MTHFR

protein-coding

methylenetetrahydrofolate reductase

Gene summary

The protein encoded by this gene catalyzes the conversion of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate, a co-substrate for homocysteine remethylation to methionine. Genetic variation in this gene influences susceptibility to occlusive vascular disease, neural tube defects, colon cancer and acute leukemia, and mutations in this gene are associated with methylenetetrahydrofolate reductase deficiency.[provided by RefSeq, Oct 2009]

MANE transcript

NM_005957.5

Inheritance

AR

ClinVar variants

P:214U:223B:317

Top phenotype

Homocystinuria due to MTHFR deficiency

gnomAD constraint

pLI —, LoF o/e 0.63

Max pathogenic AF

—

Genomic locus

chr1:11,785,723-11,806,455

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~20.7 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

homocystinuria due to methylene tetrahydrofolate reductase deficiencyDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009353

Submitter: Natera

homocystinuria due to methylene tetrahydrofolate reductase deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009353

Submitter: PanelApp Australia

homocystinuria due to methylene tetrahydrofolate reductase deficiencySUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009353

Submitter: Orphanet

homocystinuria due to methylene tetrahydrofolate reductase deficiencyDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009353

Submitter: G2P

homocystinuria due to methylene tetrahydrofolate reductase deficiencyDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009353

Submitter: ClinGen

The relationship between MTHFR and homocystinuria due to methylene tetrahydrofolate reductase deficiency (autosomal recessive) was evaluated using the ClinGen Clinical Validity Framework as of June, 2019. MTHFR encodes methylenetetrahydrofolate reductase which converts 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate, a cosubstrate for homocysteine remethylation to methionine. Deficiency of MTHFR is associated with elevated homocysteine and decreased methionine, Variants in MTHFR were first reported in humans with this deficiency in 1994 (Goyette et al., PMID 7920641. At least 109 unique variants (missense, nonsense, frameshift, splicing, deletion) have been identified in humans (Froese et al., 2016; PMID 26872964). Evidence supporting this gene-disease relationship includes case-level and experimental data. This gene-disease relationship is supported by biochemical assays, in vitro studies and a mouse model. In summary, MTHFR is definitively associated with autosomal recessive homocystinuria due to methylene tetrahydrofolate reductase deficiency. This has been repeatedly demonstrated in both the research and clinical diagnostic settings and has been upheld over time. This classification was approved by the ClinGen Aminoacidopathy Gene Curation Expert Panel on 6/18/19 (SOP Version 6). Of note, MTHFR polymorphisms have been associated with susceptibility to neural tube defects, schizophrenia, thromboembolism, and vascular disease. However, at this time, these entities are not included for analysis using the ClinGen Clinical Validity Framework.

homocystinuria due to methylene tetrahydrofolate reductase deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009353

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Homocystinuria due to MTHFR deficiencyAR

Manifestation: Biochemical; Cardiovascular; Hematologic; Neurologic

Intervention: Biochemical; Cardiovascular; Hematologic

Rationale: Medical therapy (eg, with folate, betaine, riboflavin, hydroxycobalamin) can be effective; In individuals with heterozygous variants, there may be an increased risk of thrombophilia, and considerations may be warranted in certain situations

Comments: Variants in MTHFR may interact with variants in other genes, such as F5 to result in susceptibility to hematologic manifestations

Refs: 3889647; 1998339; 1866027; 1627352; 8456826; 7920641; 7647779; 7726158; 7564788; 8691945; 8826441; 8892013; 8940272; 8994411; 9133512; 9341863; 9244205; 9372726; 9068801; 9878639; 10323741; 10384377; 10536004; 10679944; 10862840; 10923034; 10961793; 11508552; 11170082; 11274424; 11938441; 12142069; 12673793; 15896655; 15979034; 16145688; 16216822; 17409006; 18658082; 18708589; 19697151; 20236116; 20356773; 20850942; 22578003; 22646290; 22665071; 22721898; 22773907; 22807619; 22856671; 22947400; 23124942Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MTHFR variants in ClinVar

26 Conditions Cataloged
Homocystinuria due to methylene tetrahydrofolate reductase deficiencyTotal: 811
not providedTotal: 116
Neural tube defects, folate-sensitiveTotal: 112
Inborn genetic diseasesTotal: 105
Thrombophilia due to thrombin defectTotal: 41
SchizophreniaTotal: 38
not specifiedTotal: 34
MTHFR-related disorderTotal: 33

