NM_005957.5(MTHFR):c.157T>C (p.Leu53=) AND Homocystinuria due to methylene tetrahydrofolate reductase deficiency

Germline classification:: Likely benign (2 submissions)
Last evaluated:: May 22, 2020
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:: RCV001419715.8

Allele description [Variation Report for NM_005957.5(MTHFR):c.157T>C (p.Leu53=)]

NM_005957.5(MTHFR):c.157T>C (p.Leu53=)

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.157T>C (p.Leu53=)

HGVS:

NC_000001.11:g.11802960A>G
NG_008766.1:g.1811A>G
NG_013351.1:g.8144T>C
NM_001330358.2:c.280T>C
NM_005957.5:c.157T>CMANE SELECT
NP_001317287.1:p.Leu94=
NP_005948.3:p.Leu53=
LRG_726:g.8144T>C
NC_000001.10:g.11863017A>G

Links:

dbSNP: rs1205350004

NCBI 1000 Genomes Browser:

rs1205350004

Molecular consequence:

NM_001330358.2:c.280T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_005957.5:c.157T>C - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Homocystinuria due to methylene tetrahydrofolate reductase deficiency
Synonyms:: HOMOCYSTINURIA DUE TO DEFICIENCY OF N(5,10)-METHYLENETETRAHYDROFOLATE REDUCTASE ACTIVITY; Homocysteinemia due to MTHFR deficiency; Homocysteinemia due to methylenetetrahydro-folate reductase deficiency; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009353; MedGen: C1856061; Orphanet: 395; OMIM: 236250

Recent activity

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alanine dehydrogenase [Cutibacterium acnes]
alanine dehydrogenase [Cutibacterium acnes]
gi|499497382|ref|WP_011184022.1|

Protein
Mus musculus kinesin family member 2B, mRNA (cDNA clone MGC:163687 IMAGE:4013033...
Mus musculus kinesin family member 2B, mRNA (cDNA clone MGC:163687 IMAGE:40130333), complete cds
gi|124297335|gb|BC132056.1|

Nucleotide
232b10D DNA segment, 232b10D [Mus musculus]
232b10D DNA segment, 232b10D [Mus musculus]
Gene ID:53092

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001621975	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (May 22, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002094654	Natera, Inc.	no assertion criteria provided	Likely benign (Jul 29, 2021)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001621975

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(May 22, 2020)

germline

clinical testing

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

SCV002094654

Natera, Inc.

no assertion criteria provided

Likely benign
(Jul 29, 2021)

germline

clinical testing

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 Invitae, SCV001621975.4

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

#	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

From Natera, Inc., SCV002094654.1

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

#	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: Sep 16, 2024

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