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.
rs5030850
Current Build 156
Released September 21, 2022
- Organism
- Homo sapiens
- Position
-
chr12:102852876 (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>A / G>C
- Variation Type
- SNV Single Nucleotide Variation
- Frequency
-
A=0.000038 (10/264690, TOPMED)A=0.000014 (2/140168, GnomAD)A=0.000008 (1/121376, ExAC) (+ 2 more)
- Clinical Significance
- Reported in ClinVar
- Gene : Consequence
- PAH : Stop Gained
- Publications
- 21 citations
- Genomic View
- See rs on genome
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.
| Population | Group | Sample Size | Ref Allele | Alt Allele |
|---|---|---|---|---|
| Total | Global | 65852 | G=0.99995 | A=0.00005 |
| European | Sub | 59104 | G=0.99995 | A=0.00005 |
| African | Sub | 3868 | G=1.0000 | A=0.0000 |
| African Others | Sub | 132 | G=1.000 | A=0.000 |
| African American | Sub | 3736 | G=1.0000 | A=0.0000 |
| Asian | Sub | 414 | G=1.000 | A=0.000 |
| East Asian | Sub | 356 | G=1.000 | A=0.000 |
| Other Asian | Sub | 58 | G=1.00 | A=0.00 |
| Latin American 1 | Sub | 194 | G=1.000 | A=0.000 |
| Latin American 2 | Sub | 870 | G=1.000 | A=0.000 |
| South Asian | Sub | 132 | G=1.000 | A=0.000 |
| Other | Sub | 1270 | G=1.0000 | A=0.0000 |
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=0.999962 | A=0.000038 |
| gnomAD - Genomes | Global | Study-wide | 140168 | G=0.999986 | A=0.000014 |
| gnomAD - Genomes | European | Sub | 75904 | G=0.99999 | A=0.00001 |
| gnomAD - Genomes | African | Sub | 42020 | G=0.99998 | A=0.00002 |
| gnomAD - Genomes | American | Sub | 13634 | G=1.00000 | A=0.00000 |
| gnomAD - Genomes | Ashkenazi Jewish | Sub | 3322 | G=1.0000 | A=0.0000 |
| gnomAD - Genomes | East Asian | Sub | 3134 | G=1.0000 | A=0.0000 |
| gnomAD - Genomes | Other | Sub | 2154 | G=1.0000 | A=0.0000 |
| ExAC | Global | Study-wide | 121376 | G=0.999992 | A=0.000008 |
| ExAC | Europe | Sub | 73344 | G=0.99999 | A=0.00001 |
| ExAC | Asian | Sub | 25164 | G=1.00000 | A=0.00000 |
| ExAC | American | Sub | 11556 | G=1.00000 | A=0.00000 |
| ExAC | African | Sub | 10404 | G=1.00000 | A=0.00000 |
| ExAC | Other | Sub | 908 | G=1.000 | A=0.000 |
| Allele Frequency Aggregator | Total | Global | 65852 | G=0.99995 | A=0.00005 |
| Allele Frequency Aggregator | European | Sub | 59104 | G=0.99995 | A=0.00005 |
| Allele Frequency Aggregator | African | Sub | 3868 | G=1.0000 | A=0.0000 |
| Allele Frequency Aggregator | Other | Sub | 1270 | G=1.0000 | A=0.0000 |
| Allele Frequency Aggregator | Latin American 2 | Sub | 870 | G=1.000 | A=0.000 |
| Allele Frequency Aggregator | Asian | Sub | 414 | G=1.000 | A=0.000 |
| Allele Frequency Aggregator | Latin American 1 | Sub | 194 | G=1.000 | A=0.000 |
| Allele Frequency Aggregator | South Asian | Sub | 132 | G=1.000 | A=0.000 |
| Ancient Sardinia genome-wide 1240k capture data generation and analysis | Global | Study-wide | 100 | G=1.00 | A=0.00 |
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 12 | NC_000012.12:g.102852876G>A |
| GRCh38.p14 chr 12 | NC_000012.12:g.102852876G>C |
| GRCh37.p13 chr 12 | NC_000012.11:g.103246654G>A |
| GRCh37.p13 chr 12 | NC_000012.11:g.103246654G>C |
| PAH RefSeqGene | NG_008690.2:g.110535C>T |
| PAH RefSeqGene | NG_008690.2:g.110535C>G |
| Molecule type | Change | Amino acid[Codon] | SO Term |
|---|---|---|---|
| PAH transcript variant 1 | NM_000277.3:c.781C>T | R [CGA] > * [TGA] | Coding Sequence Variant |
| phenylalanine-4-hydroxylase | NP_000268.1:p.Arg261Ter | R (Arg) > * (Ter) | Stop Gained |
| PAH transcript variant 1 | NM_000277.3:c.781C>G | R [CGA] > G [GGA] | Coding Sequence Variant |
| phenylalanine-4-hydroxylase | NP_000268.1:p.Arg261Gly | R (Arg) > G (Gly) | Missense Variant |
| PAH transcript variant 2 | NM_001354304.2:c.781C>T | R [CGA] > * [TGA] | Coding Sequence Variant |
| phenylalanine-4-hydroxylase | NP_001341233.1:p.Arg261Ter | R (Arg) > * (Ter) | Stop Gained |
| PAH transcript variant 2 | NM_001354304.2:c.781C>G | R [CGA] > G [GGA] | Coding Sequence Variant |
| phenylalanine-4-hydroxylase | NP_001341233.1:p.Arg261Gly | R (Arg) > G (Gly) | Missense Variant |
| PAH transcript variant X1 | XM_017019370.2:c. | N/A | Genic Downstream Transcript 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.
