NM_002454.3(MTRR):c.538G>A (p.Val180Met) AND Methylcobalamin deficiency type cblE

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 17, 2021
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:: RCV002623790.2

Allele description [Variation Report for NM_002454.3(MTRR):c.538G>A (p.Val180Met)]

NM_002454.3(MTRR):c.538G>A (p.Val180Met)

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.538G>A (p.Val180Met)

HGVS:

NC_000005.10:g.7878080G>A
NG_008856.2:g.32223G>A
NM_001364440.2:c.538G>A
NM_001364441.2:c.538G>A
NM_001364442.2:c.538G>A
NM_002454.2:c.538G>A
NM_002454.3:c.538G>AMANE SELECT
NM_024010.4:c.538G>A
NP_001351369.1:p.Val180Met
NP_001351370.1:p.Val180Met
NP_001351371.1:p.Val180Met
NP_002445.2:p.Val180Met
NP_076915.3:p.Val180Met
NC_000005.9:g.7878193G>A
NG_008856.1:g.13977G>A
NR_134480.2:n.617G>A
NR_134481.2:n.631G>A
NR_134482.2:n.477G>A
NR_157168.2:n.591G>A
NR_157169.2:n.451G>A
NR_157170.2:n.477G>A
NR_157171.2:n.451G>A
NR_157172.2:n.477G>A
NR_157173.2:n.605G>A
NR_157174.2:n.477G>A
NR_157175.2:n.631G>A
NR_157176.2:n.631G>A
NR_157177.2:n.626G>A
NR_157178.2:n.631G>A

Protein change:

V180M

Molecular consequence:

NM_001364440.2:c.538G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001364441.2:c.538G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001364442.2:c.538G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002454.3:c.538G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_024010.4:c.538G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_134480.2:n.617G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_134481.2:n.631G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_134482.2:n.477G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157168.2:n.591G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157169.2:n.451G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157170.2:n.477G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157171.2:n.451G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157172.2:n.477G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157173.2:n.605G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157174.2:n.477G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157175.2:n.631G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157176.2:n.631G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157177.2:n.626G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157178.2:n.631G>A - 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; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009354; MedGen: C1856057; Orphanet: 2169; Orphanet: 622; OMIM: 236270

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gi|1953085862|ref|XM_038543222.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003511344	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 17, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003511344

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 17, 2021)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV003511344.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change replaces valine with methionine at codon 180 of the MTRR protein (p.Val180Met). The valine residue is moderately conserved and there is a small physicochemical difference between valine and methionine. This variant is present in population databases (rs143978300, ExAC 0.01%). This variant has not been reported in the literature in individuals with MTRR-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The methionine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 8, 2024

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