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.
rs1478521238
Current Build 156
Released September 21, 2022
- Organism
- Homo sapiens
- Position
-
chr16:15001791 (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
- G>C
- Variation Type
- SNV Single Nucleotide Variation
- Frequency
-
None
- Clinical Significance
- Not Reported in ClinVar
- Gene : Consequence
-
PDXDC1 : Synonymous VariantLOC124900586 : Synonymous Variant
- Publications
- 0 citations
- Genomic View
- See rs on genome
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").
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.
| Sequence name | Change |
|---|---|
| GRCh38.p14 chr 16 | NC_000016.10:g.15001791G>C |
| GRCh37.p13 chr 16 | NC_000016.9:g.15095648G>C |
| GRCh38.p14 chr 16 alt locus HSCHR16_1_CTG1 | NT_187607.1:g.841138G>C |
| Molecule type | Change | Amino acid[Codon] | SO Term |
|---|---|---|---|
| PDXDC1 transcript variant 2 |
NM_001285444.2:c.162-2396… NM_001285444.2:c.162-2396G>C |
N/A | Intron Variant |
| PDXDC1 transcript variant 3 |
NM_001285445.2:c.159-2396… NM_001285445.2:c.159-2396G>C |
N/A | Intron Variant |
| PDXDC1 transcript variant 5 |
NM_001285448.1:c.116+3386… NM_001285448.1:c.116+3386G>C |
N/A | Intron Variant |
| PDXDC1 transcript variant 10 |
NM_001324021.2:c.162-2396… NM_001324021.2:c.162-2396G>C |
N/A | Intron Variant |
| PDXDC1 transcript variant 4 | NM_001285447.1:c.132G>C | V [GTG] > V [GTC] | Coding Sequence Variant |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 4 | NP_001272376.1:p.Val44= | V (Val) > V (Val) | Synonymous Variant |
| PDXDC1 transcript variant 1 | NM_015027.4:c.177G>C | V [GTG] > V [GTC] | Coding Sequence Variant |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 1 | NP_055842.2:p.Val59= | V (Val) > V (Val) | Synonymous Variant |
| PDXDC1 transcript variant 7 | NM_001285450.2:c.177G>C | V [GTG] > V [GTC] | Coding Sequence Variant |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 7 | NP_001272379.1:p.Val59= | V (Val) > V (Val) | Synonymous Variant |
| PDXDC1 transcript variant 8 | NM_001324019.2:c.174G>C | V [GTG] > V [GTC] | Coding Sequence Variant |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 8 | NP_001310948.1:p.Val58= | V (Val) > V (Val) | Synonymous Variant |
| PDXDC1 transcript variant 9 | NM_001324020.2:c.174G>C | V [GTG] > V [GTC] | Coding Sequence Variant |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 9 | NP_001310949.1:p.Val58= | V (Val) > V (Val) | Synonymous Variant |
| PDXDC1 transcript variant 6 | NM_001285449.2:c.177G>C | V [GTG] > V [GTC] | Coding Sequence Variant |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 6 | NP_001272378.1:p.Val59= | V (Val) > V (Val) | Synonymous Variant |
| PDXDC1 transcript variant X4 |
XM_006720865.3:c.117-2396… XM_006720865.3:c.117-2396G>C |
N/A | Intron Variant |
| PDXDC1 transcript variant X13 |
XM_024450197.2:c.117-2396… XM_024450197.2:c.117-2396G>C |
N/A | Intron Variant |
| PDXDC1 transcript variant X2 |
XM_047433788.1:c.117-2396… XM_047433788.1:c.117-2396G>C |
N/A | Intron Variant |
| PDXDC1 transcript variant X10 |
XM_047433790.1:c.117-2396… XM_047433790.1:c.117-2396G>C |
N/A | Intron Variant |
| PDXDC1 transcript variant X1 | XM_017023059.2:c.132G>C | V [GTG] > V [GTC] | Coding Sequence Variant |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1 | XP_016878548.1:p.Val44= | V (Val) > V (Val) | Synonymous Variant |
| PDXDC1 transcript variant X3 | XM_017023060.2:c.204G>C | V [GTG] > V [GTC] | Coding Sequence Variant |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X3 | XP_016878549.1:p.Val68= | V (Val) > V (Val) | Synonymous Variant |
| PDXDC1 transcript variant X5 | XM_017023061.3:c.132G>C | V [GTG] > V [GTC] | Coding Sequence Variant |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1 | XP_016878550.1:p.Val44= | V (Val) > V (Val) | Synonymous Variant |
| PDXDC1 transcript variant X6 | XM_017023063.2:c.132G>C | V [GTG] > V [GTC] | Coding Sequence Variant |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X4 | XP_016878552.1:p.Val44= | V (Val) > V (Val) | Synonymous Variant |
| PDXDC1 transcript variant X7 | XM_047433789.1:c.177G>C | V [GTG] > V [GTC] | Coding Sequence Variant |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X5 | XP_047289745.1:p.Val59= | V (Val) > V (Val) | Synonymous Variant |
| PDXDC1 transcript variant X8 | XM_017023065.2:c.132G>C | V [GTG] > V [GTC] | Coding Sequence Variant |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X6 | XP_016878554.1:p.Val44= | V (Val) > V (Val) | Synonymous Variant |
| PDXDC1 transcript variant X9 | XM_024450194.2:c.132G>C | V [GTG] > V [GTC] | Coding Sequence Variant |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X7 | XP_024305962.1:p.Val44= | V (Val) > V (Val) | Synonymous Variant |
| PDXDC1 transcript variant X11 | XM_024450195.2:c.132G>C | V [GTG] > V [GTC] | Coding Sequence Variant |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X6 | XP_024305963.2:p.Val44= | V (Val) > V (Val) | Synonymous Variant |
| PDXDC1 transcript variant X12 | XM_047433791.1:c.204G>C | V [GTG] > V [GTC] | Coding Sequence Variant |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X9 | XP_047289747.1:p.Val68= | V (Val) > V (Val) | Synonymous Variant |
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.