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005957.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
4
clinvar
5
clinvar
290
clinvar
2
clinvar
302
missense
12
clinvar
52
clinvar
214
clinvar
22
clinvar
3
clinvar
303
nonsense
19
clinvar
29
clinvar
1
clinvar
49
start loss
2
clinvar
2
clinvar
4
frameshift
27
clinvar
35
clinvar
1
clinvar
63
splice donor/acceptor (+/-2bp)
8
clinvar
23
clinvar
2
clinvar
33
Total691452233125754

Highest pathogenic variant AF is 0.0005057931

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 37 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_005957.5RefSeqNP_005948.311MANE Select
ENST00000376590.9EnsemblENSP00000365775.311MANE Select
NM_001330358.2RefSeqNP_001317287.112Standard
NM_001410750.1RefSeqNP_001397679.112Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Fluoropyrimidine Pathway, Pharmacodynamics
  • Antimetabolite Pathway - Folate Cycle, Pharmacodynamics
  • One carbon pool by folate - Homo sapiens (human)
  • Methotrexate Pathway (Cancer Cell), Pharmacodynamics
  • Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics

Biological Process

  • response to hypoxia
  • neural tube closure
  • cellular amino acid metabolic process
  • methionine metabolic process
  • one-carbon metabolic process

Molecular Function

  • methylenetetrahydrofolate reductase (NAD(P)H) activity
  • protein-containing complex binding
  • flavin adenine dinucleotide binding
  • NADP binding
  • FAD binding

Cellular Component

  • cytosol
  • synapse

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000376592
Coding exons
11
Length
21198
Individuals with no LoFs
125699
Homozygous LoFs
0
Heterozygous LoFs
49
Defined
125748
p
0.000195
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.8963423920.8730.00002514306
Missense (PolyPhen)124156.370.7931746
Synonymous-1.371821601.140.00001061283
Loss of Function1.902031.50.6340.00000167338

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.0000870.000087rare
Ashkenazi Jewish00.0absent
East Asian0.000330.00033rare
Finnish0.0000460.000046rare
European (Non-Finnish)0.000270.00026rare
South Asian0.000260.00026rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Catalyzes the conversion of 5,10- methylenetetrahydrofolate to 5-methyltetrahydrofolate, a co- substrate for homocysteine remethylation to methionine. {ECO:0000269|PubMed:25736335}.;
Disease
DISEASE: Methylenetetrahydrofolate reductase deficiency (MTHFRD) [MIM:236250]: Autosomal recessive disorder with a wide range of features including homocysteinuria, homocysteinemia [MIM:603174], developmental delay, severe mental retardation, perinatal death, psychiatric disturbances, and later-onset neurodegenerative disorders. {ECO:0000269|PubMed:10679944, ECO:0000269|PubMed:20236116, ECO:0000269|PubMed:25736335, ECO:0000269|PubMed:25818041, ECO:0000269|PubMed:7726158, ECO:0000269|PubMed:8940272, ECO:0000269|PubMed:9781030}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Ischemic stroke (ISCHSTR) [MIM:601367]: A stroke is an acute neurologic event leading to death of neural tissue of the brain and resulting in loss of motor, sensory and/or cognitive function. Ischemic strokes, resulting from vascular occlusion, is considered to be a highly complex disease consisting of a group of heterogeneous disorders with multiple genetic and environmental risk factors. {ECO:0000269|PubMed:15534175}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Neural tube defects, folate-sensitive (NTDFS) [MIM:601634]: The most common NTDs are open spina bifida (myelomeningocele) and anencephaly. {ECO:0000269|PubMed:10323741, ECO:0000269|PubMed:7564788, ECO:0000269|PubMed:8826441}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Schizophrenia (SCZD) [MIM:181500]: A complex, multifactorial psychotic disorder or group of disorders characterized by disturbances in the form and content of thought (e.g. delusions, hallucinations), in mood (e.g. inappropriate affect), in sense of self and relationship to the external world (e.g. loss of ego boundaries, withdrawal), and in behavior (e.g bizarre or apparently purposeless behavior). Although it affects emotions, it is distinguished from mood disorders in which such disturbances are primary. Similarly, there may be mild impairment of cognitive function, and it is distinguished from the dementias in which disturbed cognitive function is considered primary. Some patients manifest schizophrenic as well as bipolar disorder symptoms and are often given the diagnosis of schizoaffective disorder. {ECO:0000269|PubMed:15729744, ECO:0000269|PubMed:18583979}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.909

Intolerance Scores

LoFtool
0.210
RVIS EVS
0.09
RVIS percentile EVS
60.71

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
1.00

Gene Damage Prediction

AllRecessiveDominant
MendelianHighMediumMedium
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh
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