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NM_014049.5(ACAD9):c.1674_1692+34del AND Mitochondrial complex I deficiency

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Dec 12, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV002509733.1

Allele description [Variation Report for NM_014049.5(ACAD9):c.1674_1692+34del]

NM_014049.5(ACAD9):c.1674_1692+34del

Genes:
ACAD9:acyl-CoA dehydrogenase family member 9 [Gene - OMIM - HGNC]
CFAP92:cilia and flagella associated protein 92 (putative) [Gene - HGNC]
Variant type:
Deletion
Cytogenetic location:
3q21.3
Genomic location:
Preferred name:
NM_014049.5(ACAD9):c.1674_1692+34del
HGVS:
  • NC_000003.12:g.128910131_128910183del
  • NG_017064.1:g.35642_35694del
  • NM_001348520.2:c.*120_*172del
  • NM_001348521.2:c.*120_*172del
  • NM_001394090.1:c.*120_*172delMANE SELECT
  • NM_014049.5:c.1674_1692+34delMANE SELECT
  • NC_000003.11:g.128628970_128629022del
  • NC_000003.11:g.128628974_128629026del
  • NM_014049.4:c.1674_1692+34del53
Links:
dbSNP: rs2107664575
NCBI 1000 Genomes Browser:
rs2107664575
Molecular consequence:
  • NM_001348520.2:c.*120_*172del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001348521.2:c.*120_*172del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001394090.1:c.*120_*172del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_014049.5:c.1674_1692+34del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Mitochondrial complex I deficiency
Synonyms:
Complex 1 mitochondrial respiratory chain deficiency; NADH coenzyme Q reductase deficiency
Identifiers:
MONDO: MONDO:0100133; MedGen: C1838979; Orphanet: 2609

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002819493Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely pathogenic
(Dec 12, 2022) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002819493.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: ACAD9 c.1674_1692+34del53 deletes part of exon 16 and the adjacent intron, affecting a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a canonical 5' splicing donor site. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 250612 control chromosomes. To our knowledge, no occurrence of c.1674_1692+34del53 in individuals affected with Mitochondrial Complex I Deficiency, Nuclear Type 20 and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014, classifying the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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

Last Updated: Mar 30, 2024