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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.

rs398123091

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr17:7221993 (GRCh38.p13) 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
A=0.000019 (5/264690, TOPMED)
A=0.000007 (1/140152, GnomAD)
A=0.00004 (1/23038, ALFA)
Clinical Significance
Reported in ClinVar
Gene : Consequence
ACADVL : Missense Variant
DLG4 : 2KB Upstream Variant
Publications
7 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.p13 chr 17 NC_000017.11:g.7221993G>A
GRCh38.p13 chr 17 NC_000017.11:g.7221993G>C
GRCh37.p13 chr 17 NC_000017.10:g.7125312G>A
GRCh37.p13 chr 17 NC_000017.10:g.7125312G>C
DLG4 RefSeqGene NG_008391.2:g.3058C>T
DLG4 RefSeqGene NG_008391.2:g.3058C>G
ACADVL RefSeqGene NG_007975.1:g.7160G>A
ACADVL RefSeqGene NG_007975.1:g.7160G>C
Gene: DLG4, discs large MAGUK scaffold protein 4 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
DLG4 transcript variant 3 NM_001321074.1:c. N/A Upstream Transcript Variant
DLG4 transcript variant 1 NM_001365.4:c. N/A Upstream Transcript Variant
DLG4 transcript variant 2 NM_001128827.4:c. N/A N/A
DLG4 transcript variant 4 NM_001321075.3:c. N/A N/A
DLG4 transcript variant 5 NM_001321076.3:c. N/A N/A
DLG4 transcript variant 6 NM_001321077.3:c. N/A N/A
DLG4 transcript variant 8 NM_001369566.3:c. N/A N/A
DLG4 transcript variant 7 NR_135527.1:n. N/A Upstream Transcript Variant
DLG4 transcript variant X2 XM_005256491.1:c. N/A N/A
DLG4 transcript variant X1 XM_011523699.2:c. N/A N/A
DLG4 transcript variant X8 XM_011523702.1:c. N/A N/A
DLG4 transcript variant X4 XM_017024288.2:c. N/A N/A
DLG4 transcript variant X5 XM_017024289.2:c. N/A N/A
DLG4 transcript variant X3 XM_024450629.1:c. N/A N/A
DLG4 transcript variant X7 XR_934005.2:n. N/A N/A
Gene: ACADVL, acyl-CoA dehydrogenase very long chain (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ACADVL transcript variant 1 NM_000018.4:c.664G>A G [GGG] > R [AGG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 1 precursor NP_000009.1:p.Gly222Arg G (Gly) > R (Arg) Missense Variant
ACADVL transcript variant 1 NM_000018.4:c.664G>C G [GGG] > R [CGG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 1 precursor NP_000009.1:p.Gly222Arg G (Gly) > R (Arg) Missense Variant
ACADVL transcript variant 2 NM_001033859.3:c.598G>A G [GGG] > R [AGG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 2 precursor NP_001029031.1:p.Gly200Arg G (Gly) > R (Arg) Missense Variant
ACADVL transcript variant 2 NM_001033859.3:c.598G>C G [GGG] > R [CGG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 2 precursor NP_001029031.1:p.Gly200Arg G (Gly) > R (Arg) Missense Variant
ACADVL transcript variant 4 NM_001270448.2:c.436G>A G [GGG] > R [AGG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 4 NP_001257377.1:p.Gly146Arg G (Gly) > R (Arg) Missense Variant
ACADVL transcript variant 4 NM_001270448.2:c.436G>C G [GGG] > R [CGG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 4 NP_001257377.1:p.Gly146Arg G (Gly) > R (Arg) Missense Variant
ACADVL transcript variant 3 NM_001270447.2:c.733G>A G [GGG] > R [AGG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 3 NP_001257376.1:p.Gly245Arg G (Gly) > R (Arg) Missense Variant
ACADVL transcript variant 3 NM_001270447.2:c.733G>C G [GGG] > R [CGG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 3 NP_001257376.1:p.Gly245Arg G (Gly) > R (Arg) Missense Variant
ACADVL transcript variant X1 XM_006721516.3:c.664G>A G [GGG] > R [AGG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X1 XP_006721579.2:p.Gly222Arg G (Gly) > R (Arg) Missense Variant
ACADVL transcript variant X1 XM_006721516.3:c.664G>C G [GGG] > R [CGG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X1 XP_006721579.2:p.Gly222Arg G (Gly) > R (Arg) Missense Variant
ACADVL transcript variant X2 XM_024450741.1:c.664G>A G [GGG] > R [AGG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X2 XP_024306509.1:p.Gly222Arg G (Gly) > R (Arg) Missense Variant
ACADVL transcript variant X2 XM_024450741.1:c.664G>C G [GGG] > R [CGG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X2 XP_024306509.1:p.Gly222Arg G (Gly) > R (Arg) Missense Variant
ACADVL transcript variant X3 XM_011523829.2:c.664G>A G [GGG] > R [AGG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X3 XP_011522131.1:p.Gly222Arg G (Gly) > R (Arg) Missense Variant
ACADVL transcript variant X3 XM_011523829.2:c.664G>C G [GGG] > R [CGG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X3 XP_011522131.1:p.Gly222Arg G (Gly) > R (Arg) Missense Variant
ACADVL transcript variant X4 XM_011523830.2:c.664G>A G [GGG] > R [AGG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X4 XP_011522132.1:p.Gly222Arg G (Gly) > R (Arg) Missense Variant
ACADVL transcript variant X4 XM_011523830.2:c.664G>C G [GGG] > R [CGG] Coding Sequence Variant
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X4 XP_011522132.1:p.Gly222Arg G (Gly) > R (Arg) Missense Variant
ACADVL transcript variant X5 XR_934021.2:n.723G>A N/A Non Coding Transcript Variant
ACADVL transcript variant X5 XR_934021.2:n.723G>C N/A Non Coding Transcript Variant
ACADVL transcript variant X6 XR_934022.2:n.723G>A N/A Non Coding Transcript Variant
ACADVL transcript variant X6 XR_934022.2:n.723G>C N/A Non Coding Transcript Variant
ACADVL transcript variant X7 XR_934023.2:n.723G>A N/A Non Coding Transcript Variant
ACADVL transcript variant X7 XR_934023.2:n.723G>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.

