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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

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.

rs142250261

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:236862284 (GRCh38.p14) 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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000884 (234/264690, TOPMED)
T=0.000943 (237/251338, GnomAD_exome)
T=0.001300 (277/213028, ALFA) (+ 8 more)
T=0.000906 (127/140202, GnomAD)
T=0.001104 (134/121386, ExAC)
T=0.00085 (11/13006, GO-ESP)
T=0.0002 (1/4480, Estonian)
T=0.0005 (2/3854, ALSPAC)
T=0.0013 (5/3708, TWINSUK)
T=0.002 (2/998, GoNL)
T=0.007 (4/600, NorthernSweden)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MTR : Missense Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 229432 C=0.998723 T=0.001277
European Sub 194370 C=0.998585 T=0.001415
African Sub 9358 C=1.0000 T=0.0000
African Others Sub 360 C=1.000 T=0.000
African American Sub 8998 C=1.0000 T=0.0000
Asian Sub 6360 C=1.0000 T=0.0000
East Asian Sub 4512 C=1.0000 T=0.0000
Other Asian Sub 1848 C=1.0000 T=0.0000
Latin American 1 Sub 796 C=1.000 T=0.000
Latin American 2 Sub 968 C=0.999 T=0.001
South Asian Sub 274 C=1.000 T=0.000
Other Sub 17306 C=0.99902 T=0.00098


