NM_005957.5(MTHFR):c.1538T>G (p.Leu513Ter) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: May 18, 2018
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:: RCV000657793.2

Allele description [Variation Report for NM_005957.5(MTHFR):c.1538T>G (p.Leu513Ter)]

NM_005957.5(MTHFR):c.1538T>G (p.Leu513Ter)

Gene:

MTHFR:methylenetetrahydrofolate reductase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p36.22

Genomic location:

Preferred name:

NM_005957.5(MTHFR):c.1538T>G (p.Leu513Ter)

HGVS:

NC_000001.11:g.11792372A>C
NG_013351.1:g.18732T>G
NM_001330358.2:c.1661T>G
NM_005957.5:c.1538T>GMANE SELECT
NP_001317287.1:p.Leu554Ter
NP_005948.3:p.Leu513Ter
NP_005948.3:p.Leu513Ter
LRG_726t1:c.1538T>G
LRG_726:g.18732T>G
LRG_726p1:p.Leu513Ter
NC_000001.10:g.11852429A>C
NM_005957.4:c.1538T>G

Protein change:

L513*

Links:

dbSNP: rs1553185069

NCBI 1000 Genomes Browser:

rs1553185069

Molecular consequence:

NM_001330358.2:c.1661T>G - nonsense - [Sequence Ontology: SO:0001587]
NM_005957.5:c.1538T>G - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000779546	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (May 18, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000779546

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(May 18, 2018)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000779546.2

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

Description

The L513X variant in the MTHFR gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The L513X variant is not observed in large population cohorts (Lek et al., 2016). We interpret L513X as a likely pathogenic variant.

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

Last Updated: Nov 24, 2024

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