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NM_024120.5(NDUFAF5):c.617C>T (p.Thr206Met) AND Mitochondrial complex 1 deficiency, nuclear type 16

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Sep 20, 2024
Review status:
criteria provided, conflicting classifications
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:
RCV002480914.2

Allele description [Variation Report for NM_024120.5(NDUFAF5):c.617C>T (p.Thr206Met)]

NM_024120.5(NDUFAF5):c.617C>T (p.Thr206Met)

Gene:
NDUFAF5:NADH:ubiquinone oxidoreductase complex assembly factor 5 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
20p12.1
Genomic location:
Preferred name:
NM_024120.5(NDUFAF5):c.617C>T (p.Thr206Met)
HGVS:
  • NC_000020.11:g.13801583C>T
  • NG_015811.1:g.21558C>T
  • NM_001039375.3:c.533C>T
  • NM_001352403.2:c.146C>T
  • NM_001352406.2:c.56C>T
  • NM_001352407.2:c.56C>T
  • NM_001352408.2:c.617C>T
  • NM_024120.5:c.617C>TMANE SELECT
  • NP_001034464.1:p.Thr178Met
  • NP_001339332.1:p.Thr49Met
  • NP_001339335.1:p.Thr19Met
  • NP_001339336.1:p.Thr19Met
  • NP_001339337.1:p.Thr206Met
  • NP_077025.2:p.Thr206Met
  • NC_000020.10:g.13782229C>T
  • NM_024120.4:c.617C>T
  • NR_029377.2:n.658C>T
  • NR_147978.2:n.658C>T
  • NR_147979.2:n.678C>T
  • NR_147980.2:n.554C>T
  • NR_147981.2:n.792C>T
  • NR_147982.2:n.792C>T
  • NR_147983.2:n.708C>T
Protein change:
T178M
Links:
dbSNP: rs141758325
NCBI 1000 Genomes Browser:
rs141758325
Molecular consequence:
  • NM_001039375.3:c.533C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001352403.2:c.146C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001352406.2:c.56C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001352407.2:c.56C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001352408.2:c.617C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024120.5:c.617C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_029377.2:n.658C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_147978.2:n.658C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_147979.2:n.678C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_147980.2:n.554C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_147981.2:n.792C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_147982.2:n.792C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_147983.2:n.708C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Mitochondrial complex 1 deficiency, nuclear type 16
Synonyms:
Mitochondrial complex I deficiency, nuclear type 16
Identifiers:
MONDO: MONDO:0032621; MedGen: C4748785; OMIM: 618238

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002783459Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Mar 16, 2022) 		unknownclinical testing

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

SCV0053287333billion
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely benign
(Sep 20, 2024) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Fulgent Genetics, Fulgent Genetics, SCV002783459.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From 3billion, SCV005328733.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The homozygous variant was found in patients diagnosed with another variant in a different gene, with no symptoms related to the gene containing the homozygous variant.

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

Last Updated: Nov 24, 2024