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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.

rs138382758

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr1:12004835 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00219 (539/245602, GnomAD)
A=0.00291 (365/125568, TOPMED)
A=0.00229 (265/115542, ExAC) (+ 5 more)
A=0.0025 (78/30968, GnomAD)
A=0.0019 (25/13006, GO-ESP)
A=0.002 (10/5008, 1000G)
A=0.003 (13/3854, ALSPAC)
A=0.004 (13/3708, TWINSUK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MFN2 : 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 1 NC_000001.11:g.12004835G>A
GRCh37.p13 chr 1 NC_000001.10:g.12064892G>A
MFN2 RefSeqGene (LRG_255) NG_007945.1:g.29655G>A
Gene: MFN2, mitofusin 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MFN2 transcript variant 1 NM_014874.3:c.140...

NM_014874.3:c.1403G>A

R [CGC] > H [CAC] Coding Sequence Variant
mitofusin-2 NP_055689.1:p.Arg...

NP_055689.1:p.Arg468His

R (Arg) > H (His) Missense Variant
MFN2 transcript variant 2 NM_001127660.1:c....

NM_001127660.1:c.1403G>A

R [CGC] > H [CAC] Coding Sequence Variant
mitofusin-2 NP_001121132.1:p....

NP_001121132.1:p.Arg468His

R (Arg) > H (His) Missense Variant
MFN2 transcript variant X1 XM_005263547.3:c....

XM_005263547.3:c.1403G>A

R [CGC] > H [CAC] Coding Sequence Variant
mitofusin-2 isoform X1 XP_005263604.1:p....

XP_005263604.1:p.Arg468His

R (Arg) > H (His) Missense Variant
MFN2 transcript variant X2 XM_005263545.3:c....

XM_005263545.3:c.1403G>A

R [CGC] > H [CAC] Coding Sequence Variant
mitofusin-2 isoform X1 XP_005263602.1:p....

XP_005263602.1:p.Arg468His

R (Arg) > H (His) Missense Variant
MFN2 transcript variant X3 XM_005263543.3:c....

XM_005263543.3:c.1403G>A

R [CGC] > H [CAC] Coding Sequence Variant
mitofusin-2 isoform X1 XP_005263600.1:p....

XP_005263600.1:p.Arg468His

R (Arg) > H (His) Missense Variant
MFN2 transcript variant X5 XM_005263548.3:c....

XM_005263548.3:c.1403G>A

R [CGC] > H [CAC] Coding Sequence Variant
mitofusin-2 isoform X1 XP_005263605.1:p....

XP_005263605.1:p.Arg468His

R (Arg) > H (His) 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: 17321 )
ClinVar Accession Disease Names Clinical Significance
RCV000002372.4 Charcot-Marie-Tooth disease, type 2A2A Pathogenic
RCV000196650.4 not specified Conflicting-Interpretations-Of-Pathogenicity
RCV000229623.3 Charcot-Marie-Tooth disease, type 2 Benign
RCV000312138.1 Hereditary motor and sensory neuropathy Likely-Benign
RCV000487518.3 not provided 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").

