MTHFD1L
Basic information
Region (hg38): 6:150865679-151101887
Previous symbols: [ "FTHFSDC1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (135 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTHFD1L gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015440.5. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 131 | 134 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 131 | 3 | 1 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MTHFD1L | protein_coding | protein_coding | ENST00000367321 | 27 | 236339 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.94e-12 | 1.00 | 125666 | 0 | 82 | 125748 | 0.000326 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.992 | 459 | 523 | 0.878 | 0.0000294 | 6309 |
| Missense in Polyphen | 162 | 217.99 | 0.74316 | 2388 | ||
| Synonymous | -0.226 | 208 | 204 | 1.02 | 0.0000128 | 1982 |
| Loss of Function | 3.17 | 28 | 52.9 | 0.529 | 0.00000285 | 618 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000363 | 0.000363 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000490 | 0.000489 |
| Finnish | 0.000185 | 0.000185 |
| European (Non-Finnish) | 0.000425 | 0.000422 |
| Middle Eastern | 0.000490 | 0.000489 |
| South Asian | 0.000432 | 0.000425 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May provide the missing metabolic reaction required to link the mitochondria and the cytoplasm in the mammalian model of one-carbon folate metabolism in embryonic an transformed cells complementing thus the enzymatic activities of MTHFD2. {ECO:0000250, ECO:0000269|PubMed:16171773}.;
- Pathway
- One carbon pool by folate - Homo sapiens (human);Folate malabsorption, hereditary;Methylenetetrahydrofolate Reductase Deficiency (MTHFRD);Methotrexate Action Pathway;Folate Metabolism;One Carbon Metabolism;Trans-sulfuration and one carbon metabolism;folate polyglutamylation;Folate metabolism;Metabolism;folate transformations I;Metabolism of folate and pterines;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors;Vitamin B9 (folate) metabolism
(Consensus)
Recessive Scores
- pRec
- 0.261
Intolerance Scores
- loftool
- 0.815
- rvis_EVS
- -0.35
- rvis_percentile_EVS
- 29.54
Haploinsufficiency Scores
- pHI
- 0.0847
- hipred
- Y
- hipred_score
- 0.706
- ghis
- 0.547
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.900
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mthfd1l
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); embryo phenotype; growth/size/body region phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); craniofacial phenotype;
Gene ontology
- Biological process
- neural tube closure;folic acid-containing compound metabolic process;purine nucleobase biosynthetic process;10-formyltetrahydrofolate biosynthetic process;formate metabolic process;tetrahydrofolate interconversion;folic acid metabolic process;embryonic neurocranium morphogenesis;embryonic viscerocranium morphogenesis;oxidation-reduction process
- Cellular component
- cytoplasm;mitochondrion;mitochondrial matrix;membrane
- Molecular function
- formate-tetrahydrofolate ligase activity;methylenetetrahydrofolate dehydrogenase (NADP+) activity;ATP binding;protein homodimerization activity