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NM_002454.3(MTRR):c.739C>T (p.Pro247Ser) AND Methylcobalamin deficiency type cblE

Germline classification:
Likely benign (2 submissions)
Last evaluated:
Jan 27, 2024
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV000872621.12

Allele description [Variation Report for NM_002454.3(MTRR):c.739C>T (p.Pro247Ser)]

NM_002454.3(MTRR):c.739C>T (p.Pro247Ser)

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.739C>T (p.Pro247Ser)
HGVS:
  • NC_000005.10:g.7878281C>T
  • NG_008856.1:g.14178C>T
  • NM_001364440.2:c.739C>T
  • NM_001364441.2:c.739C>T
  • NM_001364442.2:c.739C>T
  • NM_002454.3:c.739C>TMANE SELECT
  • NM_024010.4:c.739C>T
  • NP_001351369.1:p.Pro247Ser
  • NP_001351370.1:p.Pro247Ser
  • NP_001351371.1:p.Pro247Ser
  • NP_002445.2:p.Pro247Ser
  • NP_076915.3:p.Pro247Ser
  • NC_000005.9:g.7878394C>T
  • NM_002454.2:c.739C>T
  • NR_134480.2:n.818C>T
  • NR_134481.2:n.832C>T
  • NR_134482.2:n.678C>T
  • NR_157168.2:n.792C>T
  • NR_157169.2:n.652C>T
  • NR_157170.2:n.678C>T
  • NR_157171.2:n.652C>T
  • NR_157172.2:n.678C>T
  • NR_157173.2:n.806C>T
  • NR_157174.2:n.678C>T
  • NR_157175.2:n.832C>T
  • NR_157176.2:n.832C>T
  • NR_157177.2:n.827C>T
  • NR_157178.2:n.832C>T
Protein change:
P247S
Links:
dbSNP: rs114053717
NCBI 1000 Genomes Browser:
rs114053717
Molecular consequence:
  • NM_001364440.2:c.739C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001364441.2:c.739C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001364442.2:c.739C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002454.3:c.739C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024010.4:c.739C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_134480.2:n.818C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_134481.2:n.832C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_134482.2:n.678C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157168.2:n.792C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157169.2:n.652C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157170.2:n.678C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157171.2:n.652C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157172.2:n.678C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157173.2:n.806C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157174.2:n.678C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157175.2:n.832C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157176.2:n.832C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157177.2:n.827C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_157178.2:n.832C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Methylcobalamin deficiency type cblE (HMAE)
Synonyms:
VITAMIN B12-RESPONSIVE HOMOCYSTINURIA, cblE TYPE; Homocystinuria-Megaloblastic anemia due to defect in cobalamin metabolism, cblE complementation type; HOMOCYSTINURIA-MEGALOBLASTIC ANEMIA, cblE COMPLEMENTATION TYPE
Identifiers:
MONDO: MONDO:0009354; MedGen: C1856057; Orphanet: 2169; Orphanet: 622; OMIM: 236270

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001014468Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely benign
(Jan 27, 2024)
germlineclinical testing

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

SCV002077199Natera, Inc.
no assertion criteria provided
Benign
(Jan 19, 2020)
germlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
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 Invitae, SCV001014468.7

#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 Natera, Inc., SCV002077199.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 19, 2024