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.

• not_provided (36 variants)
• not_specified (20 variants)

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. These statistics are base on transcript: NM_000003776.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				6	2	8
missense			32	2		34
nonsense						0
start loss			1			1
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	33	8	2

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