Allele: A (allele ID: 98200 )
ClinVar Accession Disease Names Clinical Significance
RCV000077922.7 not provided Likely-Pathogenic
RCV000169301.4 Very long chain acyl-CoA dehydrogenase deficiency Pathogenic-Likely-Pathogenic

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 23038 G=0.99996 A=0.00004, C=0.00000
European Sub 15752 G=1.00000 A=0.00000, C=0.00000
African Sub 3492 G=1.0000 A=0.0000, C=0.0000
African Others Sub 122 G=1.000 A=0.000, C=0.000
African American Sub 3370 G=1.0000 A=0.0000, C=0.0000
Asian Sub 168 G=1.000 A=0.000, C=0.000
East Asian Sub 112 G=1.000 A=0.000, C=0.000
Other Asian Sub 56 G=1.00 A=0.00, C=0.00
Latin American 1 Sub 146 G=1.000 A=0.000, C=0.000
Latin American 2 Sub 610 G=1.000 A=0.000, C=0.000
South Asian Sub 98 G=1.00 A=0.00, C=0.00
Other Sub 2772 G=0.9996 A=0.0004, C=0.0000


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 G=0.999981 A=0.000019
gnomAD - Genomes Global Study-wide 140152 G=0.999993 A=0.000007
gnomAD - Genomes European Sub 75924 G=1.00000 A=0.00000
gnomAD - Genomes African Sub 41986 G=1.00000 A=0.00000
gnomAD - Genomes American Sub 13648 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3318 G=0.9997 A=0.0003
gnomAD - Genomes East Asian Sub 3128 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2148 G=1.0000 A=0.0000
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
GRCh38.p13 chr 17 NC_000017.11:g.7221993= NC_000017.11:g.7221993G>A NC_000017.11:g.7221993G>C
GRCh37.p13 chr 17 NC_000017.10:g.7125312= NC_000017.10:g.7125312G>A NC_000017.10:g.7125312G>C
DLG4 RefSeqGene NG_008391.2:g.3058= NG_008391.2:g.3058C>T NG_008391.2:g.3058C>G
ACADVL RefSeqGene NG_007975.1:g.7160= NG_007975.1:g.7160G>A NG_007975.1:g.7160G>C
ACADVL transcript variant 1 NM_000018.4:c.664= NM_000018.4:c.664G>A NM_000018.4:c.664G>C
ACADVL transcript variant 1 NM_000018.3:c.664= NM_000018.3:c.664G>A NM_000018.3:c.664G>C
ACADVL transcript variant 2 NM_001033859.3:c.598= NM_001033859.3:c.598G>A NM_001033859.3:c.598G>C
ACADVL transcript variant 2 NM_001033859.2:c.598= NM_001033859.2:c.598G>A NM_001033859.2:c.598G>C
ACADVL transcript variant 4 NM_001270448.2:c.436= NM_001270448.2:c.436G>A NM_001270448.2:c.436G>C
ACADVL transcript variant 4 NM_001270448.1:c.436= NM_001270448.1:c.436G>A NM_001270448.1:c.436G>C
ACADVL transcript variant 3 NM_001270447.2:c.733= NM_001270447.2:c.733G>A NM_001270447.2:c.733G>C
ACADVL transcript variant 3 NM_001270447.1:c.733= NM_001270447.1:c.733G>A NM_001270447.1:c.733G>C
ACADVL transcript variant X1 XM_006721516.3:c.664= XM_006721516.3:c.664G>A XM_006721516.3:c.664G>C
ACADVL transcript variant X5 XR_934021.2:n.723= XR_934021.2:n.723G>A XR_934021.2:n.723G>C
ACADVL transcript variant X7 XR_934023.2:n.723= XR_934023.2:n.723G>A XR_934023.2:n.723G>C
ACADVL transcript variant X3 XM_011523829.2:c.664= XM_011523829.2:c.664G>A XM_011523829.2:c.664G>C
ACADVL transcript variant X6 XR_934022.2:n.723= XR_934022.2:n.723G>A XR_934022.2:n.723G>C
ACADVL transcript variant X4 XM_011523830.2:c.664= XM_011523830.2:c.664G>A XM_011523830.2:c.664G>C
ACADVL transcript variant X2 XM_024450741.1:c.664= XM_024450741.1:c.664G>A XM_024450741.1:c.664G>C
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 1 precursor NP_000009.1:p.Gly222= NP_000009.1:p.Gly222Arg NP_000009.1:p.Gly222Arg
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 2 precursor NP_001029031.1:p.Gly200= NP_001029031.1:p.Gly200Arg NP_001029031.1:p.Gly200Arg
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 4 NP_001257377.1:p.Gly146= NP_001257377.1:p.Gly146Arg NP_001257377.1:p.Gly146Arg
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 3 NP_001257376.1:p.Gly245= NP_001257376.1:p.Gly245Arg NP_001257376.1:p.Gly245Arg
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X1 XP_006721579.2:p.Gly222= XP_006721579.2:p.Gly222Arg XP_006721579.2:p.Gly222Arg
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X3 XP_011522131.1:p.Gly222= XP_011522131.1:p.Gly222Arg XP_011522131.1:p.Gly222Arg
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X4 XP_011522132.1:p.Gly222= XP_011522132.1:p.Gly222Arg XP_011522132.1:p.Gly222Arg
very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform X2 XP_024306509.1:p.Gly222= XP_024306509.1:p.Gly222Arg XP_024306509.1:p.Gly222Arg
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#.

