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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.

rs61755798

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:42704564 (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
C=0.00000 (0/78698, PAGE_STUDY)
C=0.00005 (1/21382, ALFA)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PRPH2 : Missense Variant
Publications
7 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.

Release Version: 20231103111315
Population Group Sample Size Ref Allele Alt Allele
Total Global 21382 G=0.99995 C=0.00005
European Sub 16898 G=1.00000 C=0.00000
African Sub 20 G=1.00 C=0.00
African Others Sub 0 G=0 C=0
African American Sub 20 G=1.00 C=0.00
Asian Sub 0 G=0 C=0
East Asian Sub 0 G=0 C=0
Other Asian Sub 0 G=0 C=0
Latin American 1 Sub 354 G=1.000 C=0.000
Latin American 2 Sub 18 G=1.00 C=0.00
South Asian Sub 0 G=0 C=0
Other Sub 4092 G=0.9998 C=0.0002


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
The PAGE Study Global Study-wide 78698 G=1.00000 C=0.00000
The PAGE Study AfricanAmerican Sub 32516 G=1.00000 C=0.00000
The PAGE Study Mexican Sub 10810 G=1.00000 C=0.00000
The PAGE Study Asian Sub 8314 G=1.0000 C=0.0000
The PAGE Study PuertoRican Sub 7918 G=1.0000 C=0.0000
The PAGE Study NativeHawaiian Sub 4534 G=1.0000 C=0.0000
The PAGE Study Cuban Sub 4230 G=1.0000 C=0.0000
The PAGE Study Dominican Sub 3828 G=1.0000 C=0.0000
The PAGE Study CentralAmerican Sub 2450 G=1.0000 C=0.0000
The PAGE Study SouthAmerican Sub 1982 G=1.0000 C=0.0000
The PAGE Study NativeAmerican Sub 1260 G=1.0000 C=0.0000
The PAGE Study SouthAsian Sub 856 G=1.000 C=0.000
Allele Frequency Aggregator Total Global 21382 G=0.99995 C=0.00005
Allele Frequency Aggregator European Sub 16898 G=1.00000 C=0.00000
Allele Frequency Aggregator Other Sub 4092 G=0.9998 C=0.0002
Allele Frequency Aggregator Latin American 1 Sub 354 G=1.000 C=0.000
Allele Frequency Aggregator African Sub 20 G=1.00 C=0.00
Allele Frequency Aggregator Latin American 2 Sub 18 G=1.00 C=0.00
Allele Frequency Aggregator South Asian Sub 0 G=0 C=0
Allele Frequency Aggregator Asian Sub 0 G=0 C=0
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.p14 chr 6 NC_000006.12:g.42704564G>A
GRCh38.p14 chr 6 NC_000006.12:g.42704564G>C
GRCh37.p13 chr 6 NC_000006.11:g.42672302G>A
GRCh37.p13 chr 6 NC_000006.11:g.42672302G>C
PRPH2 RefSeqGene NG_009176.2:g.23057C>T
PRPH2 RefSeqGene NG_009176.2:g.23057C>G
Gene: PRPH2, peripherin 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PRPH2 transcript NM_000322.5:c.629C>T P [CCT] > L [CTT] Coding Sequence Variant
peripherin-2 NP_000313.2:p.Pro210Leu P (Pro) > L (Leu) Missense Variant
PRPH2 transcript NM_000322.5:c.629C>G P [CCT] > R [CGT] Coding Sequence Variant
peripherin-2 NP_000313.2:p.Pro210Arg P (Pro) > R (Arg) Missense Variant
PRPH2 transcript variant X1 XR_007059288.1:n.1074C>T N/A Non Coding Transcript Variant
PRPH2 transcript variant X1 XR_007059288.1:n.1074C>G 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: 104577 )
ClinVar Accession Disease Names Clinical Significance
RCV000084998.2 not provided Likely-Pathogenic
RCV001381219.2 PRPH2-Related Disorders Pathogenic
Allele: C (allele ID: 28212 )
ClinVar Accession Disease Names Clinical Significance
RCV000014059.26 Adult-onset foveomacular vitelliform dystrophy Pathogenic
RCV000084997.3 not provided Pathogenic
RCV000322776.6 PRPH2-Related Disorders Pathogenic-Likely-Pathogenic
RCV001074849.1 Retinal dystrophy Pathogenic
