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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.

rs267608513

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chrX:154031155 (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
G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.00001 (1/178793, GnomAD)
C=0.0000 (1/87670, ExAC)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MECP2 : 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 X NC_000023.11:g.154031155G>C
GRCh38.p7 chr X NC_000023.11:g.154031155G>T
GRCh37.p13 chr X fix patch HG1497_PATCH NW_003871103.3:g.1465134G>C
GRCh37.p13 chr X fix patch HG1497_PATCH NW_003871103.3:g.1465134G>T
MECP2 RefSeqGene NG_007107.2:g.110973C>G
MECP2 RefSeqGene NG_007107.2:g.110973C>A
GRCh37.p13 chr X NC_000023.10:g.153296606G>C
GRCh37.p13 chr X NC_000023.10:g.153296606G>T
Gene: MECP2, methyl-CpG binding protein 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MECP2 transcript variant 1 NM_004992.3:c.673C>G P [CCT] > A [GCT] Coding Sequence Variant
methyl-CpG-binding protein 2 isoform 1 NP_004983.1:p.Pro...

NP_004983.1:p.Pro225Ala

P (Pro) > A (Ala) Missense Variant
MECP2 transcript variant 1 NM_004992.3:c.673C>A P [CCT] > T [ACT] Coding Sequence Variant
methyl-CpG-binding protein 2 isoform 1 NP_004983.1:p.Pro...

NP_004983.1:p.Pro225Thr

P (Pro) > T (Thr) Missense Variant
MECP2 transcript variant 2 NM_001110792.1:c....

NM_001110792.1:c.709C>G

P [CCT] > A [GCT] Coding Sequence Variant
methyl-CpG-binding protein 2 isoform 2 NP_001104262.1:p....

NP_001104262.1:p.Pro237Ala

P (Pro) > A (Ala) Missense Variant
MECP2 transcript variant 2 NM_001110792.1:c....

NM_001110792.1:c.709C>A

P [CCT] > T [ACT] Coding Sequence Variant
methyl-CpG-binding protein 2 isoform 2 NP_001104262.1:p....

NP_001104262.1:p.Pro237Thr

P (Pro) > T (Thr) Missense Variant
MECP2 transcript variant 3 NM_001316337.1:c....

NM_001316337.1:c.394C>G

P [CCT] > A [GCT] Coding Sequence Variant
methyl-CpG-binding protein 2 isoform 3 NP_001303266.1:p....

NP_001303266.1:p.Pro132Ala

P (Pro) > A (Ala) Missense Variant
MECP2 transcript variant 3 NM_001316337.1:c....

NM_001316337.1:c.394C>A

P [CCT] > T [ACT] Coding Sequence Variant
methyl-CpG-binding protein 2 isoform 3 NP_001303266.1:p....

NP_001303266.1:p.Pro132Thr

P (Pro) > T (Thr) Missense Variant
MECP2 transcript variant X1 XM_017029533.1:c....

XM_017029533.1:c.394C>G

P [CCT] > A [GCT] Coding Sequence Variant
methyl-CpG-binding protein 2 isoform X1 XP_016885022.1:p....

XP_016885022.1:p.Pro132Ala

P (Pro) > A (Ala) Missense Variant
MECP2 transcript variant X1 XM_017029533.1:c....

XM_017029533.1:c.394C>A

P [CCT] > T [ACT] Coding Sequence Variant
methyl-CpG-binding protein 2 isoform X1 XP_016885022.1:p....

XP_016885022.1:p.Pro132Thr

P (Pro) > T (Thr) Missense Variant
MECP2 transcript variant X2 XM_005274682.4:c....

XM_005274682.4:c.394C>G

P [CCT] > A [GCT] Coding Sequence Variant
methyl-CpG-binding protein 2 isoform X1 XP_005274739.1:p....

XP_005274739.1:p.Pro132Ala

P (Pro) > A (Ala) Missense Variant
MECP2 transcript variant X2 XM_005274682.4:c....

XM_005274682.4:c.394C>A

P [CCT] > T [ACT] Coding Sequence Variant
methyl-CpG-binding protein 2 isoform X1 XP_005274739.1:p....

XP_005274739.1:p.Pro132Thr

P (Pro) > T (Thr) Missense Variant
MECP2 transcript variant X3 XM_011531166.2:c....

XM_011531166.2:c.394C>G

P [CCT] > A [GCT] Coding Sequence Variant
methyl-CpG-binding protein 2 isoform X1 XP_011529468.1:p....