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
TopMed Global Study-wide 264690 C=0.999116 T=0.000884
gnomAD - Exomes Global Study-wide 251338 C=0.999057 T=0.000943
gnomAD - Exomes European Sub 135276 C=0.998359 T=0.001641
gnomAD - Exomes Asian Sub 49008 C=0.99998 T=0.00002
gnomAD - Exomes American Sub 34588 C=0.99980 T=0.00020
gnomAD - Exomes African Sub 16256 C=0.99982 T=0.00018
gnomAD - Exomes Ashkenazi Jewish Sub 10076 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6134 C=0.9993 T=0.0007
Allele Frequency Aggregator Total Global 213028 C=0.998700 T=0.001300
Allele Frequency Aggregator European Sub 184238 C=0.998578 T=0.001422
Allele Frequency Aggregator Other Sub 15872 C=0.99912 T=0.00088
Allele Frequency Aggregator Asian Sub 6360 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 4520 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 968 C=0.999 T=0.001
Allele Frequency Aggregator Latin American 1 Sub 796 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 274 C=1.000 T=0.000
gnomAD - Genomes Global Study-wide 140202 C=0.999094 T=0.000906
gnomAD - Genomes European Sub 75926 C=0.99858 T=0.00142
gnomAD - Genomes African Sub 42022 C=0.99969 T=0.00031
gnomAD - Genomes American Sub 13650 C=0.99971 T=0.00029
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3132 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2152 C=0.9991 T=0.0009
ExAC Global Study-wide 121386 C=0.998896 T=0.001104
ExAC Europe Sub 73348 C=0.99824 T=0.00176
ExAC Asian Sub 25160 C=0.99996 T=0.00004
ExAC American Sub 11566 C=0.99991 T=0.00009
ExAC African Sub 10404 C=0.99981 T=0.00019
ExAC Other Sub 908 C=0.999 T=0.001
GO Exome Sequencing Project Global Study-wide 13006 C=0.99915 T=0.00085
GO Exome Sequencing Project European American Sub 8600 C=0.9988 T=0.0012
GO Exome Sequencing Project African American Sub 4406 C=0.9998 T=0.0002
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9998 T=0.0002
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9995 T=0.0005
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9987 T=0.0013
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.998 T=0.002
Northern Sweden ACPOP Study-wide 600 C=0.993 T=0.007
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.p14 chr 1 NC_000001.11:g.236862284C>T
GRCh37.p13 chr 1 NC_000001.10:g.237025584C>T
MTR RefSeqGene NG_008959.1:g.72004C>T
Gene: MTR, 5-methyltetrahydrofolate-homocysteine methyltransferase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MTR transcript variant 2 NM_001291939.1:c.2092C>T P [CCT] > S [TCT] Coding Sequence Variant
methionine synthase isoform 2 NP_001278868.1:p.Pro698Ser P (Pro) > S (Ser) Missense Variant
MTR transcript variant 3 NM_001291940.2:c.1024C>T P [CCT] > S [TCT] Coding Sequence Variant
methionine synthase isoform 3 NP_001278869.1:p.Pro342Ser P (Pro) > S (Ser) Missense Variant
MTR transcript variant 1 NM_000254.3:c.2245C>T P [CCT] > S [TCT] Coding Sequence Variant
methionine synthase isoform 1 NP_000245.2:p.Pro749Ser P (Pro) > S (Ser) Missense Variant
MTR transcript variant X1 XM_011544194.4:c.2413C>T P [CCT] > S [TCT] Coding Sequence Variant
methionine synthase isoform X1 XP_011542496.1:p.Pro805Ser P (Pro) > S (Ser) Missense Variant
MTR transcript variant X2 XM_017001329.3:c.2260C>T P [CCT] > S [TCT] Coding Sequence Variant
methionine synthase isoform X2 XP_016856818.1:p.Pro754Ser P (Pro) > S (Ser) Missense Variant
MTR transcript variant X3 XM_005273141.6:c.2242C>T P [CCT] > S [TCT] Coding Sequence Variant
methionine synthase isoform X3 XP_005273198.1:p.Pro748Ser P (Pro) > S (Ser) Missense Variant
MTR transcript variant X4 XM_017001330.3:c.2413C>T P [CCT] > S [TCT] Coding Sequence Variant
methionine synthase isoform X4 XP_016856819.1:p.Pro805Ser P (Pro) > S (Ser) Missense Variant
MTR transcript variant X5 XM_047421182.1:c.2089C>T P [CCT] > S [TCT] Coding Sequence Variant
methionine synthase isoform X5 XP_047277138.1:p.Pro697Ser P (Pro) > S (Ser) Missense Variant
MTR transcript variant X6 XM_047421183.1:c.2260C>T P [CCT] > S [TCT] Coding Sequence Variant
methionine synthase isoform X6 XP_047277139.1:p.Pro754Ser P (Pro) > S (Ser) Missense Variant
MTR transcript variant X7 XM_047421184.1:c.2245C>T P [CCT] > S [TCT] Coding Sequence Variant
methionine synthase isoform X7 XP_047277140.1:p.Pro749Ser P (Pro) > S (Ser) Missense Variant
