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NM_002454.3(MTRR):c.869T>C (p.Ile290Thr) AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
May 5, 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:
RCV001591019.6

Allele description [Variation Report for NM_002454.3(MTRR):c.869T>C (p.Ile290Thr)]

NM_002454.3(MTRR):c.869T>C (p.Ile290Thr)

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.869T>C (p.Ile290Thr)
HGVS:
  • NC_000005.10:g.7883243T>C
  • NG_008856.1:g.19140T>C
  • NM_001364440.2:c.869T>C
  • NM_001364441.2:c.869T>C
  • NM_001364442.2:c.869T>C
  • NM_002454.3:c.869T>CMANE SELECT
  • NM_024010.4:c.869T>C
  • NP_001351369.1:p.Ile290Thr
  • NP_001351370.1:p.Ile290Thr
  • NP_001351371.1:p.Ile290Thr
  • NP_002445.2:p.Ile290Thr
  • NP_076915.3:p.Ile290Thr
  • NC_000005.9:g.7883356T>C
  • NM_002454.2:c.869T>C
  • NR_134480.2:n.948T>C
  • NR_134481.2:n.962T>C
  • NR_134482.2:n.808T>C
  • NR_157168.2:n.922T>C
  • NR_157169.2:n.782T>C
  • NR_157170.2:n.808T>C
  • NR_157171.2:n.782T>C
  • NR_157172.2:n.808T>C
  • NR_157173.2:n.936T>C
  • NR_157174.2:n.808T>C
  • NR_157175.2:n.962T>C
  • NR_157176.2:n.962T>C
  • NR_157177.2:n.957T>C
  • NR_157178.2:n.962T>C
Protein change:
I290T
Links:
dbSNP: rs144899305
NCBI 1000 Genomes Browser:
rs144899305
Molecular consequence:
  • NM_001364440.2:c.869T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001364441.2:c.869T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001364442.2:c.869T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002454.3:c.869T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024010.4:c.869T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_134480.2:n.948T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_134481.2:n.962T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_134482.2:n.808T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157168.2:n.922T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157169.2:n.782T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157170.2:n.808T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157171.2:n.782T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157172.2:n.808T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157173.2:n.936T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157174.2:n.808T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157175.2:n.962T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157176.2:n.962T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157177.2:n.957T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157178.2:n.962T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV001824422GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Uncertain significance
(Jun 24, 2021)
germlineclinical testing

Citation Link,

SCV003800185ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2021)
Uncertain significance
(May 5, 2022)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV001824422.1

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

Description

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge, in association with a MTRR-related disorder; This variant is associated with the following publications: (PMID: 31063268, 27535533)

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

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV003800185.2

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

Description

The MTRR c.869T>C; p.Ile290Thr variant (rs144899305), to our knowledge, is not reported in an individual with homocystinuria-megaloblastic anemia, but is reported in the literature in an individual with cleft lip (Marini 2019). This variant is reported in ClinVar (Variation ID: 354357) and is found in the non-Finnish European population with an allele frequency of 0.18% (233/129,162 alleles) in the Genome Aggregation Database. The isoleucine at codon 290 is weakly conserved, and computational analyses predict that this variant is neutral (REVEL: 0.148). Due to limited information, the clinical significance of the p.Ile290Thr variant is uncertain at this time. References: Marini NJ et al. Accumulation of rare coding variants in genes implicated in risk of human cleft lip with or without cleft palate. Am J Med Genet A. 2019 Jul;179(7):1260-1269. PMID: 31063268.

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

Last Updated: May 7, 2024