ∙ Uniprot:Q9BYD6 ∙ 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 MRPL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPL1 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	4		24
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	4	0

Variants in MRPL1

This is a list of pathogenic ClinVar variants found in the MRPL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-77862858-G-A		not specified	Uncertain significance (Jan 23, 2024)
4-77871752-C-T		not specified	Uncertain significance (Apr 25, 2023)
4-77871782-G-T		not specified	Uncertain significance (Nov 20, 2024)
4-77871818-A-G		not specified	Likely benign (Jul 02, 2024)
4-77871822-G-A		not specified	Likely benign (Mar 18, 2024)
4-77871825-T-C		not specified	Uncertain significance (Jul 08, 2022)
4-77871845-G-C		not specified	Uncertain significance (Oct 12, 2022)
4-77883279-A-G		not specified	Likely benign (Nov 10, 2024)
4-77883302-A-C		not specified	Likely benign (Dec 22, 2023)
4-77883312-A-G		not specified	Uncertain significance (Jan 31, 2024)
4-77883315-A-G		not specified	Uncertain significance (Sep 09, 2024)
4-77883406-T-C		not specified	Uncertain significance (Dec 22, 2023)
4-77883447-C-A		not specified	Uncertain significance (Nov 18, 2022)
4-77883454-A-G		not specified	Uncertain significance (Sep 12, 2024)
4-77885310-G-A		not specified	Uncertain significance (Jun 05, 2024)
4-77887242-C-T		not specified	Uncertain significance (Aug 26, 2024)
4-77894206-G-A		not specified	Uncertain significance (Dec 18, 2023)
4-77894208-T-G		not specified	Uncertain significance (Feb 08, 2025)
4-77894235-C-G		not specified	Uncertain significance (Dec 09, 2023)
4-77909271-A-G		not specified	Uncertain significance (Apr 13, 2022)
4-77949801-A-G		not specified	Uncertain significance (Dec 09, 2023)
4-77949834-A-G		not specified	Uncertain significance (Oct 08, 2024)
4-77949875-T-A		not specified	Uncertain significance (Aug 08, 2023)
4-77952498-T-C		not specified	Uncertain significance (Jan 24, 2025)
4-77952515-C-T		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPL1	protein_coding	protein_coding	ENST00000315567	9	90271

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000445	0.854	125713	0	32	125745	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.411	161	176	0.913	0.00000902	2147
Missense in Polyphen		31	39.112	0.79259		533
Synonymous	0.579	53	58.6	0.904	0.00000304	585
Loss of Function	1.44	11	17.5	0.628	9.54e-7	217

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000345	0.000345
Ashkenazi Jewish	0.00	0.00
East Asian	0.000234	0.000217
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000108	0.000105
Middle Eastern	0.000234	0.000217
South Asian	0.000248	0.000229
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)

Intolerance Scores

• loftool: 0.848
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.41

Haploinsufficiency Scores

• pHI: 0.435
• hipred: N
• hipred_score: 0.486
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.988

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrpl1

Gene ontology

• Biological process: maturation of LSU-rRNA;mitochondrial translational elongation;mitochondrial translational termination
• Cellular component: mitochondrion;mitochondrial inner membrane;cytosolic large ribosomal subunit
• Molecular function: RNA binding;structural constituent of ribosome;protein binding