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NM_016011.5(MECR):c.965-11A>G AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Jul 29, 2022
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:
RCV000579084.6

Allele description [Variation Report for NM_016011.5(MECR):c.965-11A>G]

NM_016011.5(MECR):c.965-11A>G

Gene:
MECR:mitochondrial trans-2-enoyl-CoA reductase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p35.3
Genomic location:
Preferred name:
NM_016011.5(MECR):c.965-11A>G
HGVS:
  • NC_000001.11:g.29194190T>C
  • NG_053058.1:g.41769A>G
  • NM_001024732.4:c.737-11A>G
  • NM_001349711.2:c.737-11A>G
  • NM_001349712.2:c.737-11A>G
  • NM_001349713.2:c.737-11A>G
  • NM_001349714.2:c.737-11A>G
  • NM_001349715.2:c.1070-11A>G
  • NM_001349716.2:c.1049-11A>G
  • NM_001349717.2:c.815-11A>G
  • NM_016011.5:c.965-11A>GMANE SELECT
  • NC_000001.10:g.29520702T>C
  • NM_016011.2:c.965-11A>G
Links:
dbSNP: rs374970921
NCBI 1000 Genomes Browser:
rs374970921
Molecular consequence:
  • NM_001024732.4:c.737-11A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001349711.2:c.737-11A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001349712.2:c.737-11A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001349713.2:c.737-11A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001349714.2:c.737-11A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001349715.2:c.1070-11A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001349716.2:c.1049-11A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001349717.2:c.815-11A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_016011.5:c.965-11A>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000681267GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Dec 27, 2017) 		germlineclinical testing

Citation Link,

SCV002291772Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jul 29, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From GeneDx, SCV000681267.2

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

Description

The c.965-11A>G variant in the MECR gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is predicted to create a new cryptic SAS in intron 9, and may cause abnormal gene splicing, however, in the absence of RNA/functional studies, the actual effect of c.965-11A>G in this individual is unknown. The c.965-11A>G variant is observed in 5/18450 (0.027%) alleles from individuals of East Asian background, and in 27/256506 total alleles in large population cohorts (Lek et al., 2016). We interpret c.965-11A>G as a variant of uncertain significance.

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002291772.2

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

Description

This sequence change falls in intron 9 of the MECR gene. It does not directly change the encoded amino acid sequence of the MECR protein. This variant is present in population databases (rs374970921, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with MECR-related conditions. ClinVar contains an entry for this variant (Variation ID: 489272). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024