MTR transcript variant X7 XM_047421185.1:c.2242C>T P [CCT] > S [TCT] Coding Sequence Variant
methionine synthase isoform X7 XP_047277141.1:p.Pro748Ser P (Pro) > S (Ser) Missense Variant
MTR transcript variant X8 XM_047421186.1:c.2092C>T P [CCT] > S [TCT] Coding Sequence Variant
methionine synthase isoform X8 XP_047277142.1:p.Pro698Ser P (Pro) > S (Ser) Missense Variant
MTR transcript variant X9 XM_047421187.1:c.1309C>T P [CCT] > S [TCT] Coding Sequence Variant
methionine synthase isoform X9 XP_047277143.1:p.Pro437Ser P (Pro) > 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: T (allele ID: 279804 )
ClinVar Accession Disease Names Clinical Significance
RCV000372535.3 Disorders of Intracellular Cobalamin Metabolism Uncertain-Significance
RCV000756361.8 not provided Uncertain-Significance
RCV001252326.1 Intellectual disability Uncertain-Significance
RCV001850551.1 Methylcobalamin deficiency type cblG Uncertain-Significance
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= T
GRCh38.p14 chr 1 NC_000001.11:g.236862284= NC_000001.11:g.236862284C>T
GRCh37.p13 chr 1 NC_000001.10:g.237025584= NC_000001.10:g.237025584C>T
MTR RefSeqGene NG_008959.1:g.72004= NG_008959.1:g.72004C>T
MTR transcript variant 1 NM_000254.3:c.2245= NM_000254.3:c.2245C>T
MTR transcript variant 1 NM_000254.2:c.2245= NM_000254.2:c.2245C>T
MTR transcript variant 3 NM_001291940.2:c.1024= NM_001291940.2:c.1024C>T
MTR transcript variant 3 NM_001291940.1:c.1024= NM_001291940.1:c.1024C>T
MTR transcript variant 2 NM_001291939.1:c.2092= NM_001291939.1:c.2092C>T
MTR transcript variant X3 XM_005273141.6:c.2242= XM_005273141.6:c.2242C>T
MTR transcript variant X3 XM_005273141.5:c.2242= XM_005273141.5:c.2242C>T
MTR transcript variant X3 XM_005273141.4:c.2242= XM_005273141.4:c.2242C>T
MTR transcript variant X1 XM_005273141.3:c.2242= XM_005273141.3:c.2242C>T
MTR transcript variant X2 XM_005273141.2:c.2242= XM_005273141.2:c.2242C>T
MTR transcript variant X2 XM_005273141.1:c.2242= XM_005273141.1:c.2242C>T
MTR transcript variant X1 XM_011544194.4:c.2413= XM_011544194.4:c.2413C>T
MTR transcript variant X1 XM_011544194.3:c.2413= XM_011544194.3:c.2413C>T
MTR transcript variant X1 XM_011544194.2:c.2413= XM_011544194.2:c.2413C>T
MTR transcript variant X5 XM_011544194.1:c.2413= XM_011544194.1:c.2413C>T
MTR transcript variant X2 XM_017001329.3:c.2260= XM_017001329.3:c.2260C>T
MTR transcript variant X2 XM_017001329.2:c.2260= XM_017001329.2:c.2260C>T
MTR transcript variant X2 XM_017001329.1:c.2260= XM_017001329.1:c.2260C>T
MTR transcript variant X4 XM_017001330.3:c.2413= XM_017001330.3:c.2413C>T
MTR transcript variant X4 XM_017001330.2:c.2413= XM_017001330.2:c.2413C>T
MTR transcript variant X4 XM_017001330.1:c.2413= XM_017001330.1:c.2413C>T
MTR transcript variant X5 XM_047421182.1:c.2089= XM_047421182.1:c.2089C>T
MTR transcript variant X7 XM_047421184.1:c.2245= XM_047421184.1:c.2245C>T
MTR transcript variant X7 XM_047421185.1:c.2242= XM_047421185.1:c.2242C>T
MTR transcript variant 4 NM_001410942.1:c.2245= NM_001410942.1:c.2245C>T
MTR transcript variant X8 XM_047421186.1:c.2092= XM_047421186.1:c.2092C>T
MTR transcript variant X6 XM_047421183.1:c.2260= XM_047421183.1:c.2260C>T
MTR transcript variant X9 XM_047421187.1:c.1309= XM_047421187.1:c.1309C>T
methionine synthase isoform 1 NP_000245.2:p.Pro749= NP_000245.2:p.Pro749Ser
methionine synthase isoform 3 NP_001278869.1:p.Pro342= NP_001278869.1:p.Pro342Ser
methionine synthase isoform 2 NP_001278868.1:p.Pro698= NP_001278868.1:p.Pro698Ser
methionine synthase isoform X3 XP_005273198.1:p.Pro748= XP_005273198.1:p.Pro748Ser
methionine synthase isoform X1 XP_011542496.1:p.Pro805= XP_011542496.1:p.Pro805Ser
methionine synthase isoform X2 XP_016856818.1:p.Pro754= XP_016856818.1:p.Pro754Ser
methionine synthase isoform X4 XP_016856819.1:p.Pro805= XP_016856819.1:p.Pro805Ser
methionine synthase isoform X5 XP_047277138.1:p.Pro697= XP_047277138.1:p.Pro697Ser
methionine synthase isoform X7 XP_047277140.1:p.Pro749= XP_047277140.1:p.Pro749Ser
methionine synthase isoform X7 XP_047277141.1:p.Pro748= XP_047277141.1:p.Pro748Ser
methionine synthase isoform X8 XP_047277142.1:p.Pro698= XP_047277142.1:p.Pro698Ser
methionine synthase isoform X6 XP_047277139.1:p.Pro754= XP_047277139.1:p.Pro754Ser
methionine synthase isoform X9 XP_047277143.1:p.Pro437= XP_047277143.1:p.Pro437Ser
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#.

