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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs200137991

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr1:11794443 (GRCh38.p7) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
C>A / C>G
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00001 (3/246260, GnomAD)
A=0.00003 (4/125568, TOPMED)
A=0.00002 (2/121352, ExAC) (+ 2 more)
A=0.0000 (1/30908, GnomAD)
A=0.000 (1/5008, 1000G)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MTHFR : Missense Variant
Publications
1 citation
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p7 chr 1 NC_000001.11:g.11794443C>A
GRCh38.p7 chr 1 NC_000001.11:g.11794443C>G
GRCh37.p13 chr 1 NC_000001.10:g.11854500C>A
GRCh37.p13 chr 1 NC_000001.10:g.11854500C>G
MTHFR RefSeqGene (LRG_726) NG_013351.1:g.16661G>T
MTHFR RefSeqGene (LRG_726) NG_013351.1:g.16661G>C
Gene: MTHFR, methylenetetrahydrofolate reductase (NAD(P)H) (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MTHFR transcript variant 2 NM_005957.4:c.126...

NM_005957.4:c.1262G>T

W [TGG] > L [TTG] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform 2 NP_005948.3:p.Trp...

NP_005948.3:p.Trp421Leu

W (Trp) > L (Leu) Missense Variant
MTHFR transcript variant 2 NM_005957.4:c.126...

NM_005957.4:c.1262G>C

W [TGG] > S [TCG] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform 2 NP_005948.3:p.Trp...

NP_005948.3:p.Trp421Ser

W (Trp) > S (Ser) Missense Variant
MTHFR transcript variant X1 XM_005263458.3:c....

XM_005263458.3:c.1385G>T

W [TGG] > L [TTG] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X1 XP_005263515.1:p....

XP_005263515.1:p.Trp462Leu

W (Trp) > L (Leu) Missense Variant
MTHFR transcript variant X1 XM_005263458.3:c....

XM_005263458.3:c.1385G>C

W [TGG] > S [TCG] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X1 XP_005263515.1:p....

XP_005263515.1:p.Trp462Ser

W (Trp) > S (Ser) Missense Variant
MTHFR transcript variant X2 XM_011541495.2:c....

XM_011541495.2:c.1382G>T

W [TGG] > L [TTG] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X1 XP_011539797.1:p....

XP_011539797.1:p.Trp461Leu

W (Trp) > L (Leu) Missense Variant
MTHFR transcript variant X2 XM_011541495.2:c....

XM_011541495.2:c.1382G>C

W [TGG] > S [TCG] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X1 XP_011539797.1:p....

XP_011539797.1:p.Trp461Ser

W (Trp) > S (Ser) Missense Variant
MTHFR transcript variant X3 XM_011541496.2:c....

XM_011541496.2:c.1385G>T

W [TGG] > L [TTG] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X2 XP_011539798.1:p....

XP_011539798.1:p.Trp462Leu

W (Trp) > L (Leu) Missense Variant
MTHFR transcript variant X3 XM_011541496.2:c....

XM_011541496.2:c.1385G>C

W [TGG] > S [TCG] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X2 XP_011539798.1:p....

XP_011539798.1:p.Trp462Ser

W (Trp) > S (Ser) Missense Variant
MTHFR transcript variant X4 XM_005263460.4:c....

XM_005263460.4:c.1262G>T

W [TGG] > L [TTG] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X3 XP_005263517.1:p....

XP_005263517.1:p.Trp421Leu

W (Trp) > L (Leu) Missense Variant
MTHFR transcript variant X4 XM_005263460.4:c....

XM_005263460.4:c.1262G>C

W [TGG] > S [TCG] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X3 XP_005263517.1:p....

XP_005263517.1:p.Trp421Ser

W (Trp) > S (Ser) Missense Variant
MTHFR transcript variant X4 XM_005263462.4:c....

XM_005263462.4:c.1262G>T

W [TGG] > L [TTG] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X3 XP_005263519.1:p....

XP_005263519.1:p.Trp421Leu

W (Trp) > L (Leu) Missense Variant
MTHFR transcript variant X4 XM_005263462.4:c....

XM_005263462.4:c.1262G>C

W [TGG] > S [TCG] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X3 XP_005263519.1:p....

XP_005263519.1:p.Trp421Ser

W (Trp) > S (Ser) Missense Variant
MTHFR transcript variant X6 XM_017001328.1:c....

XM_017001328.1:c.1385G>T

W [TGG] > L [TTG] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X4 XP_016856817.1:p....

XP_016856817.1:p.Trp462Leu

W (Trp) > L (Leu) Missense Variant
MTHFR transcript variant X6 XM_017001328.1:c....

XM_017001328.1:c.1385G>C

W [TGG] > S [TCG] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X4 XP_016856817.1:p....

XP_016856817.1:p.Trp462Ser

W (Trp) > S (Ser) Missense Variant
MTHFR transcript variant X7 XM_005263463.3:c....

XM_005263463.3:c.1016G>T

W [TGG] > L [TTG] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X5 XP_005263520.1:p....

XP_005263520.1:p.Trp339Leu

W (Trp) > L (Leu) Missense Variant
MTHFR transcript variant X7 XM_005263463.3:c....