| ClinVar Accession | Disease Names | Clinical Significance |
|---|---|---|
| RCV000000641.26 | Phenylketonuria | Pathogenic |
| RCV000089090.14 | not provided | Pathogenic |
| ClinVar Accession | Disease Names | Clinical Significance |
|---|---|---|
| RCV000119826.2 | Phenylketonuria | Uncertain-Significance |
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.p14 chr 12 | NC_000012.12:g.102852876= | NC_000012.12:g.102852876G>A | NC_000012.12:g.102852876G>C |
| GRCh37.p13 chr 12 | NC_000012.11:g.103246654= | NC_000012.11:g.103246654G>A | NC_000012.11:g.103246654G>C |
| PAH RefSeqGene | NG_008690.2:g.110535= | NG_008690.2:g.110535C>T | NG_008690.2:g.110535C>G |
| PAH transcript variant 1 | NM_000277.3:c.781= | NM_000277.3:c.781C>T | NM_000277.3:c.781C>G |
| PAH transcript variant 1 | NM_000277.2:c.781= | NM_000277.2:c.781C>T | NM_000277.2:c.781C>G |
| PAH transcript | NM_000277.1:c.781= | NM_000277.1:c.781C>T | NM_000277.1:c.781C>G |
| PAH transcript variant 2 | NM_001354304.2:c.781= | NM_001354304.2:c.781C>T | NM_001354304.2:c.781C>G |
| PAH transcript variant 2 | NM_001354304.1:c.781= | NM_001354304.1:c.781C>T | NM_001354304.1:c.781C>G |
| phenylalanine-4-hydroxylase | NP_000268.1:p.Arg261= | NP_000268.1:p.Arg261Ter | NP_000268.1:p.Arg261Gly |
| phenylalanine-4-hydroxylase | NP_001341233.1:p.Arg261= | NP_001341233.1:p.Arg261Ter | NP_001341233.1:p.Arg261Gly |
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 | HGBASE | ss7986017 | Mar 31, 2003 (113) |
| 2 | ILLUMINA | ss161109670 | Dec 01, 2009 (131) |
| 3 | OMICIA | ss244239168 | Aug 29, 2012 (137) |
| 4 | OMIM-CURATED-RECORDS | ss252841346 | Aug 10, 2010 (132) |
| 5 | ILLUMINA | ss482077443 | May 04, 2012 (137) |
| 6 | ILLUMINA | ss483026543 | Sep 08, 2015 (146) |
| 7 | ILLUMINA | ss485814930 | May 04, 2012 (137) |
| 8 | ILLUMINA | ss485827537 | May 04, 2012 (137) |
| 9 | PAHDB_MCGILL | ss503928246 | Apr 03, 2012 (136) |
| 10 | ILLUMINA | ss537652912 | Sep 08, 2015 (146) |
| 11 | NGERE-U954 | ss647514556 | Dec 10, 2012 (137) |
| 12 | ILLUMINA | ss778654304 | Aug 21, 2014 (142) |
| 13 | ILLUMINA | ss783353308 | Aug 21, 2014 (142) |
| 14 | ILLUMINA | ss784304428 | Aug 21, 2014 (142) |
| 15 | ILLUMINA | ss832615376 | Apr 01, 2015 (144) |
| 16 | ILLUMINA | ss834112173 | Aug 21, 2014 (142) |
| 17 | EVA_EXAC | ss1691072553 | Apr 01, 2015 (144) |
| 18 | ILLUMINA | ss1752042940 | Sep 08, 2015 (146) |
| 19 | HUMAN_LONGEVITY | ss2192723689 | Dec 20, 2016 (150) |
| 20 | ILLUMINA | ss2633001316 | Nov 08, 2017 (151) |
| 21 | GNOMAD | ss2740077143 | Nov 08, 2017 (151) |
| 22 | GNOMAD | ss2748943635 | Nov 08, 2017 (151) |
| 23 | GNOMAD | ss2914552665 | Nov 08, 2017 (151) |
| 24 | ILLUMINA | ss3626954918 | Oct 12, 2018 (152) |
| 25 | ILLUMINA | ss3631008158 | Oct 12, 2018 (152) |
| 26 | ILLUMINA | ss3633032208 | Oct 12, 2018 (152) |
| 27 | ILLUMINA | ss3633733627 | Oct 12, 2018 (152) |
