Skip to main page content
Accesskeys

dbSNP Short Genetic Variations

Reference SNP (rs) Report

Alpha

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.

rs61751449

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chrX:154030864 (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>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
MECP2 : Missense Variant
Publications
6 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.p7 chr X NC_000023.11:g.154030864G>A
GRCh38.p7 chr X NC_000023.11:g.154030864G>C
GRCh37.p13 chr X fix patch HG1497_PATCH NW_003871103.3:g.1464843G>A
GRCh37.p13 chr X fix patch HG1497_PATCH NW_003871103.3:g.1464843G>C
MECP2 RefSeqGene NG_007107.2:g.111264C>T
MECP2 RefSeqGene NG_007107.2:g.111264C>G
GRCh37.p13 chr X NC_000023.10:g.153296315G>A
GRCh37.p13 chr X NC_000023.10:g.153296315G>C
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.964C>T P [CCC] > S [TCC] Coding Sequence Variant
methyl-CpG-binding protein 2 isoform 1 NP_004983.1:p.Pro...

NP_004983.1:p.Pro322Ser

P (Pro) > S (Ser) Missense Variant
MECP2 transcript variant 1 NM_004992.3:c.964C>G P [CCC] > A [GCC] Coding Sequence Variant
methyl-CpG-binding protein 2 isoform 1 NP_004983.1:p.Pro...

NP_004983.1:p.Pro322Ala

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

NM_001110792.1:c.1000C>T

P [CCC] > S [TCC] Coding Sequence Variant
methyl-CpG-binding protein 2 isoform 2 NP_001104262.1:p....

NP_001104262.1:p.Pro334Ser

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

NM_001110792.1:c.1000C>G

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

NP_001104262.1:p.Pro334Ala

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

NM_001316337.1:c.685C>T

P [CCC] > S [TCC] Coding Sequence Variant
methyl-CpG-binding protein 2 isoform 3 NP_001303266.1:p....

NP_001303266.1:p.Pro229Ser

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

NM_001316337.1:c.685C>G

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

NP_001303266.1:p.Pro229Ala

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

XM_017029533.1:c.685C>T

P [CCC] > S [TCC] Coding Sequence Variant
methyl-CpG-binding protein 2 isoform X1 XP_016885022.1:p....

XP_016885022.1:p.Pro229Ser

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

XM_017029533.1:c.685C>G

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

XP_016885022.1:p.Pro229Ala

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

XM_005274682.4:c.685C>T

P [CCC] > S [TCC] Coding Sequence Variant
methyl-CpG-binding protein 2 isoform X1 XP_005274739.1:p....

XP_005274739.1:p.Pro229Ser

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

XM_005274682.4:c.685C>G

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

XP_005274739.1:p.Pro229Ala

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

XM_011531166.2:c.685C>T

P [CCC] > S [TCC] Coding Sequence Variant
methyl-CpG-binding protein 2 isoform X1 XP_011529468.1:p....

XP_011529468.1:p.Pro229Ser

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

XM_011531166.2:c.685C>G

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

XP_011529468.1:p.Pro229Ala

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

XM_006724819.3:c.295C>T

P [CCC] > S [TCC] Coding Sequence Variant
methyl-CpG-binding protein 2 isoform X2 XP_006724882.1:p....

XP_006724882.1:p.Pro99Ser

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

XM_006724819.3:c.295C>G

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

XP_006724882.1:p.Pro99Ala

P (Pro) > A (Ala) 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: A (allele ID: 26882 )
ClinVar Accession Disease Names Clinical Significance
RCV000012617.19 Mental retardation, X-linked, syndromic 13 Pathogenic
RCV000416315.1 Rett syndrome Pathogenic
Allele: C (allele ID: 153485 )
ClinVar Accession Disease Names Clinical Significance
RCV000169949.1 Rett syndrome Uncertain-Significance
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 G= A C Note
GRCh38.p7 chr X NC_000023.11:g.15...

NC_000023.11:g.154030864G=

NC_000023.11:g.15...

NC_000023.11:g.154030864G>A

NC_000023.11:g.15...

NC_000023.11:g.154030864G>C

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

NW_003871103.3:g.1464843G=

NW_003871103.3:g....

NW_003871103.3:g.1464843G>A

NW_003871103.3:g....

NW_003871103.3:g.1464843G>C

MECP2 RefSeqGene NG_007107.2:g.111...

NG_007107.2:g.111264C=

NG_007107.2:g.111...

NG_007107.2:g.111264C>T

NG_007107.2:g.111...

NG_007107.2:g.111264C>G

MECP2 transcript variant 1 NM_004992.3:c.964C= NM_004992.3:c.964C>T NM_004992.3:c.964C>G
MECP2 transcript variant 3 NM_001316337.1:c....

NM_001316337.1:c.685C=

NM_001316337.1:c....

NM_001316337.1:c.685C>T

NM_001316337.1:c....

