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NM_001697.3(ATP5PO):c.87+3A>G AND Mitochondrial complex V (ATP synthase) deficiency, nuclear type 7

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 4, 2023
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003227945.1

Allele description [Variation Report for NM_001697.3(ATP5PO):c.87+3A>G]

NM_001697.3(ATP5PO):c.87+3A>G

Genes:
ATP5PO:ATP synthase peripheral stalk subunit OSCP [Gene - OMIM - HGNC]
LOC126653351:MED14-independent group 3 enhancer GRCh37_chr21:35285966-35287165 [Gene]
Variant type:
single nucleotide variant
Cytogenetic location:
21q22.11
Genomic location:
Preferred name:
NM_001697.3(ATP5PO):c.87+3A>G
HGVS:
  • NC_000021.9:g.33914447T>C
  • NG_081844.1:g.886T>C
  • NM_001697.3:c.87+3A>GMANE SELECT
  • NC_000021.8:g.35286751T>C
  • NM_001697.2:c.87+3A>G
Nucleotide change:
IVS2DS, A-G, +3
Links:
OMIM: 600828.0003; dbSNP: rs1987287870
NCBI 1000 Genomes Browser:
rs1987287870
Molecular consequence:
  • NM_001697.3:c.87+3A>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Mitochondrial complex V (ATP synthase) deficiency, nuclear type 7 (MC5DN7)
Identifiers:
MONDO: MONDO:0957255; MedGen: C5830482; OMIM: 620359

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV003922387OMIM
no assertion criteria provided
Pathogenic
(May 4, 2023)
germlineliterature only

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

A homozygous splice variant in ATP5PO, disrupts mitochondrial complex V function and causes Leigh syndrome in two unrelated families.

Ganapathi M, Friocourt G, Gueguen N, Friederich MW, Le Gac G, Okur V, Loaƫc N, Ludwig T, Ka C, Tanji K, Marcorelles P, Theodorou E, Lignelli-Dipple A, Voisset C, Walker MA, Briere LC, Bourhis A, Blondel M, LeDuc C, Hagen J, Cooper C, Muraresku C, et al.

J Inherit Metab Dis. 2022 Sep;45(5):996-1012. doi: 10.1002/jimd.12526. Epub 2022 Jul 11.

PubMed [citation]
PMID:
35621276
PMCID:
PMC9474623

Details of each submission

From OMIM, SCV003922387.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In 3 affected patients from 2 unrelated families (consanguineous family 1 of Moroccan origin and family 2 of Turkish origin) with mitochondrial complex V deficiency, nuclear type 7 (MC5DN7; 620359), Ganapathi et al. (2022) identified a homozygous intronic A-to-G transition (c.87+3A-G) in the ATP5PO gene, resulting in a splicing defect. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in both families. It was not present in the gnomAD database. Haplotype analysis showed that the mutation arose independently in the 2 families. Studies of patient cells showed that the mutation resulted in the skipping of exon 2 and an in-frame deletion of 17 residues. Western blot analysis of patient cells showed a strong depletion of the ATP5PO protein, and enzymatic studies showed significantly decreased ATPase activity compared to controls. Assembly of the complex V holoenzyme was disrupted, and patient fibroblasts showed impaired growth and defective mitochondrial oxidative phosphorylation in a glucose-free media. Yeast studies confirmed that the mutation impaired the function of ATP5PO, causing mitochondrial respiratory defects.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 12, 2024