NM_032601.4(MCEE):c.178A>C (p.Lys60Gln) AND Methylmalonyl-CoA epimerase deficiency

Clinical significance:Likely benign (Last evaluated: Aug 31, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000203363.4

Allele description [Variation Report for NM_032601.4(MCEE):c.178A>C (p.Lys60Gln)]

NM_032601.4(MCEE):c.178A>C (p.Lys60Gln)

Gene:
MCEE:methylmalonyl-CoA epimerase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p13.3
Genomic location:
Preferred name:
NM_032601.4(MCEE):c.178A>C (p.Lys60Gln)
Other names:
p.K60Q:AAG>CAG
HGVS:
  • NC_000002.12:g.71124406T>G
  • NG_008977.1:g.10859A>C
  • NM_032601.4:c.178A>CMANE SELECT
  • NP_115990.3:p.Lys60Gln
  • NP_115990.3:p.Lys60Gln
  • NC_000002.11:g.71351536T>G
  • NM_032601.3:c.178A>C
Protein change:
K60Q
Links:
dbSNP: rs147401037
NCBI 1000 Genomes Browser:
rs147401037
Molecular consequence:
  • NM_032601.4:c.178A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Methylmalonyl-CoA epimerase deficiency
Synonyms:
METHYLMALONYL-CoA RACEMASE DEFICIENCY; METHYLMALONIC ACIDURIA III
Identifiers:
MONDO: MONDO:0009615; MedGen: C1855100; OMIM: 251120

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000258536GeneReviewsno assertion criteria providedPathogenic
(Jan 7, 2016)
germlineliterature only

Citation Link,

SCV001115025Invitaecriteria provided, single submitter
Likely benign
(Aug 31, 2020)
germlineclinical testing

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

SCV001435154Broad Institute Rare Disease Group, Broad Institutecriteria provided, single submitter
Likely benigngermlineresearch

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedliterature only, research

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Atypical methylmalonic aciduria: frequency of mutations in the methylmalonyl CoA epimerase gene (MCEE).

Gradinger AB, Bélair C, Worgan LC, Li CD, Lavallée J, Roquis D, Watkins D, Rosenblatt DS.

Hum Mutat. 2007 Oct;28(10):1045.

PubMed [citation]
PMID:
17823972
See all PubMed Citations (3)

Details of each submission

From GeneReviews, SCV000258536.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature onlynot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV001115025.3

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

From Broad Institute Rare Disease Group, Broad Institute, SCV001435154.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (2)

Description

The homozygous p.Lys60Gln variant in MCEE has been identified in an individual with methylmalonic aciduria (PMID: 17823972), but has also been identified in >1% of South Asian chromosomes and 8 homozygotes by ExAC (http://gnomad.broadinstitute.org/). In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely benign for autosomal recessive methylmalonic aciduria.

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

Last Updated: Oct 16, 2021

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