MIPEP

mitochondrial intermediate peptidase, the group of M3 metallopeptidase family

Basic information

Region (hg38): 13:23730189-23889400

Links

ENSG00000027001

∙ NCBI:4285 ∙ OMIM:602241 ∙ HGNC:7104 ∙ Uniprot:Q99797 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

lethal left ventricular non-compaction-seizures-hypotonia-cataract-developmental delay syndrome (Supportive), mode of inheritance: AR
lethal left ventricular non-compaction-seizures-hypotonia-cataract-developmental delay syndrome (Strong), mode of inheritance: AR
mitochondrial disease (Moderate), mode of inheritance: AR
lethal left ventricular non-compaction-seizures-hypotonia-cataract-developmental delay syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Combined oxidative phosphorylation deficiency 31	AR	Cardiovascular	The condition can include hypertrophic cardiomyopathy, and awareness may allow early diagnosis and interventions	Biochemical; Cardiovascular; Craniofacial; Neurologic; Ophthalmologic	27799064

ClinVar

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

not_provided (147 variants)
Inborn_genetic_diseases (110 variants)
Lethal_left_ventricular_non-compaction-seizures-hypotonia-cataract-developmental_delay_syndrome (42 variants)
MIPEP-related_disorder (13 variants)
Cardiomyopathy (6 variants)
Left_ventricular_noncompaction (6 variants)
Floppy_infant (6 variants)
not_specified (4 variants)
Microcephaly (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MIPEP gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005932.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	36 clinvar	4 clinvar	41
missense		6 clinvar	134 clinvar	14 clinvar	7 clinvar	161
nonsense	3 clinvar	4 clinvar				7
start loss						0
frameshift	2 clinvar	2 clinvar	1 clinvar			5
splice donor/acceptor (+/-2bp)	1 clinvar	4 clinvar				5
Total	6	16	136	50	11

Highest pathogenic variant AF is 0.00014129459

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MIPEP	protein_coding	protein_coding	ENST00000382172	19	159231

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.59e-15	0.304	125622	0	126	125748	0.000501

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.222	366	378	0.968	0.0000205	4633
Missense in Polyphen		120	126.19	0.95094		1382
Synonymous	0.300	128	132	0.967	0.00000718	1350
Loss of Function	1.38	28	37.1	0.755	0.00000197	470

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000482	0.000478
Ashkenazi Jewish	0.000119	0.0000992
East Asian	0.000335	0.000326
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000657	0.000651
Middle Eastern	0.000335	0.000326
South Asian	0.000776	0.000719
Other	0.00114	0.00114

dbNSFP

Source: dbNSFP

Function: FUNCTION: Cleaves proteins, imported into the mitochondrion, to their mature size.;
Disease: DISEASE: Combined oxidative phosphorylation deficiency 31 (COXPD31) [MIM:617228]: An autosomal recessive, severe mitochondrial disease with multisystemic manifestations appearing soon after birth or in early infancy. Clinical features include left ventricular non-compaction, global developmental delay, severe hypotonia, seizures, cataract, and abnormal movements. Death may occur in early childhood. {ECO:0000269|PubMed:27799064}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec: 0.121

Intolerance Scores

loftool: 0.961
rvis_EVS: 0.62
rvis_percentile_EVS: 83.53

Haploinsufficiency Scores

pHI: 0.146
hipred: N
hipred_score: 0.426
ghis: 0.479

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.552

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Mipep
Phenotype

Gene ontology

Biological process: proteolysis;peptide metabolic process;protein processing involved in protein targeting to mitochondrion
Cellular component: mitochondrion;mitochondrial matrix
Molecular function: metalloendopeptidase activity;metal ion binding