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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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.

rs397507444

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr1:11794407 (GRCh38.p12) 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
T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
None
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MTHFR : Missense Variant
Publications
0 citations
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.p12 chr 1 NC_000001.11:g.11794407T>G
GRCh37.p13 chr 1 NC_000001.10:g.11854464T>G
MTHFR RefSeqGene (LRG_726) NG_013351.1:g.16697A>C
Gene: MTHFR, methylenetetrahydrofolate reductase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MTHFR transcript variant 2 NM_005957.4:c.1298A>C E [GAA] > A [GCA] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform 2 NP_005948.3:p.Glu433Ala E (Glu) > A (Ala) Missense Variant
MTHFR transcript variant 1 NM_001330358.1:c.1421A>C E [GAA] > A [GCA] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform 1 NP_001317287.1:p.Glu474Ala E (Glu) > A (Ala) Missense Variant
MTHFR transcript variant X4 XM_005263462.4:c.1298A>C E [GAA] > A [GCA] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X3 XP_005263519.1:p.Glu433Ala E (Glu) > A (Ala) Missense Variant
MTHFR transcript variant X1 XM_011541495.3:c.1418A>C E [GAA] > A [GCA] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X1 XP_011539797.1:p.Glu473Ala E (Glu) > A (Ala) Missense Variant
MTHFR transcript variant X2 XM_011541496.3:c.1421A>C E [GAA] > A [GCA] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X2 XP_011539798.1:p.Glu474Ala E (Glu) > A (Ala) Missense Variant
MTHFR transcript variant X3 XM_005263460.5:c.1298A>C E [GAA] > A [GCA] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X3 XP_005263517.1:p.Glu433Ala E (Glu) > A (Ala) Missense Variant
MTHFR transcript variant X5 XM_017001328.2:c.1421A>C E [GAA] > A [GCA] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X4 XP_016856817.1:p.Glu474Ala E (Glu) > A (Ala) Missense Variant
MTHFR transcript variant X6 XM_005263463.4:c.1052A>C E [GAA] > A [GCA] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X5 XP_005263520.1:p.Glu351Ala E (Glu) > A (Ala) Missense Variant
MTHFR transcript variant X7 XM_024447198.1:c.1052A>C E [GAA] > A [GCA] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X5 XP_024302966.1:p.Glu351Ala E (Glu) > A (Ala) Missense Variant
MTHFR transcript variant X8 XR_002956640.1:n.2399A>C N/A Non Coding Transcript 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.

Not Reported in ClinVar
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").

None
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 T= G Note
GRCh38.p12 chr 1 NC_000001.11:g.11794407T= NC_000001.11:g.11794407T>G
GRCh37.p13 chr 1 NC_000001.10:g.11854464T= NC_000001.10:g.11854464T>G
MTHFR RefSeqGene (LRG_726) NG_013351.1:g.16697A= NG_013351.1:g.16697A>C
MTHFR transcript variant 2 NM_005957.4:c.1298A= NM_005957.4:c.1298A>C
MTHFR transcript variant 1 NM_001330358.1:c.1421A= NM_001330358.1:c.1421A>C
MTHFR transcript variant X3 XM_005263460.5:c.1298A= XM_005263460.5:c.1298A>C
MTHFR transcript variant X3 XM_005263460.1:c.1298A= XM_005263460.1:c.1298A>C
MTHFR transcript variant X6 XM_005263463.4:c.1052A= XM_005263463.4:c.1052A>C
MTHFR transcript variant X6 XM_005263463.1:c.1052A= XM_005263463.1:c.1052A>C
MTHFR transcript variant X4 XM_005263462.4:c.1298A= XM_005263462.4:c.1298A>C
MTHFR transcript variant X5 XM_005263462.1:c.1298A= XM_005263462.1:c.1298A>C
MTHFR transcript variant X1 XM_011541495.3:c.1418A= XM_011541495.3:c.1418A>C
MTHFR transcript variant X2 XM_011541496.3:c.1421A= XM_011541496.3:c.1421A>C
MTHFR transcript variant X5 XM_017001328.2:c.1421A= XM_017001328.2:c.1421A>C
MTHFR transcript variant X8 XR_002956640.1:n.2399A= XR_002956640.1:n.2399A>C
MTHFR transcript variant X7 XM_024447198.1:c.1052A= XM_024447198.1:c.1052A>C
methylenetetrahydrofolate reductase isoform 2 NP_005948.3:p.Glu433= NP_005948.3:p.Glu433Ala
methylenetetrahydrofolate reductase isoform 1 NP_001317287.1:p.Glu474= NP_001317287.1:p.Glu474Ala
methylenetetrahydrofolate reductase isoform X3 XP_005263517.1:p.Glu433= XP_005263517.1:p.Glu433Ala
methylenetetrahydrofolate reductase isoform X5 XP_005263520.1:p.Glu351= XP_005263520.1:p.Glu351Ala
methylenetetrahydrofolate reductase isoform X3 XP_005263519.1:p.Glu433= XP_005263519.1:p.Glu433Ala
methylenetetrahydrofolate reductase isoform X1 XP_011539797.1:p.Glu473= XP_011539797.1:p.Glu473Ala
methylenetetrahydrofolate reductase isoform X2 XP_011539798.1:p.Glu474= XP_011539798.1:p.Glu474Ala
methylenetetrahydrofolate reductase isoform X4 XP_016856817.1:p.Glu474= XP_016856817.1:p.Glu474Ala
methylenetetrahydrofolate reductase isoform X5 XP_024302966.1:p.Glu351= XP_024302966.1:p.Glu351Ala
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#.

1 SubSNP submissions
No Submitter Submission ID Date (Build)
1 CLINVAR ss831879118 Nov 05, 2013 (136)
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
ss831879118 NC_000001.11:11794406:T:G NC_000001.11:11794406:T:G (self)
Help

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

No publications for rs397507444

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: 2.0.1.post104+4a6ee9c