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NM_015506.3(MMACHC):c.394C>T (p.Arg132Ter) AND Cobalamin C disease

Germline classification:
Pathogenic (17 submissions)
Last evaluated:
Mar 26, 2024
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:
RCV000001488.45

Allele description [Variation Report for NM_015506.3(MMACHC):c.394C>T (p.Arg132Ter)]

NM_015506.3(MMACHC):c.394C>T (p.Arg132Ter)

Gene:
MMACHC:metabolism of cobalamin associated C [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p34.1
Genomic location:
Preferred name:
NM_015506.3(MMACHC):c.394C>T (p.Arg132Ter)
Other names:
p.R132*:CGA>TGA
HGVS:
  • NC_000001.11:g.45508329C>T
  • NG_013378.1:g.13146C>T
  • NM_001330540.2:c.223C>T
  • NM_015506.3:c.394C>TMANE SELECT
  • NP_001317469.1:p.Arg75Ter
  • NP_056321.2:p.Arg132Ter
  • NC_000001.10:g.45974001C>T
  • NM_015506.2:c.394C>T
  • NP_056321.2:p.Arg132*
  • p.R132X
Protein change:
R132*; ARG132TER
Links:
OMIM: 609831.0003; dbSNP: rs121918241
NCBI 1000 Genomes Browser:
rs121918241
Molecular consequence:
  • NM_001330540.2:c.223C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_015506.3:c.394C>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
3

Condition(s)

Name:
Cobalamin C disease
Synonyms:
Cobalamin-C methylmalonic acidemia and homocystinuria; Methylmalonic acidemia and homocystinuria cblC type; Methylmalonic aciduria and homocystinuria, Vitamin B12-responsive; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010184; MedGen: C1848561; Orphanet: 26; Orphanet: 79282; OMIM: 277400

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000021643OMIM
no assertion criteria provided
Pathogenic
(Jul 1, 2009)
germlineliterature only

PubMed (4)
[See all records that cite these PMIDs]

SCV000267132Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital - ORGANIC ACIDURIAS
no assertion criteria provided
Pathogenic
(Jan 25, 2016)
germlineresearch

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

SCV000485871Counsyl
criteria provided, single submitter

(Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015))
Pathogenic
(Nov 2, 2016)
unknownclinical testing

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

mdi-5618_320494_Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015).pdf,

Citation Link,

SCV000611284Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Aug 11, 2021)
unknownclinical testing

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

SCV000640288Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jan 25, 2024)
germlineclinical testing

PubMed (8)
[See all records that cite these PMIDs]

SCV000699398Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Pathogenic
(Aug 3, 2020)
germlineclinical testing

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

Citation Link,

SCV000746493Genomic Research Center, Shahid Beheshti University of Medical Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Dec 3, 2017)
inheritedclinical testing

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

SCV001162905Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 26, 2024)
unknownclinical testing

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

SCV001786618Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSLVariantClassificationCriteria RUGD 01 April 2020)
Pathogenic
(Nov 2, 2020)
unknownclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Citation Link,

SCV0020123483billion
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 2, 2021)
paternalclinical testing

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

SCV003821673Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Feb 17, 2023)
germlineclinical testing

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

SCV003922054Lifecell International Pvt. Ltd
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicgermlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

SCV004101511Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicgermlineclinical testing

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

SCV004101777Clinical Genomics Laboratory, Stanford Medicine
no assertion criteria provided
Pathogenic
(Mar 4, 2021)
germlineclinical testing

SCV004178164Genome-Nilou Lab
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Apr 11, 2023)
germlineclinical testing

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

SCV004805005Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 17, 2024)
germlineresearch

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

SCV004814217Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 25, 2023)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, research
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedpaternalyes1not providednot provided1not providedclinical testing
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
not providedinheritedyesnot providednot providednot providednot providednot providedclinical testing
Asiangermlineyes1not providednot providednot providednot providedclinical testing
Indiansgermlineyes16not providednot providednot providednot providedresearch

Citations

PubMed

Nothing to display

See all PubMed Citations (13)

Details of each submission

From OMIM, SCV000021643.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (4)

Description

In a survey of 204 individuals with methylmalonic aciduria and homocystinuria cblC type (MAHCC; 277400), Lerner-Ellis et al. (2006) found 34 examples of the 394C-T mutant allele of the MMACHC gene, predicted to result in an arg132-to-ter mutation (R132X). The R132X mutation was primarily associated with late-onset disease and was noted in the homozygous state among published individuals in Asiatic-Indian, Pakistani, or Middle Eastern descent and reported by Morel et al. (2006) in an additional 9 unpublished patients from their database who were either of Asiatic-Indian, Pakistani, or Middle Eastern descent.

