MRPL9

protein-coding

mitochondrial ribosomal protein L9, the group of Mitochondrial ribosomal proteins

Gene summary

This is a nuclear gene encoding a protein component of the 39S subunit of the mitochondrial ribosome. Alternative splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 8. [provided by RefSeq, Jul 2014]

MANE transcript

NM_031420.4

Inheritance

—

ClinVar variants

U:66B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.58

Max pathogenic AF

—

Genomic locus

chr1:151,759,647-151,763,496

External References & Databases

Ensembl (ENSG00000143436)

Transcript & Mutation Effects

hg38 • Region Span ~3.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MRPL9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 55

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031420.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	1 clinvar		4
missense			57 clinvar	1 clinvar		58
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	66	2	0	68

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031420.4	RefSeq	NP_113608.1	7	MANE Select
ENST00000368830.8	Ensembl	ENSP00000357823.3	7	MANE Select
NM_001300733.2	RefSeq	NP_001287662.1	6	Standard
ENST00000368829.3	Ensembl	ENSP00000357822.3	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ribosome - Homo sapiens (human)
Mitochondrial translation initiation
Translation
Metabolism of proteins
Mitochondrial translation elongation

Biological Process

translation
mitochondrial translational elongation
mitochondrial translational termination

Molecular Function

RNA binding
structural constituent of ribosome
protein binding

Cellular Component

mitochondrion
mitochondrial inner membrane
mitochondrial ribosome
mitochondrial large ribosomal subunit

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368830
Coding exons: 7
Length: 3922
Individuals with no LoFs: 125711
Homozygous LoFs: 0
Heterozygous LoFs: 37
Defined: 125748
p: 0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.263	141	150	0.939	0.00000747	1659
Missense (PolyPhen)		26	32.896	0.79038		359
Synonymous	-0.753	70	62.4	1.12	0.00000289	557
Loss of Function	1.43	8	13.7	0.583	6.44e-7	162

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.00033	0.00033	rare
Other	0.00072	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0910

Intolerance Scores

LoFtool: 0.729
RVIS EVS: 1.02
RVIS percentile EVS: 90.86

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.522

Gene Damage Prediction

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