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 |
|---|---|---|
| GRCh38.p14 chr 16 | NC_000016.10:g.15001791= | NC_000016.10:g.15001791G>C |
| GRCh37.p13 chr 16 | NC_000016.9:g.15095648= | NC_000016.9:g.15095648G>C |
| GRCh38.p14 chr 16 alt locus HSCHR16_1_CTG1 | NT_187607.1:g.841138= | NT_187607.1:g.841138G>C |
| PDXDC1 transcript variant 1 | NM_015027.4:c.177= | NM_015027.4:c.177G>C |
| PDXDC1 transcript variant 1 | NM_015027.3:c.177= | NM_015027.3:c.177G>C |
| PDXDC1 transcript | NM_015027.2:c.177= | NM_015027.2:c.177G>C |
| PDXDC1 transcript variant X6 | XM_017023063.2:c.132= | XM_017023063.2:c.132G>C |
| PDXDC1 transcript variant X8 | XM_017023063.1:c.132= | XM_017023063.1:c.132G>C |
| PDXDC1 transcript variant 7 | NM_001285450.2:c.177= | NM_001285450.2:c.177G>C |
| PDXDC1 transcript variant 7 | NM_001285450.1:c.177= | NM_001285450.1:c.177G>C |
| PDXDC1 transcript variant 6 | NM_001285449.2:c.177= | NM_001285449.2:c.177G>C |
| PDXDC1 transcript variant 6 | NM_001285449.1:c.177= | NM_001285449.1:c.177G>C |
| PDXDC1 transcript variant 9 | NM_001324020.2:c.174= | NM_001324020.2:c.174G>C |
| PDXDC1 transcript variant 9 | NM_001324020.1:c.174= | NM_001324020.1:c.174G>C |
| PDXDC1 transcript variant X8 | XM_017023065.2:c.132= | XM_017023065.2:c.132G>C |
| PDXDC1 transcript variant X10 | XM_017023065.1:c.132= | XM_017023065.1:c.132G>C |
| PDXDC1 transcript variant X11 | XM_024450195.2:c.132= | XM_024450195.2:c.132G>C |
| PDXDC1 transcript variant X12 | XM_024450195.1:c.231= | XM_024450195.1:c.231G>C |
| PDXDC1 transcript variant X9 | XM_024450194.2:c.132= | XM_024450194.2:c.132G>C |
| PDXDC1 transcript variant X11 | XM_024450194.1:c.132= | XM_024450194.1:c.132G>C |
| PDXDC1 transcript variant X7 | XM_047433789.1:c.177= | XM_047433789.1:c.177G>C |
| PDXDC1 transcript variant 8 | NM_001324019.2:c.174= | NM_001324019.2:c.174G>C |
| PDXDC1 transcript variant 8 | NM_001324019.1:c.174= | NM_001324019.1:c.174G>C |
| PDXDC1 transcript variant X5 | XM_017023061.3:c.132= | XM_017023061.3:c.132G>C |
| PDXDC1 transcript variant X6 | XM_017023061.2:c.132= | XM_017023061.2:c.132G>C |
| PDXDC1 transcript variant X6 | XM_017023061.1:c.132= | XM_017023061.1:c.132G>C |
| PDXDC1 transcript variant X1 | XM_017023059.2:c.132= | XM_017023059.2:c.132G>C |
| PDXDC1 transcript variant X1 | XM_017023059.1:c.132= | XM_017023059.1:c.132G>C |
| PDXDC1 transcript variant X3 | XM_017023060.2:c.204= | XM_017023060.2:c.204G>C |
| PDXDC1 transcript variant X3 | XM_017023060.1:c.204= | XM_017023060.1:c.204G>C |
| PDXDC1 transcript variant X12 | XM_047433791.1:c.204= | XM_047433791.1:c.204G>C |
| PDXDC1 transcript variant 4 | NM_001285447.1:c.132= | NM_001285447.1:c.132G>C |
| LOC124900586 transcript variant X1 | XM_047442849.1:c.231= | XM_047442849.1:c.231G>C |
| LOC124900586 transcript variant X18 | XM_047442865.1:c.177= | XM_047442865.1:c.177G>C |
| LOC124900586 transcript variant X12 | XM_047442859.1:c.231= | XM_047442859.1:c.231G>C |
| LOC124900586 transcript variant X17 | XM_047442864.1:c.231= | XM_047442864.1:c.231G>C |
| LOC124900586 transcript variant X3 | XM_047442851.1:c.204= | XM_047442851.1:c.204G>C |
| LOC124900586 transcript variant X5 | XM_047442853.1:c.177= | XM_047442853.1:c.177G>C |
| LOC124900586 transcript variant X10 | XM_047442857.1:c.132= | XM_047442857.1:c.132G>C |
| LOC124900586 transcript variant X2 | XM_047442850.1:c.219= | XM_047442850.1:c.219G>C |