XP_011529468.1:p.Pro132Ala

P (Pro) > A (Ala) Missense Variant
MECP2 transcript variant X3 XM_011531166.2:c....

XM_011531166.2:c.394C>A

P [CCT] > T [ACT] Coding Sequence Variant
methyl-CpG-binding protein 2 isoform X1 XP_011529468.1:p....

XP_011529468.1:p.Pro132Thr

P (Pro) > T (Thr) Missense Variant
MECP2 transcript variant X4 XM_006724819.3:c....

XM_006724819.3:c.4C>G

P [CCT] > A [GCT] Coding Sequence Variant
methyl-CpG-binding protein 2 isoform X2 XP_006724882.1:p....

XP_006724882.1:p.Pro2Ala

P (Pro) > A (Ala) Missense Variant
MECP2 transcript variant X4 XM_006724819.3:c....

XM_006724819.3:c.4C>A

P [CCT] > T [ACT] Coding Sequence Variant
methyl-CpG-binding protein 2 isoform X2 XP_006724882.1:p....

XP_006724882.1:p.Pro2Thr

P (Pro) > T (Thr) 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: 153384 )
ClinVar Accession Disease Names Clinical Significance
RCV000133192.2 not provided Pathogenic
RCV000193090.1 Rett syndrome 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
The Genome Aggregation Database Global Study-wide 178793 G=0.99999 C=0.00001
The Genome Aggregation Database European Sub 96601 G=1.0000 C=0.0000
The Genome Aggregation Database Asian Sub 32015 G=1.0000 C=0.0000
The Genome Aggregation Database American Sub 26579 G=1.0000 C=0.0000
The Genome Aggregation Database African Sub 12246 G=1.0000 C=0.0000
The Genome Aggregation Database Ashkenazi Jewish Sub 7295 G=1.000 C=0.000
The Genome Aggregation Database Other Sub 4057 G=1.000 C=0.000
The Exome Aggregation Consortium Global Study-wide 87670 G=1.0000 C=0.0000
The Exome Aggregation Consortium Europe Sub 52459 G=1.0000 C=0.0000
The Exome Aggregation Consortium Asian Sub 16761 G=1.0000 C=0.0000
The Exome Aggregation Consortium American Sub 9322 G=1.000 C=0.000
The Exome Aggregation Consortium African Sub 8495 G=1.000 C=0.000
The Exome Aggregation Consortium Other Sub 633 G=1.00 C=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 G= C T Note
GRCh38.p7 chr X NC_000023.11:g.15...

NC_000023.11:g.154031155G=

NC_000023.11:g.15...

NC_000023.11:g.154031155G>C

NC_000023.11:g.15...

NC_000023.11:g.154031155G>T

GRCh37.p13 chr X fix patch HG1497_PATCH NW_003871103.3:g....

NW_003871103.3:g.1465134G=

NW_003871103.3:g....

NW_003871103.3:g.1465134G>C

NW_003871103.3:g....

NW_003871103.3:g.1465134G>T

MECP2 RefSeqGene NG_007107.2:g.110...

NG_007107.2:g.110973C=

NG_007107.2:g.110...

NG_007107.2:g.110973C>G

NG_007107.2:g.110...

NG_007107.2:g.110973C>A

MECP2 transcript variant 1 NM_004992.3:c.673C= NM_004992.3:c.673C>G NM_004992.3:c.673C>A
MECP2 transcript variant 3 NM_001316337.1:c....

NM_001316337.1:c.394C=

NM_001316337.1:c....

NM_001316337.1:c.394C>G

NM_001316337.1:c....

NM_001316337.1:c.394C>A

MECP2 transcript variant 2 NM_001110792.1:c....

NM_001110792.1:c.709C=

NM_001110792.1:c....

NM_001110792.1:c.709C>G

NM_001110792.1:c....

NM_001110792.1:c.709C>A

GRCh37.p13 chr X NC_000023.10:g.15...

NC_000023.10:g.153296606G=

NC_000023.10:g.15...

NC_000023.10:g.153296606G>C

NC_000023.10:g.15...

NC_000023.10:g.153296606G>T

MECP2 transcript variant X2 XM_005274682.4:c....

XM_005274682.4:c.394C=

XM_005274682.4:c....

XM_005274682.4:c.394C>G

XM_005274682.4:c....

XM_005274682.4:c.394C>A

MECP2 transcript variant X2 XM_005274682.1:c....