39 SubSNP, 11 Frequency, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342038655 May 09, 2011 (134)
2 EXOME_CHIP ss491313131 May 04, 2012 (137)
3 CLINSEQ_SNP ss491618315 May 04, 2012 (137)
4 ILLUMINA ss780764489 Sep 08, 2015 (146)
5 ILLUMINA ss783443742 Sep 08, 2015 (146)
6 EVA-GONL ss976295739 Aug 21, 2014 (142)
7 EVA_DECODE ss1585697618 Apr 01, 2015 (144)
8 EVA_UK10K_ALSPAC ss1602442015 Apr 01, 2015 (144)
9 EVA_UK10K_TWINSUK ss1645436048 Apr 01, 2015 (144)
10 EVA_EXAC ss1686130369 Apr 01, 2015 (144)
11 ILLUMINA ss1751907260 Sep 08, 2015 (146)
12 ILLUMINA ss1917744478 Feb 12, 2016 (147)
13 ILLUMINA ss1946027879 Feb 12, 2016 (147)
14 JJLAB ss2020285232 Sep 14, 2016 (149)
15 HUMAN_LONGEVITY ss2171246117 Dec 20, 2016 (150)
16 ILLUMINA ss2710698043 Nov 08, 2017 (151)
17 GNOMAD ss2732391410 Nov 08, 2017 (151)
18 GNOMAD ss2746597597 Nov 08, 2017 (151)
19 GNOMAD ss2767806095 Nov 08, 2017 (151)
20 SWEGEN ss2988684964 Nov 08, 2017 (151)
21 ILLUMINA ss3626342484 Oct 11, 2018 (152)
22 ILLUMINA ss3634380707 Oct 11, 2018 (152)
23 ILLUMINA ss3640088060 Oct 11, 2018 (152)
24 ILLUMINA ss3644523882 Oct 11, 2018 (152)
25 EGCUT_WGS ss3656643817 Jul 12, 2019 (153)
26 EVA_DECODE ss3688910909 Jul 12, 2019 (153)
27 ACPOP ss3727988021 Jul 12, 2019 (153)
28 ILLUMINA ss3744362340 Jul 12, 2019 (153)
29 ILLUMINA ss3744681614 Jul 12, 2019 (153)
30 ILLUMINA ss3772182388 Jul 12, 2019 (153)
31 EVA ss3823731953 Apr 25, 2020 (154)
32 EVA ss3825591911 Apr 25, 2020 (154)
33 NORTHRUP_AU ss3983905862 Apr 25, 2021 (155)
34 EVA ss3986165556 Apr 25, 2021 (155)
35 TOPMED ss4488463458 Apr 25, 2021 (155)
36 EVA ss5325688891 Oct 12, 2022 (156)
37 EVA ss5847579930 Oct 12, 2022 (156)
38 EVA ss5848289810 Oct 12, 2022 (156)
39 EVA ss5939579036 Oct 12, 2022 (156)
40 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 237025584 Oct 11, 2018 (152)
41 Genetic variation in the Estonian population NC_000001.10 - 237025584 Oct 11, 2018 (152)
42 ExAC NC_000001.10 - 237025584 Oct 11, 2018 (152)
43 gnomAD - Genomes NC_000001.11 - 236862284 Apr 25, 2021 (155)
44 gnomAD - Exomes NC_000001.10 - 237025584 Jul 12, 2019 (153)
45 GO Exome Sequencing Project NC_000001.10 - 237025584 Oct 11, 2018 (152)
46 Genome of the Netherlands Release 5 NC_000001.10 - 237025584 Apr 25, 2020 (154)
47 Northern Sweden NC_000001.10 - 237025584 Jul 12, 2019 (153)
48 TopMed NC_000001.11 - 236862284 Apr 25, 2021 (155)
49 UK 10K study - Twins NC_000001.10 - 237025584 Oct 11, 2018 (152)
50 ALFA NC_000001.11 - 236862284 Apr 25, 2021 (155)
51 ClinVar RCV000372535.3 Oct 12, 2022 (156)
52 ClinVar RCV000756361.8 Oct 12, 2022 (156)
53 ClinVar RCV001252326.1 Apr 25, 2021 (155)
54 ClinVar RCV001850551.1 Oct 12, 2022 (156)
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
ss491618315, ss1585697618 NC_000001.9:235092206:C:T NC_000001.11:236862283:C:T (self)
3371449, 2382065, 5372640, 1430249, 190455, 1474762, 1272886, 3371449, ss342038655, ss491313131, ss780764489, ss783443742, ss976295739, ss1602442015, ss1645436048, ss1686130369, ss1751907260, ss1917744478, ss1946027879, ss2020285232, ss2710698043, ss2732391410, ss2746597597, ss2767806095, ss2988684964, ss3626342484, ss3634380707, ss3640088060, ss3644523882, ss3656643817, ss3727988021, ss3744362340, ss3744681614, ss3772182388, ss3823731953, ss3825591911, ss3983905862, ss3986165556, ss5325688891, ss5847579930, ss5848289810, ss5939579036 NC_000001.10:237025583:C:T NC_000001.11:236862283:C:T (self)
RCV000372535.3, RCV000756361.8, RCV001252326.1, RCV001850551.1, 43621640, 52069793, 6058421653, ss2171246117, ss3688910909, ss4488463458 NC_000001.11:236862283:C:T NC_000001.11:236862283:C:T (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 rs142250261

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

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.post761+d5e8e07