| LOC124900586 transcript variant X15 | XM_047442862.1:c.204= | XM_047442862.1:c.204G>C |
| LOC124900586 transcript variant X16 | XM_047442863.1:c.204= | XM_047442863.1:c.204G>C |
| LOC124900586 transcript variant X19 | XM_047442866.1:c.177= | XM_047442866.1:c.177G>C |
| LOC124900586 transcript variant X6 | XM_047442854.1:c.132= | XM_047442854.1:c.132G>C |
| LOC124900586 transcript variant X4 | XM_047442852.1:c.132= | XM_047442852.1:c.132G>C |
| LOC124900586 transcript variant X13 | XM_047442860.1:c.219= | XM_047442860.1:c.219G>C |
| LOC124900586 transcript variant X7 | XR_007068665.1:n.306= | XR_007068665.1:n.306G>C |
| LOC124900586 transcript variant X20 | XM_047442867.1:c.177= | XM_047442867.1:c.177G>C |
| LOC124900586 transcript variant X9 | XM_047442856.1:c.132= | XM_047442856.1:c.132G>C |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 1 | NP_055842.2:p.Val59= | NP_055842.2:p.Val59= |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X4 | XP_016878552.1:p.Val44= | XP_016878552.1:p.Val44= |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 7 | NP_001272379.1:p.Val59= | NP_001272379.1:p.Val59= |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 6 | NP_001272378.1:p.Val59= | NP_001272378.1:p.Val59= |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 9 | NP_001310949.1:p.Val58= | NP_001310949.1:p.Val58= |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X6 | XP_016878554.1:p.Val44= | XP_016878554.1:p.Val44= |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X6 | XP_024305963.2:p.Val44= | XP_024305963.2:p.Val44= |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X7 | XP_024305962.1:p.Val44= | XP_024305962.1:p.Val44= |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X5 | XP_047289745.1:p.Val59= | XP_047289745.1:p.Val59= |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 8 | NP_001310948.1:p.Val58= | NP_001310948.1:p.Val58= |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1 | XP_016878550.1:p.Val44= | XP_016878550.1:p.Val44= |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1 | XP_016878548.1:p.Val44= | XP_016878548.1:p.Val44= |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X3 | XP_016878549.1:p.Val68= | XP_016878549.1:p.Val68= |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X9 | XP_047289747.1:p.Val68= | XP_047289747.1:p.Val68= |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 4 | NP_001272376.1:p.Val44= | NP_001272376.1:p.Val44= |
| PDXDC1 transcript variant 2 | NM_001285444.2:c.162-2396= | NM_001285444.2:c.162-2396G>C |
| PDXDC1 transcript variant 3 | NM_001285445.2:c.159-2396= | NM_001285445.2:c.159-2396G>C |
| PDXDC1 transcript variant 5 | NM_001285448.1:c.116+3386= | NM_001285448.1:c.116+3386G>C |
| PDXDC1 transcript variant 10 | NM_001324021.2:c.162-2396= | NM_001324021.2:c.162-2396G>C |
| PDXDC1 transcript variant X6 | XM_005255178.1:c.186-2396= | XM_005255178.1:c.186-2396G>C |
| PDXDC1 transcript variant X7 | XM_005255179.1:c.162-2396= | XM_005255179.1:c.162-2396G>C |
| PDXDC1 transcript variant X8 | XM_005255180.1:c.159-2396= | XM_005255180.1:c.159-2396G>C |
| PDXDC1 transcript variant X9 | XM_005255181.1:c.116+3386= | XM_005255181.1:c.116+3386G>C |
| PDXDC1 transcript variant X4 | XM_006720865.3:c.117-2396= | XM_006720865.3:c.117-2396G>C |
| PDXDC1 transcript variant X13 | XM_024450197.2:c.117-2396= | XM_024450197.2:c.117-2396G>C |
| PDXDC1 transcript variant X2 | XM_047433788.1:c.117-2396= | XM_047433788.1:c.117-2396G>C |