XM_005263463.3:c.1016G>C

W [TGG] > S [TCG] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X5 XP_005263520.1:p....

XP_005263520.1:p.Trp339Ser

W (Trp) > S (Ser) Missense Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: G (allele ID: 185771 )
ClinVar Accession Disease Names Clinical Significance
RCV000167612.1 Homocysteinemia due to MTHFR deficiency Pathogenic
Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
Trans-Omics for Precision Medicine Global Study-wide 125568 C=0.99997 A=0.00003
The Exome Aggregation Consortium Global Study-wide 121352 C=0.99998 A=0.00002
The Exome Aggregation Consortium Europe Sub 73346 C=1.0000 A=0.0000
The Exome Aggregation Consortium Asian Sub 25166 C=0.9999 A=0.0001
The Exome Aggregation Consortium American Sub 11578 C=1.0000 A=0.0000
The Exome Aggregation Consortium African Sub 10354 C=1.0000 A=0.0000
The Exome Aggregation Consortium Other Sub 908 C=1.00 A=0.00
The Genome Aggregation Database Global Study-wide 30908 C=1.0000 A=0.0000
The Genome Aggregation Database European Sub 18464 C=0.9999 A=0.0001
The Genome Aggregation Database African Sub 8710 C=1.000 A=0.000
The Genome Aggregation Database East Asian Sub 1620 C=1.000 A=0.000
The Genome Aggregation Database Other Sub 976 C=1.00 A=0.00
The Genome Aggregation Database American Sub 838 C=1.00 A=0.00
The Genome Aggregation Database Ashkenazi Jewish Sub 300 C=1.00 A=0.00
1000Genomes Global Study-wide 5008 C=1.000 A=0.000
1000Genomes African Sub 1322 C=1.000 A=0.000
1000Genomes East Asian Sub 1008 C=0.999 A=0.001
1000Genomes Europe Sub 1006 C=1.000 A=0.000
1000Genomes South Asian Sub 978 C=1.00 A=0.00
1000Genomes American Sub 694 C=1.00 A=0.00
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement C= A G Note
GRCh38.p7 chr 1 NC_000001.11:g.11...

NC_000001.11:g.11794443C=

NC_000001.11:g.11...

NC_000001.11:g.11794443C>A

NC_000001.11:g.11...

NC_000001.11:g.11794443C>G

GRCh37.p13 chr 1 NC_000001.10:g.11...

NC_000001.10:g.11854500C=

NC_000001.10:g.11...

NC_000001.10:g.11854500C>A

NC_000001.10:g.11...

NC_000001.10:g.11854500C>G

MTHFR RefSeqGene (LRG_726) NG_013351.1:g.166...

NG_013351.1:g.16661G=

NG_013351.1:g.166...

NG_013351.1:g.16661G>T

NG_013351.1:g.166...

NG_013351.1:g.16661G>C

MTHFR transcript variant 2 NM_005957.4:c.1262G= NM_005957.4:c.126...

NM_005957.4:c.1262G>T

NM_005957.4:c.126...

NM_005957.4:c.1262G>C

MTHFR transcript variant X4 XM_005263460.4:c....

XM_005263460.4:c.1262G=

XM_005263460.4:c....

XM_005263460.4:c.1262G>T

XM_005263460.4:c....

XM_005263460.4:c.1262G>C

MTHFR transcript variant X3 XM_005263460.1:c....

XM_005263460.1:c.1262G=

XM_005263460.1:c....

XM_005263460.1:c.1262G>T

XM_005263460.1:c....

XM_005263460.1:c.1262G>C

MTHFR transcript variant X4 XM_005263462.4:c....

XM_005263462.4:c.1262G=

XM_005263462.4:c....

XM_005263462.4:c.1262G>T

XM_005263462.4:c....

XM_005263462.4:c.1262G>C

MTHFR transcript variant X5 XM_005263462.1:c....

XM_005263462.1:c.1262G=

XM_005263462.1:c....

XM_005263462.1:c.1262G>T

XM_005263462.1:c....

XM_005263462.1:c.1262G>C

MTHFR transcript variant X1 XM_005263458.3:c....

XM_005263458.3:c.1385G=

XM_005263458.3:c....

XM_005263458.3:c.1385G>T

XM_005263458.3:c....

XM_005263458.3:c.1385G>C

MTHFR transcript variant X7 XM_005263463.3:c....

XM_005263463.3:c.1016G=

XM_005263463.3:c....

XM_005263463.3:c.1016G>T

XM_005263463.3:c....

XM_005263463.3:c.1016G>C

MTHFR transcript variant X6 XM_005263463.1:c....

XM_005263463.1:c.1016G=

XM_005263463.1:c....

XM_005263463.1:c.1016G>T

XM_005263463.1:c....

XM_005263463.1:c.1016G>C

MTHFR transcript variant X2 XM_011541495.2:c....

XM_011541495.2:c.1382G=

XM_011541495.2:c....

XM_011541495.2:c.1382G>T

XM_011541495.2:c....

XM_011541495.2:c.1382G>C

MTHFR transcript variant X3 XM_011541496.2:c....