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Study Population Group Sample Size Ref Allele Alt Allele
The Genome Aggregation Database Global Study-wide 245602 G=0.99781 A=0.00219
The Genome Aggregation Database European Sub 133536 G=0.99675 A=0.00325
The Genome Aggregation Database Asian Sub 47940 G=0.9999 A=0.0001
The Genome Aggregation Database American Sub 33558 G=0.9979 A=0.0021
The Genome Aggregation Database African Sub 15260 G=0.9996 A=0.0004
The Genome Aggregation Database Ashkenazi Jewish Sub 9834 G=1.000 A=0.000
The Genome Aggregation Database Other Sub 5474 G=0.996 A=0.004
Trans-Omics for Precision Medicine Global Study-wide 125568 G=0.99709 A=0.00291
The Exome Aggregation Consortium Global Study-wide 115542 G=0.99771 A=0.00229
The Exome Aggregation Consortium Europe Sub 69702 G=0.9967 A=0.0033
The Exome Aggregation Consortium Asian Sub 23962 G=0.9998 A=0.0002
The Exome Aggregation Consortium American Sub 11080 G=0.9978 A=0.0022
The Exome Aggregation Consortium African Sub 9936 G=0.999 A=0.001
The Exome Aggregation Consortium Other Sub 862 G=1.00 A=0.00
The Genome Aggregation Database Global Study-wide 30968 G=0.9975 A=0.0025
The Genome Aggregation Database European Sub 18496 G=0.9963 A=0.0037
The Genome Aggregation Database African Sub 8728 G=1.000 A=0.000
The Genome Aggregation Database East Asian Sub 1622 G=1.000 A=0.000
The Genome Aggregation Database Other Sub 982 G=1.00 A=0.00
The Genome Aggregation Database American Sub 838 G=1.00 A=0.00
The Genome Aggregation Database Ashkenazi Jewish Sub 302 G=1.00 A=0.00
GO Exome Sequencing Project Global Study-wide 13006 G=0.9981 A=0.0019
GO Exome Sequencing Project European American Sub 8600 G=0.998 A=0.002
GO Exome Sequencing Project African American Sub 4406 G=0.999 A=0.001
1000Genomes Global Study-wide 5008 G=0.998 A=0.002
1000Genomes African Sub 1322 G=0.999 A=0.001
1000Genomes East Asian Sub 1008 G=1.000 A=0.000
1000Genomes Europe Sub 1006 G=0.994 A=0.006
1000Genomes South Asian Sub 978 G=1.00 A=0.00
1000Genomes American Sub 694 G=1.00 A=0.00
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.997 A=0.003
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.996 A=0.004
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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 Note
GRCh38.p7 chr 1 NC_000001.11:g.12004835G= NC_000001.11:g.12004835G>A
GRCh37.p13 chr 1 NC_000001.10:g.12064892G= NC_000001.10:g.12064892G>A
MFN2 RefSeqGene (LRG_255) NG_007945.1:g.29655G= NG_007945.1:g.29655G>A
MFN2 transcript variant 1 NM_014874.3:c.1403G= NM_014874.3:c.1403G>A
MFN2 transcript variant 2 NM_001127660.1:c.1403G= NM_001127660.1:c.1403G>A
MFN2 transcript variant X3 XM_005263543.3:c.1403G= XM_005263543.3:c.1403G>A
MFN2 transcript variant X1 XM_005263543.1:c.1403G= XM_005263543.1:c.1403G>A
MFN2 transcript variant X5 XM_005263548.3:c.1403G= XM_005263548.3:c.1403G>A
MFN2 transcript variant X6 XM_005263548.1:c.1403G= XM_005263548.1:c.1403G>A
MFN2 transcript variant X1 XM_005263547.3:c.1403G= XM_005263547.3:c.1403G>A
MFN2 transcript variant X5 XM_005263547.1:c.1403G= XM_005263547.1:c.1403G>A
MFN2 transcript variant X2 XM_005263545.3:c.1403G= XM_005263545.3:c.1403G>A
MFN2 transcript variant X3 XM_005263545.1:c.1403G= XM_005263545.1:c.1403G>A
mitofusin-2 NP_055689.1:p.Arg468= NP_055689.1:p.Arg468His
mitofusin-2 NP_001121132.1:p.Arg468= NP_001121132.1:p.Arg468His
mitofusin-2 isoform X1 XP_005263600.1:p.Arg468= XP_005263600.1:p.Arg468His
mitofusin-2 isoform X1 XP_005263605.1:p.Arg468= XP_005263605.1:p.Arg468His
mitofusin-2 isoform X1 XP_005263604.1:p.Arg468= XP_005263604.1:p.Arg468His
mitofusin-2 isoform X1 XP_005263602.1:p.Arg468= XP_005263602.1:p.Arg468His
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#.