Ben-Omran et al. (2007) reported 2 unrelated girls of Pakistani and Bengali origin, respectively, with cblC disease caused by a homozygous R132X mutation. The girls presented with neuropsychiatric symptoms at ages 14 and 10 years, respectively.

In a study of 118 patients with cblC disease, Lerner-Ellis et al. (2009) found that individuals with the R132X mutation tended to present with late-onset disease. Transcript and RT-PCR analysis of cblC fibroblasts showed that the R132X mutation resulted in significantly higher levels of transcript compared to cell lines homozygous for the early-onset mutations. The authors postulated that nonsense-mediated decay may not occur with this mutation, or that it may occur to a lesser extent. Alternatively, the mutation may result in a truncated protein with residual function. Lerner-Ellis et al. (2009) identified the R132X mutation in 20% of pathogenic alleles from 118 patients with cblC.

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

From Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital - ORGANIC ACIDURIAS, SCV000267132.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Indians16not providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided16not providednot providednot provided

From Counsyl, SCV000485871.2

#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 Fulgent Genetics, Fulgent Genetics, SCV000611284.2

#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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000640288.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (8)

Description

This sequence change creates a premature translational stop signal (p.Arg132*) in the MMACHC gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 151 amino acid(s) of the MMACHC protein. This variant is present in population databases (rs121918241, gnomAD 0.07%). This premature translational stop signal has been observed in individual(s) with methylmalonic acidemia and hyperhomocysteinemia of the cobalamin C (cblC) type (PMID: 16311595, 19760748, 20631720, 24577983, 25511120, 26149271, 26563984). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 1423). For these reasons, this variant has been classified as Pathogenic.

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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000699398.2

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

Description

Variant summary: MMACHC c.394C>T (p.Arg132X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 9.6e-05 in 249398 control chromosomes. c.394C>T has been reported in the literature in multiple individuals affected with Cobalamin C Disease (Methylmalonic Aciduria With Homocystinuria) (example, Lerner-Ellis_2009). These data indicate that the variant is very likely to be associated with disease. Eight clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

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

From Genomic Research Center, Shahid Beheshti University of Medical Sciences, SCV000746493.1

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

From Baylor Genetics, SCV001162905.2

#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 Illumina Laboratory Services, Illumina, SCV001786618.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

The MMACHC c.394C>T (p.Arg132Ter) variant is a stop-gained variant that is predicted to result in a premature termination of the protein. Across a selection of the available literature, the p.Arg132Ter variant is found in at least 57 individuals with the cblC type of methylmalonic aciduria and homocystinuria, the most common inborn error of cobalamin metabolism, including in a homozygous state in at least 31 individuals and in a compound heterozygous state in 26 individuals (Lerner-Ellis et al. 2006; Richard et al. 2009; Lerner-Ellis et al. 2009; Liu et al. 2010; Kılıç et al. 2013). Additionally, this variant has been identified in 20% of disease alleles in individuals from India, Pakistan, and Middle East, and in 5.7% of disease alleles in Chinese population (Lerner-Ellis et al. 2006; Lerner-Ellis et al. 2009; Liu et al. 2010). The p.Arg132Ter variant is associated with late onset disease characterized by acute neurological deterioration without systemic symptoms (Lerner-Ellis et al. 2006). The p.Arg132Ter variant was absent from 155 control subjects (Lerner-Ellis et al. 2006; Lerner-Ellis et al. 2009) but is reported at a frequency of 0.000719 in the South Asian population of the Genome Aggregation Database. Functional assays in patient cell lines indicate that the p.Arg132Ter variant may result in the production of a truncated protein product with residual function (Lerner-Ellis et al. 2009). Furthermore, patient skin fibroblasts do not show an increase in reactive oxygen species levels compared to control cells, however, there was an increase in basal level of apoptosis (Richard et al. 2009). Based on the collective evidence and application of the ACMG criteria, the p.Arg132Ter variant is classified as pathogenic for disorders of intracellular cobalamin metabolism.