XM_011541496.2:c.1385G=

XM_011541496.2:c....

XM_011541496.2:c.1385G>T

XM_011541496.2:c....

XM_011541496.2:c.1385G>C

MTHFR transcript variant X6 XM_017001328.1:c....

XM_017001328.1:c.1385G=

XM_017001328.1:c....

XM_017001328.1:c.1385G>T

XM_017001328.1:c....

XM_017001328.1:c.1385G>C

methylenetetrahydrofolate reductase isoform 2 NP_005948.3:p.Trp...

NP_005948.3:p.Trp421=

NP_005948.3:p.Trp...

NP_005948.3:p.Trp421Leu

NP_005948.3:p.Trp...

NP_005948.3:p.Trp421Ser

methylenetetrahydrofolate reductase isoform X3 XP_005263517.1:p....

XP_005263517.1:p.Trp421=

XP_005263517.1:p....

XP_005263517.1:p.Trp421Leu

XP_005263517.1:p....

XP_005263517.1:p.Trp421Ser

methylenetetrahydrofolate reductase isoform X3 XP_005263519.1:p....

XP_005263519.1:p.Trp421=

XP_005263519.1:p....

XP_005263519.1:p.Trp421Leu

XP_005263519.1:p....

XP_005263519.1:p.Trp421Ser

methylenetetrahydrofolate reductase isoform X1 XP_005263515.1:p....

XP_005263515.1:p.Trp462=

XP_005263515.1:p....

XP_005263515.1:p.Trp462Leu

XP_005263515.1:p....

XP_005263515.1:p.Trp462Ser

methylenetetrahydrofolate reductase isoform X5 XP_005263520.1:p....

XP_005263520.1:p.Trp339=

XP_005263520.1:p....

XP_005263520.1:p.Trp339Leu

XP_005263520.1:p....

XP_005263520.1:p.Trp339Ser

methylenetetrahydrofolate reductase isoform X1 XP_011539797.1:p....

XP_011539797.1:p.Trp461=

XP_011539797.1:p....

XP_011539797.1:p.Trp461Leu

XP_011539797.1:p....

XP_011539797.1:p.Trp461Ser

methylenetetrahydrofolate reductase isoform X2 XP_011539798.1:p....

XP_011539798.1:p.Trp462=

XP_011539798.1:p....

XP_011539798.1:p.Trp462Leu

XP_011539798.1:p....

XP_011539798.1:p.Trp462Ser

methylenetetrahydrofolate reductase isoform X4 XP_016856817.1:p....

XP_016856817.1:p.Trp462=

XP_016856817.1:p....

XP_016856817.1:p.Trp462Leu

XP_016856817.1:p....

XP_016856817.1:p.Trp462Ser

Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

5 Frequency, 8 SubSNP, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss488652097 May 04, 2012 (137)
2 1000GENOMES ss1289701098 Aug 21, 2014 (142)
3 EVA_EXAC ss1685304137 Apr 01, 2015 (144)
4 CLINVAR ss1751113078 May 21, 2015 (144)
5 GNOMAD ss2731121606 Nov 08, 2017 (151)
6 GNOMAD ss2746215807 Nov 08, 2017 (151)
7 GNOMAD ss2751673902 Nov 08, 2017 (151)
8 TOPMED ss3068711136 Nov 08, 2017 (151)
9 1000Genomes NC_000001.10 - 11854500 Jul 19, 2018 (151)
10 The Exome Aggregation Consortium NC_000001.10 - 11854500 Jul 19, 2018 (151)
11 The Genome Aggregation Database NC_000001.10 - 11854500 Jul 19, 2018 (151)
12 The Genome Aggregation Database NC_000001.10 - 11854500 Jul 19, 2018 (151)
13 Trans-Omics for Precision Medicine NC_000001.11 - 11794443 Jul 19, 2018 (151)
14 ClinVar RCV000167612.1 Jul 19, 2018 (151)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
377815, 4483571, 1073101, 136341, ss488652097, ss1289701098, ss1685304137, ss2731121606, ss2746215807, ss2751673902 NC_000001.10:11854499:C= NC_000001.11:11794442:C= (self)
1876546, ss1751113078, ss3068711136 NC_000001.11:11794442:C= NC_000001.11:11794442:C= (self)
377815, 4483571, 1073101, 136341, ss488652097, ss1289701098, ss1685304137, ss2731121606, ss2746215807, ss2751673902 NC_000001.10:11854499:C>A NC_000001.11:11794442:C>A (self)
1876546, ss3068711136 NC_000001.11:11794442:C>A NC_000001.11:11794442:C>A (self)
136341, ss2731121606 NC_000001.10:11854499:C>G NC_000001.11:11794442:C>G (self)
RCV000167612.1, ss1751113078 NC_000001.11:11794442:C>G NC_000001.11:11794442:C>G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs200137991
PMID Title Author Year Journal
25736335 Insights into severe 5,10-methylenetetrahydrofolate reductase deficiency: molecular genetic and enzymatic characterization of 76 patients. Burda P et al. 2015 Human mutation

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 0.1.4.post833+d3ba21e