8 Frequency, 33 SubSNP, 5 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss328417680 May 09, 2011 (134)
2 NHLBI-ESP ss341933707 May 09, 2011 (134)
3 1000GENOMES ss489721360 May 04, 2012 (137)
4 EXOME_CHIP ss491286345 May 04, 2012 (137)
5 NCBI-CURATED-RECORDS ss537713868 Jan 04, 2013 (137)
6 ILLUMINA ss780760515 Sep 08, 2015 (146)
7 ILLUMINA ss783439429 Sep 08, 2015 (146)
8 EVA-GONL ss974862003 Aug 21, 2014 (142)
9 1000GENOMES ss1289708192 Aug 21, 2014 (142)
10 EVA_DECODE ss1584220097 Apr 01, 2015 (144)
11 EVA_UK10K_ALSPAC ss1599560982 Apr 01, 2015 (144)
12 EVA_UK10K_TWINSUK ss1642555015 Apr 01, 2015 (144)
13 EVA_EXAC ss1685307678 Apr 01, 2015 (144)
14 EVA_MGP ss1710888602 Apr 01, 2015 (144)
15 ILLUMINA ss1751867357 Sep 08, 2015 (146)
16 ILLUMINA ss1917722776 Feb 12, 2016 (147)
17 ILLUMINA ss1945984854 Feb 12, 2016 (147)
18 ILLUMINA ss1958241941 Feb 12, 2016 (147)
19 JJLAB ss2019544913 Sep 14, 2016 (149)
20 HUMAN_LONGEVITY ss2160100170 Dec 20, 2016 (150)
21 TOPMED ss2322258455 Dec 20, 2016 (150)
22 ILLUMINA ss2710665921 Nov 08, 2017 (151)
23 GNOMAD ss2731126738 Nov 08, 2017 (151)
24 GNOMAD ss2746217343 Nov 08, 2017 (151)
25 GNOMAD ss2751693125 Nov 08, 2017 (151)
26 AFFY ss2984845488 Nov 08, 2017 (151)
27 SWEGEN ss2986306403 Nov 08, 2017 (151)
28 ILLUMINA ss3021055025 Nov 08, 2017 (151)
29 TOPMED ss3068754690 Nov 08, 2017 (151)
30 ILLUMINA ss3626027564 Jul 19, 2018 (151)
31 ILLUMINA ss3634307206 Jul 19, 2018 (151)
32 ILLUMINA ss3640014570 Jul 19, 2018 (151)
33 ILLUMINA ss3644480709 Jul 19, 2018 (151)
34 1000Genomes NC_000001.10 - 12064892 Jul 19, 2018 (151)
35 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 12064892 Jul 19, 2018 (151)
36 The Exome Aggregation Consortium NC_000001.10 - 12064892 Jul 19, 2018 (151)
37 The Genome Aggregation Database NC_000001.10 - 12064892 Jul 19, 2018 (151)
38 The Genome Aggregation Database NC_000001.10 - 12064892 Jul 19, 2018 (151)
39 GO Exome Sequencing Project NC_000001.10 - 12064892 Jul 19, 2018 (151)
40 Trans-Omics for Precision Medicine NC_000001.11 - 12004835 Jul 19, 2018 (151)
41 UK 10K study - Twins NC_000001.10 - 12064892 Jul 19, 2018 (151)
42 ClinVar RCV000002372.4 Jul 19, 2018 (151)
43 ClinVar RCV000196650.4 Jul 19, 2018 (151)
44 ClinVar RCV000229623.3 Jul 19, 2018 (151)
45 ClinVar RCV000312138.1 Jul 19, 2018 (151)
46 ClinVar RCV000487518.3 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
ss1584220097 NC_000001.9:11987478:G= NC_000001.11:12004834:G= (self)
385165, 200844, 4487332, 1092324, 141473, 19762, 200844, ss328417680, ss341933707, ss489721360, ss491286345, ss780760515, ss783439429, ss974862003, ss1289708192, ss1599560982, ss1642555015, ss1685307678, ss1710888602, ss1751867357, ss1917722776, ss1945984854, ss1958241941, ss2019544913, ss2322258455, ss2710665921, ss2731126738, ss2746217343, ss2751693125, ss2984845488, ss2986306403, ss3021055025, ss3626027564, ss3634307206, ss3640014570, ss3644480709 NC_000001.10:12064891:G= NC_000001.11:12004834:G= (self)
1911930, ss537713868, ss2160100170, ss3068754690 NC_000001.11:12004834:G= NC_000001.11:12004834:G= (self)
ss1584220097 NC_000001.9:11987478:G>A NC_000001.11:12004834:G>A (self)
385165, 200844, 4487332, 1092324, 141473, 19762, 200844, ss328417680, ss341933707, ss489721360, ss491286345, ss780760515, ss783439429, ss974862003, ss1289708192, ss1599560982, ss1642555015, ss1685307678, ss1710888602, ss1751867357, ss1917722776, ss1945984854, ss1958241941, ss2019544913, ss2322258455, ss2710665921, ss2731126738, ss2746217343, ss2751693125, ss2984845488, ss2986306403, ss3021055025, ss3626027564, ss3634307206, ss3640014570, ss3644480709 NC_000001.10:12064891:G>A NC_000001.11:12004834:G>A (self)
RCV000002372.4, RCV000196650.4, RCV000229623.3, RCV000312138.1, RCV000487518.3, 1911930, ss537713868, ss2160100170, ss3068754690 NC_000001.11:12004834:G>A NC_000001.11:12004834:G>A (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 rs138382758
PMID Title Author Year Journal
16762064 Charcot-Marie-Tooth neuropathy type 2A: novel mutations in the mitofusin 2 gene (MFN2). Engelfried K et al. 2006 BMC medical genetics
19889647 Phenotypic spectrum of MFN2 mutations in the Spanish population. Casasnovas C et al. 2010 Journal of medical genetics
20350294 MFN2 point mutations occur in 3.4% of Charcot-Marie-Tooth families. An investigation of 232 Norwegian CMT families. Braathen GJ et al. 2010 BMC medical genetics
21258814 Mutation screening of mitofusin 2 in Charcot-Marie-Tooth disease type 2. McCorquodale DS 3rd et al. 2011 Journal of neurology
21519004 Simultaneous MFN2 and GDAP1 mutations cause major mitochondrial defects in a patient with CMT. Cassereau J et al. 2011 Neurology
26392352 Application of targeted multi-gene panel testing for the diagnosis of inherited peripheral neuropathy provides a high diagnostic yield with unexpected phenotype-genotype variability. Antoniadi T et al. 2015 BMC medical genetics

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