| PDXDC1 transcript variant X10 | XM_047433790.1:c.117-2396= | XM_047433790.1:c.117-2396G>C |
| LOC124900586 transcript variant X8 | XM_047442855.1:c.117-2396= | XM_047442855.1:c.117-2396G>C |
| LOC124900586 transcript variant X11 | XM_047442858.1:c.189-2396= | XM_047442858.1:c.189-2396G>C |
| LOC124900586 transcript variant X14 | XM_047442861.1:c.162-2396= | XM_047442861.1:c.162-2396G>C |
| LOC124900586 transcript variant X21 | XM_047442868.1:c.162-2396= | XM_047442868.1:c.162-2396G>C |
| LOC124900586 transcript variant X22 | XM_047442869.1:c.162-2396= | XM_047442869.1:c.162-2396G>C |
| LOC124900586 transcript variant X23 | XM_047442870.1:c.162-2396= | XM_047442870.1:c.162-2396G>C |
| putative pyridoxal-dependent decarboxylase domain-containing protein 2 isoform X1 | XP_047298805.1:p.Val77= | XP_047298805.1:p.Val77= |
| putative pyridoxal-dependent decarboxylase domain-containing protein 2 isoform X2 | XP_047298806.1:p.Val73= | XP_047298806.1:p.Val73= |
| putative pyridoxal-dependent decarboxylase domain-containing protein 2 isoform X3 | XP_047298807.1:p.Val68= | XP_047298807.1:p.Val68= |
| putative pyridoxal-dependent decarboxylase domain-containing protein 2 isoform X4 | XP_047298808.1:p.Val44= | XP_047298808.1:p.Val44= |
| putative pyridoxal-dependent decarboxylase domain-containing protein 2 isoform X5 | XP_047298809.1:p.Val59= | XP_047298809.1:p.Val59= |
| putative pyridoxal-dependent decarboxylase domain-containing protein 2 isoform X6 | XP_047298810.1:p.Val44= | XP_047298810.1:p.Val44= |
| pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X8 | XP_047298812.1:p.Val44= | XP_047298812.1:p.Val44= |
| putative pyridoxal-dependent decarboxylase domain-containing protein 2 isoform X9 | XP_047298813.1:p.Val44= | XP_047298813.1:p.Val44= |
| putative pyridoxal-dependent decarboxylase domain-containing protein 2 isoform X11 | XP_047298815.1:p.Val77= | XP_047298815.1:p.Val77= |
| putative pyridoxal-dependent decarboxylase domain-containing protein 2 isoform X12 | XP_047298816.1:p.Val73= | XP_047298816.1:p.Val73= |
| putative pyridoxal-dependent decarboxylase domain-containing protein 2 isoform X14 | XP_047298818.1:p.Val68= | XP_047298818.1:p.Val68= |
| putative pyridoxal-dependent decarboxylase domain-containing protein 2 isoform X15 | XP_047298819.1:p.Val68= | XP_047298819.1:p.Val68= |
| putative pyridoxal-dependent decarboxylase domain-containing protein 2 isoform X16 | XP_047298820.1:p.Val77= | XP_047298820.1:p.Val77= |
| putative pyridoxal-dependent decarboxylase domain-containing protein 2 isoform X17 | XP_047298821.1:p.Val59= | XP_047298821.1:p.Val59= |
| putative pyridoxal-dependent decarboxylase domain-containing protein 2 isoform X18 | XP_047298822.1:p.Val59= | XP_047298822.1:p.Val59= |
| putative pyridoxal-dependent decarboxylase domain-containing protein 2 isoform X19 | XP_047298823.1:p.Val59= | XP_047298823.1:p.Val59= |
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#.
| No | Submitter | Submission ID | Date (Build) |
|---|---|---|---|
| 1 | GNOMAD | ss2741771381 | Nov 08, 2017 (151) |
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).
Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.
No publications for rs1478521238
The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.
Genomic regions, transcripts, and products
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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.
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.