NM_002454.3(MTRR):c.589G>A (p.Asp197Asn) AND Methylcobalamin deficiency type cblE

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 12, 2022
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:: RCV002001993.3

Allele description [Variation Report for NM_002454.3(MTRR):c.589G>A (p.Asp197Asn)]

NM_002454.3(MTRR):c.589G>A (p.Asp197Asn)

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.589G>A (p.Asp197Asn)

HGVS:

NC_000005.10:g.7878131G>A
NG_008856.1:g.14028G>A
NM_001364440.2:c.589G>A
NM_001364441.2:c.589G>A
NM_001364442.2:c.589G>A
NM_002454.3:c.589G>AMANE SELECT
NM_024010.4:c.589G>A
NP_001351369.1:p.Asp197Asn
NP_001351370.1:p.Asp197Asn
NP_001351371.1:p.Asp197Asn
NP_002445.2:p.Asp197Asn
NP_076915.3:p.Asp197Asn
NC_000005.9:g.7878244G>A
NR_134480.2:n.668G>A
NR_134481.2:n.682G>A
NR_134482.2:n.528G>A
NR_157168.2:n.642G>A
NR_157169.2:n.502G>A
NR_157170.2:n.528G>A
NR_157171.2:n.502G>A
NR_157172.2:n.528G>A
NR_157173.2:n.656G>A
NR_157174.2:n.528G>A
NR_157175.2:n.682G>A
NR_157176.2:n.682G>A
NR_157177.2:n.677G>A
NR_157178.2:n.682G>A

Protein change:

D197N

Links:

dbSNP: rs748186027

NCBI 1000 Genomes Browser:

rs748186027

Molecular consequence:

NM_001364440.2:c.589G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001364441.2:c.589G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001364442.2:c.589G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002454.3:c.589G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_024010.4:c.589G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_134480.2:n.668G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_134481.2:n.682G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_134482.2:n.528G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157168.2:n.642G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157169.2:n.502G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157170.2:n.528G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157171.2:n.502G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157172.2:n.528G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157173.2:n.656G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157174.2:n.528G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157175.2:n.682G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157176.2:n.682G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157177.2:n.677G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157178.2:n.682G>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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002216141	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 12, 2022)	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

SCV002216141

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 12, 2022)

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, SCV002216141.2

#	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 aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 197 of the MTRR protein (p.Asp197Asn). This variant is present in population databases (rs748186027, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with MTRR-related conditions. ClinVar contains an entry for this variant (Variation ID: 1436051). 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 asparagine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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

ClinVar

Relating variation to medicine