MRPL40

mitochondrial ribosomal protein L40, the group of Large subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins

Basic information

Region (hg38): 22:19432545-19436075

Previous symbols: [ "NLVCF" ]

Links

ENSG00000185608 ∙ NCBI:64976 ∙ OMIM:605089 ∙ HGNC:14491 ∙ Uniprot:Q9NQ50 ∙ 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 MRPL40 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPL40 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				3	2	5
missense			22	2	2	26
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				5	2	7
Total	0	0	23	10	6

Variants in MRPL40

This is a list of pathogenic ClinVar variants found in the MRPL40 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-19432556-T-C			Uncertain significance (Sep 27, 2022)
22-19432564-T-C			Uncertain significance (Dec 22, 2023)
22-19432565-C-A			Uncertain significance (Jan 28, 2025)
22-19432566-C-T			Likely benign (Dec 06, 2024)
22-19432567-G-C		not specified	Uncertain significance (Feb 17, 2023)
22-19432581-C-G			Uncertain significance (Jun 15, 2023)
22-19432586-T-C			Benign (Feb 03, 2025)
22-19432597-C-T		not specified	Uncertain significance (Jan 22, 2024)
22-19432607-G-A			Uncertain significance (Jun 09, 2024)
22-19433245-C-T			Likely benign (Oct 03, 2023)
22-19433247-T-C			Likely benign (Oct 03, 2023)
22-19433255-T-A			Benign (Dec 26, 2024)
22-19433269-C-T			Likely benign (Oct 15, 2024)
22-19433285-C-G			Uncertain significance (Oct 27, 2023)
22-19433300-C-T		not specified	Uncertain significance (Dec 24, 2024)
22-19433328-C-G		not specified	Uncertain significance (Apr 06, 2023)
22-19433338-A-G		not specified	Uncertain significance (Dec 31, 2024)
22-19433357-C-CA			Likely benign (Nov 23, 2021)
22-19434717-T-C			Likely benign (Apr 16, 2023)
22-19434798-G-A			Uncertain significance (Sep 16, 2024)
22-19434867-C-T			Uncertain significance (Nov 23, 2024)
22-19434884-G-A			Uncertain significance (Nov 21, 2023)
22-19434901-A-C			Likely benign (Oct 29, 2024)
22-19434912-G-A			Likely benign (Oct 20, 2023)
22-19434914-G-C			Benign (Oct 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRPL40	protein_coding	protein_coding	ENST00000333130	4	4174

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0529	0.929	125698	1	49	125748	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.525	122	107	1.14	0.00000558	1318
Missense in Polyphen		39	32.356	1.2053		412
Synonymous	-0.799	48	41.5	1.16	0.00000206	396
Loss of Function	2.05	4	11.5	0.347	6.84e-7	122

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000428	0.000425
Ashkenazi Jewish	0.00	0.00
East Asian	0.000169	0.000163
Finnish	0.000416	0.000416
European (Non-Finnish)	0.0000977	0.0000791
Middle Eastern	0.000169	0.000163
South Asian	0.000740	0.000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0615

Intolerance Scores

• loftool: 0.738
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.0442
• hipred: Y
• hipred_score: 0.587
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.999

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mrpl40

Gene ontology

• Biological process: anatomical structure morphogenesis;mitochondrial translational elongation;mitochondrial translational termination
• Cellular component: nucleus;mitochondrion;mitochondrial inner membrane;mitochondrial ribosome;mitochondrial large ribosomal subunit
• Molecular function: RNA binding;protein binding