MTERF2

protein-coding

mitochondrial transcription termination factor 2

Gene summary

Enables DNA binding activity. Predicted to be involved in termination of mitochondrial transcription. Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

MTERFD3

MANE transcript

NM_001033050.3

Inheritance

—

ClinVar variants

U:48B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr12:106,973,120-106,987,163

External References & Databases

Ensembl (ENSG00000120832)

Transcript & Mutation Effects

hg38 • Region Span ~14.0 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 MTERF2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 52

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001033050.3. 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				1 clinvar		1
missense			48 clinvar	4 clinvar	3 clinvar	55
nonsense						0
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)						0
Total	0	0	48	6	3	57

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001033050.3	RefSeq	NP_001028222.1	1	MANE Select
ENST00000240050.9	Ensembl	ENSP00000240050.4	1	MANE Select
NM_025198.5	RefSeq	NP_079474.2	1	Standard
ENST00000392830.6	Ensembl	ENSP00000376575.2	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription, DNA-templated
termination of mitochondrial transcription

Molecular Function

DNA binding
double-stranded DNA binding

Cellular Component

mitochondrion
mitochondrial nucleoid

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000552029
Coding exons: 1
Length: 9876
Individuals with no LoFs: 125538
Homozygous LoFs: 1
Heterozygous LoFs: 207
Defined: 125746
p: 0.000827

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.243	198	189	1.05	0.00000874	2520
Missense (PolyPhen)		57	54.615	1.0437		803
Synonymous	0.517	67	72.6	0.923	0.00000343	733
Loss of Function	0.749	10	12.9	0.775	6.23e-7	186

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0079	0.0078	notable
Latino/Admixed American	0.00043	0.00043	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00030	0.00030	rare
South Asian	0.00079	0.00075	rare
Other	0.00098	0.00098	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds mitochondrial DNA and plays a role in the regulation of transcription of mitochondrial mRNA and rRNA species. {ECO:0000269|PubMed:16226716, ECO:0000269|PubMed:19366608, ECO:0000269|PubMed:21558281}.;

Recessive Scores

pRec: 0.0782

Intolerance Scores

RVIS EVS: 0.64
RVIS percentile EVS: 83.9

Essentials

Essential (gene trap): N