| 28 | ILLUMINA | ss3634520727 | Oct 12, 2018 (152) |
| 29 | ILLUMINA | ss3635424137 | Oct 12, 2018 (152) |
| 30 | ILLUMINA | ss3636206806 | Oct 12, 2018 (152) |
| 31 | ILLUMINA | ss3637175136 | Oct 12, 2018 (152) |
| 32 | ILLUMINA | ss3640228060 | Oct 12, 2018 (152) |
| 33 | ILLUMINA | ss3725352001 | Jul 13, 2019 (153) |
| 34 | ILLUMINA | ss3744821532 | Jul 13, 2019 (153) |
| 35 | ILLUMINA | ss3772320771 | Jul 13, 2019 (153) |
| 36 | EVA | ss3985610981 | Apr 26, 2021 (155) |
| 37 | TOPMED | ss4930848738 | Apr 26, 2021 (155) |
| 38 | EVA | ss5237517558 | Apr 26, 2021 (155) |
| 39 | HUGCELL_USP | ss5486661812 | Oct 16, 2022 (156) |
| 40 | EVA | ss5847681363 | Oct 16, 2022 (156) |
| 41 | EVA | ss5979402103 | Oct 16, 2022 (156) |
| 42 | ExAC | NC_000012.11 - 103246654 | Oct 12, 2018 (152) |
| 43 | gnomAD - Genomes | NC_000012.12 - 102852876 | Apr 26, 2021 (155) |
| 44 |
gnomAD - Exomes
Submission ignored due to conflicting rows: |
- | Jul 13, 2019 (153) |
| 45 |
gnomAD - Exomes
Submission ignored due to conflicting rows: |
- | Jul 13, 2019 (153) |
| 46 | Ancient Sardinia genome-wide 1240k capture data generation and analysis | NC_000012.11 - 103246654 | Apr 26, 2021 (155) |
| 47 | TopMed | NC_000012.12 - 102852876 | Apr 26, 2021 (155) |
| 48 | ALFA | NC_000012.12 - 102852876 | Apr 26, 2021 (155) |
| 49 | ClinVar | RCV000000641.26 | Oct 16, 2022 (156) |
| 50 | ClinVar | RCV000089090.14 | Oct 16, 2022 (156) |
| 51 | ClinVar | RCV000119826.2 | Apr 26, 2021 (155) |
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).
| Associated ID | History Updated (Build) |
|---|---|
| rs386626637 | Aug 06, 2014 (136) |
| Submission IDs | Observation SPDI | Canonical SPDI | Source RSIDs |
|---|---|---|---|
| ss485827537 | NC_000012.10:101770783:G:A | NC_000012.12:102852875:G:A | (self) |
| 1383605, 836908, ss482077443, ss483026543, ss485814930, ss537652912, ss778654304, ss783353308, ss784304428, ss832615376, ss834112173, ss1691072553, ss1752042940, ss2633001316, ss2740077143, ss2748943635, ss2914552665, ss3626954918, ss3631008158, ss3633032208, ss3633733627, ss3634520727, ss3635424137, ss3636206806, ss3637175136, ss3640228060, ss3744821532, ss3772320771, ss3985610981, ss5237517558, ss5847681363, ss5979402103 | NC_000012.11:103246653:G:A | NC_000012.12:102852875:G:A | (self) |
| RCV000000641.26, RCV000089090.14, 417729952, 146394395, 9448193055, ss244239168, ss252841346, ss503928246, ss2192723689, ss3725352001, ss4930848738, ss5486661812 | NC_000012.12:102852875:G:A | NC_000012.12:102852875:G:A | (self) |
| ss7986017, ss161109670 | NT_029419.12:65389959:G:A | NC_000012.12:102852875:G:A | (self) |
| ss2740077143 | NC_000012.11:103246653:G:C | NC_000012.12:102852875:G:C | (self) |
| RCV000119826.2, ss647514556 | NC_000012.12:102852875:G:C | NC_000012.12:102852875:G:C | (self) |
Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.
