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NM_002454.3(MTRR):c.166G>A (p.Val56Met) AND not provided

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
Mar 14, 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:
RCV001532514.20

Allele description [Variation Report for NM_002454.3(MTRR):c.166G>A (p.Val56Met)]

NM_002454.3(MTRR):c.166G>A (p.Val56Met)

Gene:
MTRR:5-methyltetrahydrofolate-homocysteine methyltransferase reductase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5p15.31
Genomic location:
Preferred name:
NM_002454.3(MTRR):c.166G>A (p.Val56Met)
HGVS:
  • NC_000005.10:g.7873409G>A
  • NG_008856.1:g.9306G>A
  • NG_033101.1:g.629C>T
  • NM_001364440.2:c.166G>A
  • NM_001364441.2:c.166G>A
  • NM_001364442.2:c.166G>A
  • NM_002454.3:c.166G>AMANE SELECT
  • NM_024010.4:c.166G>A
  • NP_001351369.1:p.Val56Met
  • NP_001351370.1:p.Val56Met
  • NP_001351371.1:p.Val56Met
  • NP_002445.2:p.Val56Met
  • NP_076915.3:p.Val56Met
  • NC_000005.9:g.7873522G>A
  • NM_002454.2:c.166G>A
  • NR_134480.2:n.259G>A
  • NR_134481.2:n.259G>A
  • NR_157168.2:n.233G>A
  • NR_157173.2:n.233G>A
  • NR_157175.2:n.259G>A
  • NR_157176.2:n.259G>A
  • NR_157177.2:n.259G>A
  • NR_157178.2:n.259G>A
Protein change:
V56M
Links:
dbSNP: rs761061866
NCBI 1000 Genomes Browser:
rs761061866
Molecular consequence:
  • NM_001364440.2:c.166G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001364441.2:c.166G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001364442.2:c.166G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002454.3:c.166G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024010.4:c.166G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_134480.2:n.259G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_134481.2:n.259G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157168.2:n.233G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157173.2:n.233G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157175.2:n.259G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157176.2:n.259G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157177.2:n.259G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157178.2:n.259G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
2

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001748116CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Pathogenic
(Oct 1, 2023)
germlineclinical testing

Citation Link,

SCV001765914GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Likely pathogenic
(Mar 14, 2024)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes2not providednot providednot providednot providedclinical testing

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV001748116.17

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided

Description

MTRR: PM3:Strong, PM2, PP4:Moderate, PS3:Moderate

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided2not providednot providednot provided

From GeneDx, SCV001765914.2

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

Description

Observed in apparent homozygous state or with another MTRR variant in patients referred for genetic testing at GeneDx or in published literature with features suggestive of homocystinuria, cblE complementation type, but it is not known whether the variants occurred on the same (in cis) or on different (in trans) chromosomes in some cases (PMID: 22887477, 10484769); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 10484769, 22887477)

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

Last Updated: Jul 23, 2024