MIEF2

mitochondrial elongation factor 2

Basic information

Region (hg38): 17:18260597-18266552

Previous symbols: [ "SMCR7" ]

Links

ENSG00000177427 ∙ NCBI:125170 ∙ OMIM:615498 ∙ HGNC:17920 ∙ Uniprot:Q96C03 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• combined oxidative phosphorylation deficiency 49 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Combined oxidative phosphorylation deficiency 49	AR	Biochemical	The condition has been described as involving muscle weakness and pain, and medical management (eg, with riboflavin and coenzyme Q10) has been described as beneficial	Biochemical; Musculoskeletal	29361167

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MIEF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MIEF2 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				4		4
missense			50	3		53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	50	8	0

Variants in MIEF2

This is a list of pathogenic ClinVar variants found in the MIEF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-18261140-G-A		not specified	Uncertain significance (Sep 07, 2022)
17-18261152-A-G		not specified	Uncertain significance (Nov 10, 2024)
17-18262751-C-T		not specified	Uncertain significance (Aug 04, 2024)
17-18262755-G-A		not specified	Uncertain significance (Apr 20, 2024)
17-18262758-G-T		not specified	Uncertain significance (Apr 25, 2022)
17-18262760-G-A		not specified	Uncertain significance (Aug 21, 2024)
17-18262763-G-A		not specified	Uncertain significance (Dec 02, 2024)
17-18262781-G-A		not specified	Uncertain significance (Jan 24, 2023)
17-18262820-G-A		not specified	Uncertain significance (Nov 17, 2023)
17-18263101-A-G		not specified	Uncertain significance (Oct 16, 2023)
17-18263105-G-A		not specified	Uncertain significance (Jul 02, 2024)
17-18263111-G-A		not specified	Uncertain significance (Oct 26, 2022)
17-18263168-C-T		not specified	Uncertain significance (Mar 06, 2023)
17-18263170-C-T		not specified	Uncertain significance (Mar 13, 2023)
17-18263179-C-T		Combined oxidative phosphorylation deficiency 49	Pathogenic (Sep 23, 2020)
17-18263185-C-T		not specified	Uncertain significance (Sep 14, 2022)
17-18263216-T-C		not specified	Uncertain significance (Mar 20, 2023)
17-18263230-C-T		not specified	Uncertain significance (Jan 26, 2023)
17-18263234-C-T		not specified	Uncertain significance (Apr 25, 2022)
17-18263436-G-A			Likely benign (Apr 01, 2023)
17-18263764-C-T			Uncertain significance (Aug 01, 2023)
17-18263789-G-C		not specified	Uncertain significance (Jul 05, 2024)
17-18263814-G-A		not specified	Uncertain significance (Nov 14, 2023)
17-18263827-C-G		not specified	Uncertain significance (Aug 23, 2021)
17-18263858-T-C		not specified	Likely benign (Sep 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MIEF2	protein_coding	protein_coding	ENST00000395706	4	6019

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0160	0.962	124881	0	9	124890	0.0000360

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.513	269	294	0.916	0.0000201	2909
Missense in Polyphen		75	93.85	0.79915		1068
Synonymous	0.574	130	139	0.938	0.00000963	1070
Loss of Function	1.99	5	12.7	0.395	6.29e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.000100	0.0000994
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000274	0.0000265
Middle Eastern	0.000110	0.000109
South Asian	0.0000677	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mitochondrial outer membrane protein which regulates mitochondrial fission. Promotes the recruitment and association of the fission mediator dynamin-related protein 1 (DNM1L) to the mitochondrial surface independently of the mitochondrial fission FIS1 and MFF proteins. Regulates DNM1L GTPase activity. {ECO:0000269|PubMed:21508961, ECO:0000269|PubMed:23283981, ECO:0000269|PubMed:23530241, ECO:0000269|PubMed:23921378}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.78

Haploinsufficiency Scores

• pHI: 0.0960
• hipred: N
• hipred_score: 0.242
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mief2

Gene ontology

• Biological process: mitochondrion organization;mitochondrial fusion;positive regulation of protein homooligomerization;positive regulation of mitochondrial fission;positive regulation of protein targeting to membrane
• Cellular component: mitochondrion;mitochondrial outer membrane;peroxisome;integral component of membrane
• Molecular function: protein binding;identical protein binding