NM_001316337.1:c.685C>G

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

NM_001110792.1:c.1000C=

NM_001110792.1:c....

NM_001110792.1:c.1000C>T

NM_001110792.1:c....

NM_001110792.1:c.1000C>G

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

NC_000023.10:g.153296315G=

NC_000023.10:g.15...

NC_000023.10:g.153296315G>A

NC_000023.10:g.15...

NC_000023.10:g.153296315G>C

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

XM_005274682.4:c.685C=

XM_005274682.4:c....

XM_005274682.4:c.685C>T

XM_005274682.4:c....

XM_005274682.4:c.685C>G

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

XM_005274682.1:c.685C=

XM_005274682.1:c....

XM_005274682.1:c.685C>T

XM_005274682.1:c....

XM_005274682.1:c.685C>G

MECP2 transcript variant X4 XM_006724819.3:c....

XM_006724819.3:c.295C=

XM_006724819.3:c....

XM_006724819.3:c.295C>T

XM_006724819.3:c....

XM_006724819.3:c.295C>G

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

XM_011531166.2:c.685C=

XM_011531166.2:c....

XM_011531166.2:c.685C>T

XM_011531166.2:c....

XM_011531166.2:c.685C>G

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

XM_017029533.1:c.685C=

XM_017029533.1:c....

XM_017029533.1:c.685C>T

XM_017029533.1:c....

XM_017029533.1:c.685C>G

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

NP_004983.1:p.Pro322=

NP_004983.1:p.Pro...

NP_004983.1:p.Pro322Ser

NP_004983.1:p.Pro...

NP_004983.1:p.Pro322Ala

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

NP_001303266.1:p.Pro229=

NP_001303266.1:p....

NP_001303266.1:p.Pro229Ser

NP_001303266.1:p....

NP_001303266.1:p.Pro229Ala

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

NP_001104262.1:p.Pro334=

NP_001104262.1:p....

NP_001104262.1:p.Pro334Ser

NP_001104262.1:p....

NP_001104262.1:p.Pro334Ala

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

XP_005274739.1:p.Pro229=

XP_005274739.1:p....

XP_005274739.1:p.Pro229Ser

XP_005274739.1:p....

XP_005274739.1:p.Pro229Ala

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

XP_006724882.1:p.Pro99=

XP_006724882.1:p....

XP_006724882.1:p.Pro99Ser

XP_006724882.1:p....

XP_006724882.1:p.Pro99Ala

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

XP_011529468.1:p.Pro229=

XP_011529468.1:p....

XP_011529468.1:p.Pro229Ser

XP_011529468.1:p....

XP_011529468.1:p.Pro229Ala

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

XP_016885022.1:p.Pro229=

XP_016885022.1:p....

XP_016885022.1:p.Pro229Ser

XP_016885022.1:p....

XP_016885022.1:p.Pro229Ala

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#.

3 ClinVar, 4 SubSNP submissions
No Submitter Submission ID Date (Build)
1 OMICIA ss244239962 Sep 17, 2012 (137)
2 OMIM-CURATED-RECORDS ss295476541 Feb 04, 2011 (133)
3 CHWRETT ss538296672 Aug 08, 2012 (137)
4 CHWRETT ss538296673 Aug 08, 2012 (137)
5 ClinVar RCV000012617.19 Jul 20, 2018 (151)
6 ClinVar RCV000169949.1 Jul 20, 2018 (151)
7 ClinVar RCV000416315.1 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
ss244239962, ss295476541, ss538296672, ss538296673 NC_000023.11:154030863:G= NC_000023.11:154030863:G= (self)
RCV000012617.19, RCV000416315.1, ss244239962, ss295476541, ss538296673 NC_000023.11:154030863:G>A NC_000023.11:154030863:G>A (self)
RCV000169949.1, ss538296672 NC_000023.11:154030863:G>C NC_000023.11:154030863:G>C (self)
Help

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

6 citations for rs61751449
PMID Title Author Year Journal
11462237 DHPLC analysis of the MECP2 gene in Italian Rett patients. Nicolao P et al. 2001 Human mutation
15173251 Screening of MECP2 coding sequence in patients with phenotypes of decreasing likelihood for Rett syndrome: a cohort of 171 cases. Kammoun F et al. 2004 Journal of medical genetics
16473305 Spectrum and distribution of MECP2 mutations in 424 Rett syndrome patients: a molecular update. Philippe C et al. 2006 European journal of medical genetics
16966553 A novel familial MECP2 mutation in a young boy: clinical and molecular findings. Ventura P et al. 2006 Neurology
18174559 Rett syndrome: prevalence among Chinese and a comparison of MECP2 mutations of classic Rett syndrome with other neurodevelopmental disorders. Wong VC et al. 2007 Journal of child neurology
21954873 Molecular screening of MECP2 gene in a cohort of Lebanese patients suspected with Rett syndrome: report on a mild case with a novel indel mutation. Corbani S et al. 2012 Journal of intellectual disability research

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