chr14:64442127:G>A Detail (hg38) (MTHFD1)

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Summary
Information
Links
Disease area statistics
MGeND
ClinVar
CIViC
DisGeNET
Annotation
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Information

Genome

Assembly	Position
hg19	chr14:64,908,845-64,908,845 View the variant detail on this assembly version.
hg38	chr14:64,442,127-64,442,127

HGVS

MTHFD1

Type	Transcript	Protein
RefSeq
Ensemble	ENST00000545908.6:c.1958G>A	ENST00000545908.6:p.Arg653Gln
	ENST00000554768.6:c.1715G>A	ENST00000554768.6:p.Arg572Gln
	ENST00000557370.3:c.1958G>A	ENST00000557370.3:p.Arg653Gln
	ENST00000557539.2:c.1715G>A	ENST00000557539.2:p.Arg572Gln
	ENST00000652337.1:c.1958G>A	ENST00000652337.1:p.Arg653Gln
	ENST00000697168.1:c.1958G>A	ENST00000697168.1:p.Arg653Gln
	ENST00000697173.1:c.1715G>A	ENST00000697173.1:p.Arg572Gln
	ENST00000697174.1:c.1709G>A	ENST00000697174.1:p.Arg570Gln

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:0.286
	ToMMo:0.287
	NCBN:[No Data.]
	NCBN(Hondo):[No Data.]
	NCBN(Ryukyu):[No Data.]
East asia	ExAC:0.223

Prediction

ClinVar

Clinical Significance	Benign Likely benign
Review star
Show details

Links

MTHFD1

Type	Database	ID	Link
Gene	MIM	172460	OMIM
	HGNC	7432	HGNC
	Ensembl	ENSG00000100714	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv51074616	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
risk factor	2008-03-01	no assertion criteria provided	Neural tube defects, folate-sensitive, susceptibility to	germline	Detail
Benign Likely benign	2021-12-03	criteria provided, multiple submitters, no conflicts	not specified	germline	Detail
Benign	2024-02-01	criteria provided, multiple submitters, no conflicts	not provided	germline	Detail
Benign	2021-09-05	criteria provided, single submitter	Combined immunodeficiency and megaloblastic anemia with or without hyperhomocysteinemia	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.003	cervix carcinoma	Employing PCR-RFLPs and HRM analyses, we examined the prevalence of BHMT Arg239G...	BeFree	21349258	Detail
0.004	ovarian carcinoma	Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890)...	BeFree	22183302	Detail
0.013	Malignant neoplasm of ovary	Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890)...	BeFree	22183302	Detail
0.006	Malignant tumor of cervix	Employing PCR-RFLPs and HRM analyses, we examined the prevalence of BHMT Arg239G...	BeFree	21349258	Detail
<0.001	ovarian carcinoma	Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890)...	BeFree	22183302	Detail
0.001	Malignant tumor of cervix	Employing PCR-RFLPs and HRM analyses, we examined the prevalence of BHMT Arg239G...	BeFree	21349258	Detail
0.003	Malignant neoplasm of ovary	Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890)...	BeFree	22183302	Detail
0.010	cervix carcinoma	Employing PCR-RFLPs and HRM analyses, we examined the prevalence of BHMT Arg239G...	BeFree	21349258	Detail
0.003	Down syndrome	In conclusion, our meta-analysis suggested that the MTRR c.66A>G (rs1801394) ...	BeFree	25544792	Detail
0.040	Down syndrome	In conclusion, our meta-analysis suggested that the MTRR c.66A>G (rs1801394) ...	BeFree	25544792	Detail
0.005	Migraine Disorders	Association study of MTHFD1 coding polymorphisms R134K and R653Q with migraine s...	BeFree	25039261	Detail
<0.001	Common Migraine	The R134K and R653Q variants in MTHFD1 were genotyped in an Australian cohort of...	BeFree	25039261	Detail
<0.001	Diabetes Mellitus, Non-Insulin-Dependent	Subjects with the genotype AA of the MTHFD variant (rs2236225) had a significant...	BeFree	25074646	Detail
0.007	Precursor Cell Lymphoblastic Leukemia Lymphoma	[Polymorphisms in folate-related genes and risk of pediatric acute lymphoblastic...	GAD	19020309	Detail
0.005	Migraine Disorders	Thymidylate synthase promoter tandem repeat and MTHFD1 R653Q polymorphisms modul...	BeFree	15953655	Detail
0.005	Migraine Disorders	Thymidylate synthase promoter tandem repeat and MTHFD1 R653Q polymorphisms modul...	BeFree	15953655	Detail
0.054	Migraine Disorders	Thymidylate synthase promoter tandem repeat and MTHFD1 R653Q polymorphisms modul...	BeFree	15953655	Detail
0.015	colorectal cancer	We examined whether polymorphisms in these genes, i.e., cSHMT L474F, MTHFD1 R653...	BeFree	15122597	Detail
0.008	congenital heart defects	MTHFD1 p.R653Q has been proposed as a risk factor for neural tube defects (NTDs)...	BeFree	23704330	Detail
0.240	Neural tube defect, folate-sensitive	The MTHFD1 p.Arg653Gln variant alters enzyme function and increases risk for con...	UNIPROT	18767138	Detail
0.008	colorectal cancer	We examined whether polymorphisms in these genes, i.e., cSHMT L474F, MTHFD1 R653...	BeFree	15122597	Detail
0.008	congenital heart defects	The MTHFD1 p.Arg653Gln variant alters enzyme function and increases risk for con...	BeFree	18767138	Detail
<0.001	colorectal carcinoma	We examined whether polymorphisms in these genes, i.e., cSHMT L474F, MTHFD1 R653...	BeFree	15122597	Detail
0.001	colorectal carcinoma	We examined whether polymorphisms in these genes, i.e., cSHMT L474F, MTHFD1 R653...	BeFree	15122597	Detail
0.001	attention deficit hyperactivity disorder	We hypothesized that ADHD related cognitive deficit could be attributed to abnor...	BeFree	25079255	Detail