5 SubSNP, 5 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EGL ss947846749 Jan 23, 2014 (138)
2 GNOMAD ss2742385654 Nov 08, 2017 (151)
3 TOPMED ss3256594219 Nov 08, 2017 (151)
4 GNOMAD ss4307501969 Apr 27, 2021 (155)
5 TOPMED ss5028550400 Apr 27, 2021 (155)
6 gnomAD - Genomes NC_000017.11 - 7221993 Apr 27, 2021 (155)
7 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 11683090 (NC_000017.10:7125311:G:G 251381/251384, NC_000017.10:7125311:G:A 3/251384)
Row 11683091 (NC_000017.10:7125311:G:G 251383/251384, NC_000017.10:7125311:G:C 1/251384)

- Jul 13, 2019 (153)
8 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 11683090 (NC_000017.10:7125311:G:G 251381/251384, NC_000017.10:7125311:G:A 3/251384)
Row 11683091 (NC_000017.10:7125311:G:G 251383/251384, NC_000017.10:7125311:G:C 1/251384)

- Jul 13, 2019 (153)
9 TopMed NC_000017.11 - 7221993 Apr 27, 2021 (155)
10 ALFA NC_000017.11 - 7221993 Apr 27, 2021 (155)
11 ClinVar RCV000077922.7 Jul 13, 2019 (153)
12 ClinVar RCV000169301.4 Apr 27, 2021 (155)
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
ss2742385654 NC_000017.10:7125311:G:A NC_000017.11:7221992:G:A (self)
RCV000077922.7, RCV000169301.4, 500716053, 152330434, 244096062, 10243923657, ss947846749, ss3256594219, ss4307501969, ss5028550400 NC_000017.11:7221992:G:A NC_000017.11:7221992:G:A (self)
ss2742385654 NC_000017.10:7125311:G:C NC_000017.11:7221992:G:C (self)
10243923657 NC_000017.11:7221992:G:C NC_000017.11:7221992:G:C
Help

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

7 citations for rs398123091
PMID Title Author Year Journal
16443431 Rhabdomyolysis caused by an inherited metabolic disease: very long-chain acyl-CoA dehydrogenase deficiency. Voermans NC et al. 2006 The American journal of medicine
20060901 Compared effects of missense mutations in Very-Long-Chain Acyl-CoA Dehydrogenase deficiency: Combined analysis by structural, functional and pharmacological approaches. Gobin-Limballe S et al. 2010 Biochimica et biophysica acta
21378393 Exposure to resveratrol triggers pharmacological correction of fatty acid utilization in human fatty acid oxidation-deficient fibroblasts. Bastin J et al. 2011 Human molecular genetics
23757202 Free the data: one laboratory's approach to knowledge-based genomic variant classification and preparation for EMR integration of genomic data. Bean LJ et al. 2013 Human mutation
24801231 Clinical features and mutations in seven Chinese patients with very long chain acyl-CoA dehydrogenase deficiency. Zhang RN et al. 2014 World journal of pediatrics
24898617 Stilbenes and resveratrol metabolites improve mitochondrial fatty acid oxidation defects in human fibroblasts. Aires V et al. 2014 Orphanet journal of rare diseases
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
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.post596+ae089ad