MTRF1

protein-coding

mitochondrial translation release factor 1, the group of Mitochondrial translation release factor family

Gene summary

The protein encoded by this gene was determined by in silico methods to be a mitochondrial protein with similarity to the peptide chain release factors (RFs) discovered in bacteria and yeast. The peptide chain release factors direct the termination of translation in response to the peptide chain termination codons. Initially thought to have a role in the termination of mitochondria protein synthesis, a recent publication found no mitochondrial translation release functionality. Multiple alternatively spliced transcript variants have been suggested by mRNA and EST data; however, their full-length natures are not clear. [provided by RefSeq, Jul 2008]

MANE transcript

NM_004294.4

Inheritance

—

ClinVar variants

U:59B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chr13:41,216,369-41,263,577

External References & Databases

Ensembl (ENSG00000120662)

Transcript & Mutation Effects

hg38 • Region Span ~47.2 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 MTRF1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 57

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004294.4. 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	3
missense			57 clinvar	2 clinvar	1 clinvar	60
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	59	2	4	65

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 183 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004294.4	RefSeq	NP_004285.2	9	MANE Select
ENST00000379480.9	Ensembl	ENSP00000368793.3	9	MANE Select
NM_001354073.1	RefSeq	NP_001341002.1	9	Standard
NM_001354074.1	RefSeq	NP_001341003.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

translational termination
regulation of translational termination
mitochondrial translational termination

Molecular Function

translation release factor activity
translation release factor activity, codon specific
ribosome binding

Cellular Component

mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000379480
Coding exons: 9
Length: 47238
Individuals with no LoFs: 125667
Homozygous LoFs: 0
Heterozygous LoFs: 78
Defined: 125745
p: 0.000310

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.596	213	239	0.891	0.0000124	2932
Missense (PolyPhen)		67	82.438	0.81273		994
Synonymous	0.697	76	84.1	0.903	0.00000425	794
Loss of Function	1.69	20	30.0	0.667	0.00000186	299

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00038	0.00038	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.00049	0.00048	rare
South Asian	0.000033	0.000033	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Mitochondrial peptide chain release factor that directs the termination of translation in response to the peptide chain non-cognate termination stop codons AGG and AGA.;

Recessive Scores

pRec: 0.0975

Intolerance Scores

LoFtool: 0.938
RVIS EVS: 0.64
RVIS percentile EVS: 83.98

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.726

Gene Damage Prediction

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