NM_002488.5(NDUFA2):c.225del (p.Asn76fs) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Dec 29, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000514072.4

Allele description [Variation Report for NM_002488.5(NDUFA2):c.225del (p.Asn76fs)]

NM_002488.5(NDUFA2):c.225del (p.Asn76fs)

Genes:

NDUFA2:NADH:ubiquinone oxidoreductase subunit A2 [Gene - OMIM - HGNC]
TMCO6:transmembrane and coiled-coil domains 6 [Gene - HGNC]

Variant type:

Deletion

Cytogenetic location:

5q31.3

Genomic location:

Preferred name:

NM_002488.5(NDUFA2):c.225del (p.Asn76fs)

HGVS:

NC_000005.10:g.140645662del
NG_021417.1:g.7124del
NM_001185012.2:c.*41del
NM_002488.5:c.225delMANE SELECT
NP_002479.1:p.Asn76fs
NP_002479.1:p.Asn76fs
NC_000005.9:g.140025247del
NM_002488.4:c.225del
NM_002488.4:c.225del
NM_002488.4:c.225delG
NR_033697.2:n.392del
p.N76MfsX4

Protein change:

N76fs

Links:

OMIM: 602137.0003; dbSNP: rs863224084

NCBI 1000 Genomes Browser:

rs863224084

Molecular consequence:

NM_001185012.2:c.*41del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_002488.5:c.225del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_033697.2:n.392del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000251792	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Dec 29, 2023)	germline	clinical testing	Citation Link,
SCV000610210	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (May 30, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000251792

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Dec 29, 2023)

germline

clinical testing

Citation Link,

SCV000610210

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(May 30, 2017)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical 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 GeneDx, SCV000251792.7

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Not observed at significant frequency in large population cohorts (gnomAD); Frameshift variant predicted to result in abnormal protein length as the last 24 amino acids are replaced with 3 different amino acids; This variant is associated with the following publications: (PMID: 27159321, 32154054, 28857146, 33233646, 32304865)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, SCV000610210.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	0.000185	not provided	not provided

Last Updated: Jul 23, 2024

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