MTHFR
protein-codingmethylenetetrahydrofolate 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
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~20.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0009353
Submitter: Natera
Inheritance Pattern: AR
Disease ID:MONDO:0009353
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0009353
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0009353
Submitter: G2P
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.
Inheritance Pattern: AR
Disease ID:MONDO:0009353
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MTHFR variants in ClinVar
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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 4 | 5 | 290 | 2 | 302 |
| missense | 12 | 52 | 214 | 22 | 3 | 303 |
| nonsense | 19 | 29 | 1 | 49 | ||
| start loss | 2 | 2 | 4 | |||
| frameshift | 27 | 35 | 1 | 63 | ||
| splice donor/acceptor (+/-2bp) | 8 | 23 | 2 | 33 | ||
| Total | 69 | 145 | 223 | 312 | 5 | 754 |
Highest pathogenic variant AF is 0.0005057931
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005948.3 | 11 | MANE Select | |
| Ensembl | ENSP00000365775.3 | 11 | MANE Select | |
| RefSeq | NP_001317287.1 | 12 | Standard | |
| RefSeq | NP_001397679.1 | 12 | Standard |
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:
- 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-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.896 | 342 | 392 | 0.873 | 0.0000251 | 4306 |
| Missense (PolyPhen) | 124 | 156.37 | 0.793 | 1746 | ||
| Synonymous | -1.37 | 182 | 160 | 1.14 | 0.0000106 | 1283 |
| Loss of Function | 1.90 | 20 | 31.5 | 0.634 | 0.00000167 | 338 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00033 | 0.00033 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00027 | 0.00026 | rare |
| South Asian | 0.00026 | 0.00026 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | Medium | Medium |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |