MIEF1

mitochondrial elongation factor 1

Basic information

Region (hg38): 22:39499431-39518132

Previous symbols: [ "SMCR7L" ]

Links

ENSG00000100335 ∙ NCBI:54471 ∙ OMIM:615497 ∙ HGNC:25979 ∙ Uniprot:L0R8F8, Q9NQG6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Optic atrophy 14	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	33632269

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MIEF1 gene.

• Inborn genetic diseases (22 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MIEF1 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					1	1
missense			21	2	2	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	3

Variants in MIEF1

This is a list of pathogenic ClinVar variants found in the MIEF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-39511344-G-A		not specified	Uncertain significance (Sep 20, 2023)
22-39511347-C-T		not specified	Uncertain significance (Oct 03, 2023)
22-39511437-G-A		not specified	Uncertain significance (Mar 22, 2022)
22-39511873-C-G		not specified	Uncertain significance (Nov 02, 2023)
22-39511901-C-T		not specified	Uncertain significance (Jan 24, 2023)
22-39511946-G-A		not specified	Uncertain significance (May 04, 2022)
22-39511970-C-T			Benign (Dec 31, 2019)
22-39511981-C-T		not specified	Uncertain significance (Apr 08, 2022)
22-39511991-A-G		not specified	Uncertain significance (Aug 30, 2022)
22-39512244-C-A		not specified	Uncertain significance (Jan 04, 2022)
22-39512339-C-T		not specified	Uncertain significance (Dec 03, 2021)
22-39512345-C-T		Optic atrophy 14	Pathogenic (Oct 24, 2023)
22-39512408-G-A		not specified	Uncertain significance (Jul 09, 2021)
22-39512466-T-C		not specified	Uncertain significance (Apr 13, 2022)
22-39512486-G-A		not specified	Uncertain significance (Oct 25, 2023)
22-39513535-A-G		not specified	Uncertain significance (Oct 12, 2022)
22-39513595-G-A			Likely benign (Sep 01, 2022)
22-39513604-A-G		not specified	Uncertain significance (Feb 14, 2023)
22-39513649-T-A		Optic atrophy 14	Pathogenic (Oct 24, 2023)
22-39513717-C-T			Benign (Dec 31, 2019)
22-39513763-G-A		not specified	Uncertain significance (May 05, 2023)
22-39513793-C-T		not specified	Uncertain significance (May 27, 2022)
22-39513806-C-T		not specified	Uncertain significance (Aug 08, 2023)
22-39513842-G-A			Benign (Aug 11, 2017)
22-39513877-G-C		not specified	Uncertain significance (Dec 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MIEF1	protein_coding	protein_coding	ENST00000325301	4	18701

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0117	0.981	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.816	246	285	0.864	0.0000189	2957
Missense in Polyphen		101	121.09	0.83409		1315
Synonymous	1.58	97	119	0.816	0.00000735	1018
Loss of Function	2.34	6	16.2	0.371	9.82e-7	170

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000971	0.0000967
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the regulation of mitochondrial fission mediated by DNM1L (PubMed:29083303). May play a role in ribosome biogenesis by preventing premature association of the 28S and 39S ribosomal subunits. {ECO:0000269|PubMed:29083303, ECO:0000305|PubMed:28892042}.

Recessive Scores

• pRec: 0.0999

Intolerance Scores

• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.16

Haploinsufficiency Scores

• pHI: 0.123
• hipred: N
• hipred_score: 0.391
• ghis: 0.504

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: Mief1

Gene ontology

• Biological process: mitochondrial fission;mitochondrial fusion;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;GDP binding;identical protein binding;ADP binding