XM_005274682.1:c.394C=

XM_005274682.1:c....

XM_005274682.1:c.394C>G

XM_005274682.1:c....

XM_005274682.1:c.394C>A

MECP2 transcript variant X4 XM_006724819.3:c.4C= XM_006724819.3:c....

XM_006724819.3:c.4C>G

XM_006724819.3:c....

XM_006724819.3:c.4C>A

MECP2 transcript variant X3 XM_011531166.2:c....

XM_011531166.2:c.394C=

XM_011531166.2:c....

XM_011531166.2:c.394C>G

XM_011531166.2:c....

XM_011531166.2:c.394C>A

MECP2 transcript variant X1 XM_017029533.1:c....

XM_017029533.1:c.394C=

XM_017029533.1:c....

XM_017029533.1:c.394C>G

XM_017029533.1:c....

XM_017029533.1:c.394C>A

methyl-CpG-binding protein 2 isoform 1 NP_004983.1:p.Pro...

NP_004983.1:p.Pro225=

NP_004983.1:p.Pro...

NP_004983.1:p.Pro225Ala

NP_004983.1:p.Pro...

NP_004983.1:p.Pro225Thr

methyl-CpG-binding protein 2 isoform 3 NP_001303266.1:p....

NP_001303266.1:p.Pro132=

NP_001303266.1:p....

NP_001303266.1:p.Pro132Ala

NP_001303266.1:p....

NP_001303266.1:p.Pro132Thr

methyl-CpG-binding protein 2 isoform 2 NP_001104262.1:p....

NP_001104262.1:p.Pro237=

NP_001104262.1:p....

NP_001104262.1:p.Pro237Ala

NP_001104262.1:p....

NP_001104262.1:p.Pro237Thr

methyl-CpG-binding protein 2 isoform X1 XP_005274739.1:p....

XP_005274739.1:p.Pro132=

XP_005274739.1:p....

XP_005274739.1:p.Pro132Ala

XP_005274739.1:p....

XP_005274739.1:p.Pro132Thr

methyl-CpG-binding protein 2 isoform X2 XP_006724882.1:p....

XP_006724882.1:p.Pro2=

XP_006724882.1:p....

XP_006724882.1:p.Pro2Ala

XP_006724882.1:p....

XP_006724882.1:p.Pro2Thr

methyl-CpG-binding protein 2 isoform X1 XP_011529468.1:p....

XP_011529468.1:p.Pro132=

XP_011529468.1:p....

XP_011529468.1:p.Pro132Ala

XP_011529468.1:p....

XP_011529468.1:p.Pro132Thr

methyl-CpG-binding protein 2 isoform X1 XP_016885022.1:p....

XP_016885022.1:p.Pro132=

XP_016885022.1:p....

XP_016885022.1:p.Pro132Ala

XP_016885022.1:p....

XP_016885022.1:p.Pro132Thr

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#.

2 Frequency, 5 SubSNP, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CHWRETT ss538296569 Aug 08, 2012 (137)
2 EVA_EXAC ss1694655211 Apr 09, 2015 (144)
3 GNOMAD ss2745614122 Jul 20, 2018 (151)
4 ILLUMINA ss3626004250 Jul 20, 2018 (151)
5 ILLUMINA ss3626004251 Jul 20, 2018 (151)
6 The Exome Aggregation Consortium NC_000023.10 - 153296606 Jul 20, 2018 (151)
7 The Genome Aggregation Database NC_000023.10 - 153296606 Jul 20, 2018 (151)
8 ClinVar RCV000133192.2 Jul 20, 2018 (151)
9 ClinVar RCV000193090.1 Jul 20, 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
10166681, 14628857, ss1694655211, ss2745614122, ss3626004250, ss3626004251 NC_000023.10:153296605:G= NC_000023.11:154031154:G= (self)
ss538296569 NC_000023.11:154031154:G= NC_000023.11:154031154:G= (self)
10166681, 14628857, ss1694655211, ss2745614122, ss3626004250 NC_000023.10:153296605:G>C NC_000023.11:154031154:G>C (self)
ss3626004251 NC_000023.10:153296605:G>T NC_000023.11:154031154:G>T
RCV000133192.2, RCV000193090.1, ss538296569 NC_000023.11:154031154:G>T NC_000023.11:154031154:G>T (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 rs267608513
PMID Title Author Year Journal
18414213 ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007. Richards CS et al. 2008 Genetics in medicine

Genomic regions, transcripts, and products
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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