| PMID | Title | Author | Year | Journal |
|---|---|---|---|---|
| 1682234 | Recurrent nonsense mutation in exon 7 of the phenylalanine hydroxylase gene. | Dworniczak B et al. | 1991 | Human genetics |
| 1769645 | Aberrant splicing of phenylalanine hydroxylase mRNA: the major cause for phenylketonuria in parts of southern Europe. | Dworniczak B et al. | 1991 | Genomics |
| 10598814 | Mutational spectrum of phenylalanine hydroxylase deficiency in the population resident in Catalonia: genotype-phenotype correlation. | Mallolas J et al. | 1999 | Human genetics |
| 10693064 | Should genetic analysis in newborn screening and a heterozygote test for hyperphenylalaninaemia be recommended? An Italian study. | Rottoli A et al. | 1999 | Journal of medical screening |
| 11180595 | Mutations of the phenylalanine hydroxylase (PAH) gene in Brazilian patients with phenylketonuria. | Acosta A et al. | 2001 | Human mutation |
| 11385716 | Molecular analysis of phenylketonuria (PKU) in newborns from Texas. | Yang Y et al. | 2001 | Human mutation |
| 12409276 | Two novel genetic lesions and a common BH4-responsive mutation of the PAH gene in Italian patients with hyperphenylalaninemia. | Bardelli T et al. | 2002 | Molecular genetics and metabolism |
| 12655553 | Mutational spectrum in German patients with phenylalanine hydroxylase deficiency. | Aulehla-Scholz C et al. | 2003 | Human mutation |
| 12765842 | Molecular characterization of phenylketonuria in South Brazil. | Santana da Silva LC et al. | 2003 | Molecular genetics and metabolism |
| 15503242 | The molecular basis of phenylketonuria in Koreans. | Lee DH et al. | 2004 | Journal of human genetics |
| 16601866 | The spectrum of phenylalanine variations under tetrahydrobiopterin load in subjects affected by phenylalanine hydroxylase deficiency. | Leuzzi V et al. | 2006 | Journal of inherited metabolic disease |
| 16755493 | Frequencies of phenylalanine hydroxylase mutations I65T, R252W, R261Q, R261X, IVS10nt11, V388M, R408W, Y414C, and IVS12nt1 in Minas Gerais, Brazil. | Santos LL et al. | 2006 | Genetics and molecular research |
| 16879198 | Molecular and phenotypic characteristics of patients with phenylketonuria in Serbia and Montenegro. | Stojiljkovic M et al. | 2006 | Clinical genetics |
| 17935162 | Molecular genetics of tetrahydrobiopterin-responsive phenylalanine hydroxylase deficiency. | Zurflüh MR et al. | 2008 | Human mutation |
| 19062537 | Predicting a clinical/biochemical phenotype for PKU/MHP patients with PAH gene mutations. | Kasnauskiene J et al. | 2008 | Genetika |
| 19394257 | Genotype-predicted tetrahydrobiopterin (BH4)-responsiveness and molecular genetics in Croatian patients with phenylalanine hydroxylase (PAH) deficiency. | Karacić I et al. | 2009 | Molecular genetics and metabolism |
| 20920871 | Mutation spectrum of phenylketonuria in Iranian population. | Zare-Karizi Sh et al. | 2011 | Molecular genetics and metabolism |
| 23500595 | Molecular epidemiology and BH4-responsiveness in patients with phenylalanine hydroxylase deficiency from Galicia region of Spain. | Couce ML et al. | 2013 | Gene |
| 24048906 | Mutation analysis of PAH gene in patients with PKU in western Iran and its association with polymorphisms: identification of four novel mutations. | Alibakhshi R et al. | 2014 | Metabolic brain disease |
| 24401910 | The mutation spectrum of the phenylalanine hydroxylase (PAH) gene and associated haplotypes reveal ethnic heterogeneity in the Taiwanese population. | Liang Y et al. | 2014 | Journal of human genetics |
| 25525159 | RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. | Xiong HY et al. | 2015 | Science (New York, N.Y.) |
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.