Annotation

Annotations

Descrption	Source	Links
NM_005956.4(MTHFD1):c.1958G>A (p.Arg653Gln) AND Neural tube defects, folate-sensitive, susceptibilit...	ClinVar	Detail
NM_005956.4(MTHFD1):c.1958G>A (p.Arg653Gln) AND not specified	ClinVar	Detail
NM_005956.4(MTHFD1):c.1958G>A (p.Arg653Gln) AND not provided	ClinVar	Detail
NM_005956.4(MTHFD1):c.1958G>A (p.Arg653Gln) AND Combined immunodeficiency and megaloblastic anemia w...	ClinVar	Detail
Employing PCR-RFLPs and HRM analyses, we examined the prevalence of BHMT Arg239Gln (rs3733890), MTR ...	DisGeNET	Detail
Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890), MTHFD1 (rs2236225)...	DisGeNET	Detail
Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890), MTHFD1 (rs2236225)...	DisGeNET	Detail
Employing PCR-RFLPs and HRM analyses, we examined the prevalence of BHMT Arg239Gln (rs3733890), MTR ...	DisGeNET	Detail
Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890), MTHFD1 (rs2236225)...	DisGeNET	Detail
Employing PCR-RFLPs and HRM analyses, we examined the prevalence of BHMT Arg239Gln (rs3733890), MTR ...	DisGeNET	Detail
Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890), MTHFD1 (rs2236225)...	DisGeNET	Detail
Employing PCR-RFLPs and HRM analyses, we examined the prevalence of BHMT Arg239Gln (rs3733890), MTR ...	DisGeNET	Detail
In conclusion, our meta-analysis suggested that the MTRR c.66A>G (rs1801394) polymorphism and MTH...	DisGeNET	Detail
In conclusion, our meta-analysis suggested that the MTRR c.66A>G (rs1801394) polymorphism and MTH...	DisGeNET	Detail
Association study of MTHFD1 coding polymorphisms R134K and R653Q with migraine susceptibility.	DisGeNET	Detail
The R134K and R653Q variants in MTHFD1 were genotyped in an Australian cohort of 520 unrelated migra...	DisGeNET	Detail
Subjects with the genotype AA of the MTHFD variant (rs2236225) had a significantly lower likelihood ...	DisGeNET	Detail
[Polymorphisms in folate-related genes and risk of pediatric acute lymphoblastic leukemia.]	DisGeNET	Detail
Thymidylate synthase promoter tandem repeat and MTHFD1 R653Q polymorphisms modulate the risk for mig...	DisGeNET	Detail
Thymidylate synthase promoter tandem repeat and MTHFD1 R653Q polymorphisms modulate the risk for mig...	DisGeNET	Detail
Thymidylate synthase promoter tandem repeat and MTHFD1 R653Q polymorphisms modulate the risk for mig...	DisGeNET	Detail
We examined whether polymorphisms in these genes, i.e., cSHMT L474F, MTHFD1 R653Q and GCPII H475Y, m...	DisGeNET	Detail
MTHFD1 p.R653Q has been proposed as a risk factor for neural tube defects (NTDs), congenital heart d...	DisGeNET	Detail
The MTHFD1 p.Arg653Gln variant alters enzyme function and increases risk for congenital heart defect...	DisGeNET	Detail
We examined whether polymorphisms in these genes, i.e., cSHMT L474F, MTHFD1 R653Q and GCPII H475Y, m...	DisGeNET	Detail
The MTHFD1 p.Arg653Gln variant alters enzyme function and increases risk for congenital heart defect...	DisGeNET	Detail
We examined whether polymorphisms in these genes, i.e., cSHMT L474F, MTHFD1 R653Q and GCPII H475Y, m...	DisGeNET	Detail
We examined whether polymorphisms in these genes, i.e., cSHMT L474F, MTHFD1 R653Q and GCPII H475Y, m...	DisGeNET	Detail
We hypothesized that ADHD related cognitive deficit could be attributed to abnormalities in the fola...	DisGeNET	Detail

Overlapped Transcript Coordinates

Gene	Transcript ID	Exon Number	Chromosome	Start	Stop	Type	Amino Mutation	Transcript Position	Links

Overlapped Transcript

Gene	Transcript ID	Chromosome	Start	Stop	Links

Gene: -
dbSNP: rs2236225 dbSNP
Genome: hg38
Position: chr14:64,442,127-64,442,127
Variant Type: snv
Reference Allele: G
Alternative Allele: A
Filtering Status (HGVD): PASS
# of samples (HGVD): 1177
Mean of sample read depth (HGVD): 94.94
Standard deviation of sample read depth (HGVD): 41.40
Number of reference allele (HGVD): 1680
Number of alternative allele (HGVD): 674
Allele Frequency (HGVD): 0.286321155480034
Gene Symbol (HGVD): MTHFD1
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): rs2236225
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.2869
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 4808
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16760
East Asian Chromosome Counts (ExAC): 8628
East Asian Allele Counts (ExAC): 1927
East Asian Heterozygous Counts (ExAC): 1527
East Asian Homozygous Counts (ExAC): 200
East Asian Allele Frequency (ExAC): 0.22334260547056095
Chromosome Counts in All Race (ExAC): 121370
Allele Counts in All Race (ExAC): 52844
Heterozygous Counts in All Race (ExAC): 28440
Homozygous Counts in All Race (ExAC): 12202
Allele Frequency in All Race (ExAC): 0.4353958968443602

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