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

From 3billion, SCV002012348.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

Stop-gained (nonsense): predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant (PVS1_VS). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.0000962, PM2). The variant was observed in trans with a pathogenic variant (NM_015506.2:c.609G>Ap) as compound heterozygous (3billion dataset, PM3). The variant has been reported multiple times as an established pathogenic variant (ClinVar ID: VCV000001423.16). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1paternalyes1not providednot provided1not providednot providednot provided

From Revvity Omics, Revvity, SCV003821673.2

#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 Lifecell International Pvt. Ltd, SCV003922054.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Asian1not providednot providedclinical testing PubMed (3)

Description

A Homozygote Nonsense variant c.394C>T in Exon 3 of the MMACHC gene that results in the amino acid substitution p.Arg132* was identified. The observed variant has a maximum allele frequency of 0.00010/0.00 % in gnomAD exomes and genomes, respectively. The severity of the impact of this variant on the protein is high, based on the effect of the protein and REVEL score . Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. ClinVar has also classified this variant as Pathogenic (ClinVar ID: 1423). This variant has previously been reported for cblC type of methylmalonic aciduria and homocystinuria. Functional assays in patient cell lines indicate that the p.Arg132Ter variant may result in the production of a truncated protein product with residual function (Richard E et al., 2009 and Lerner-Ellis JP et al., 2009). Based on the above evidence this variant has been classified as Pathogenic according to the ACMG guidelines.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Neuberg Centre For Genomic Medicine, NCGM, SCV004101511.2

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

Description

The observed stop gained variant c.394C>T(p.Arg132Ter) in MMACHC gene has been reported previously in homozygous and compound heterozygous state in multiple individuals with methylmalonic acidemia and hyperhomocysteinemia of the cobalamin C (cblC) type (Han B, et al., 2016, Zong Y, et al., 2015). Experimental studies show that functional assays in patient cell lines indicate that the p.Arg132Ter variant may result in the production of a truncated protein product with residual function (Lerner-Ellis et al., 2009) and also showed an increase in basal level of apoptosis (Richard et al. 2009). The c.394C>T variant is reported with 0.01% allele frequency in gnomAD Exomes. This variant has been reported to the ClinVar database as Pathogenic (multiple submissions). This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing.For these reasons, this variant has been classified as Pathogenic.

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

From Clinical Genomics Laboratory, Stanford Medicine, SCV004101777.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testingnot provided

Description

The p.Arg132* variant in the MMACHC gene has been previously reported in the homozygous or compound heterozygous state in at least 35 individuals with cobalamin C deficiency (Lerner-Ellis et al., 2006; Nogueira et al., 2008; Lerner-Ellis et al., 2009; Ricci et al., 2020). In one affected cohort, the p.Arg132* variant accounted for 20% of the pathogenic alleles identified and was associated with later onset of disease (Lerner-Ellis et al., 2009). This variant has also been identified in 22/30,600 (0.07%) South Asian chromosomes by the Genome Aggregation Database (http://gnomad.broadinstitute.org/). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. The p.Arg132* variant leads to a premature stop codon in exon 3 of 4 coding exons, and is therefore predicted to undergo nonsense-mediated decay resulting in a truncated or absent protein. Homozygous or compound heterozygous loss of function is an established mechanism of disease for the MMACHC gene. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, there is sufficient evidence to classify the p.Arg132* variant as pathogenic for autosomal recessive cobalamin C deficiency based on the information above. [ACMG evidence codes used: PVS1; PM3_Very Strong; PM2]

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Genome-Nilou Lab, SCV004178164.1

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

From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004805005.2

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

From Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India, SCV004814217.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providedclinical testing PubMed (4)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 8, 2024