RCV001250286.1 Stargardt disease Pathogenic
RCV001250287.1 Patterned dystrophy of the retinal pigment epithelium Pathogenic
RCV001250288.1 Vitelliform macular dystrophy 2 Pathogenic
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.p14 chr 6 NC_000006.12:g.42704564= NC_000006.12:g.42704564G>A NC_000006.12:g.42704564G>C
GRCh37.p13 chr 6 NC_000006.11:g.42672302= NC_000006.11:g.42672302G>A NC_000006.11:g.42672302G>C
PRPH2 RefSeqGene NG_009176.2:g.23057= NG_009176.2:g.23057C>T NG_009176.2:g.23057C>G
PRPH2 transcript NM_000322.5:c.629= NM_000322.5:c.629C>T NM_000322.5:c.629C>G
PRPH2 transcript NM_000322.4:c.629= NM_000322.4:c.629C>T NM_000322.4:c.629C>G
PRPH2 transcript variant X1 XR_007059288.1:n.1074= XR_007059288.1:n.1074C>T XR_007059288.1:n.1074C>G
peripherin-2 NP_000313.2:p.Pro210= NP_000313.2:p.Pro210Leu NP_000313.2:p.Pro210Arg
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 SubSNP, 2 Frequency, 9 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss275518336 Dec 08, 2010 (133)
2 RISN-LSDB ss562065237 Dec 21, 2012 (137)
3 RISN-LSDB ss562065274 Dec 21, 2012 (137)
4 ILLUMINA ss1958904936 Feb 12, 2016 (147)
5 ILLUMINA ss3022616361 Nov 08, 2017 (151)
6 ILLUMINA ss3653132967 Oct 12, 2018 (152)
7 ILLUMINA ss3726342809 Jul 13, 2019 (153)
8 PAGE_CC ss3771290323 Jul 13, 2019 (153)
9 The PAGE Study NC_000006.12 - 42704564 Jul 13, 2019 (153)
10 ALFA NC_000006.12 - 42704564 Apr 26, 2021 (155)
11 ClinVar RCV000014059.26 Oct 12, 2018 (152)
12 ClinVar RCV000084997.3 Oct 17, 2022 (156)
13 ClinVar RCV000084998.2 Oct 17, 2022 (156)
14 ClinVar RCV000322776.6 Oct 17, 2022 (156)
15 ClinVar RCV001074849.1 Apr 26, 2021 (155)
16 ClinVar RCV001250286.1 Apr 26, 2021 (155)
17 ClinVar RCV001250287.1 Apr 26, 2021 (155)
18 ClinVar RCV001250288.1 Apr 26, 2021 (155)
19 ClinVar RCV001381219.2 Oct 17, 2022 (156)
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
RCV000084998.2, RCV001381219.2, ss562065274 NC_000006.12:42704563:G:A NC_000006.12:42704563:G:A (self)
ss1958904936, ss3022616361, ss3653132967 NC_000006.11:42672301:G:C NC_000006.12:42704563:G:C (self)
RCV000014059.26, RCV000084997.3, RCV000322776.6, RCV001074849.1, RCV001250286.1, RCV001250287.1, RCV001250288.1, 511792, 4094091790, ss275518336, ss562065237, ss3726342809, ss3771290323 NC_000006.12:42704563:G:C NC_000006.12:42704563: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.

7 citations for rs61755798
PMID Title Author Year Journal
4142662 A clinicopathologic study of a peculiar foveomacular dystrophy. Gass JD et al. 1974 Transactions of the American Ophthalmological Society
7519821 Choroidal neovascularization in a patient with adult foveomacular dystrophy and a mutation in the retinal degeneration slow gene (Pro 210 Arg). Feist RM et al. 1994 American journal of ophthalmology
7862413 A peripherin/retinal degeneration slow mutation (Pro-210-Arg) associated with macular and peripheral retinal degeneration. Gorin MB et al. 1995 Ophthalmology
16885924 Peripherin/RDS and VMD2 mutations in macular dystrophies with adult-onset vitelliform lesion. Zhuk SA et al. 2006 Molecular vision
21071739 Cone structure in retinal degeneration associated with mutations in the peripherin/RDS gene. Duncan JL et al. 2011 Investigative ophthalmology & visual science
22863181 Molecular diagnosis of putative Stargardt Disease probands by exome sequencing. Strom SP et al. 2012 BMC medical genetics
25082885 Molecular diagnostic testing by eyeGENE: analysis of patients with hereditary retinal dystrophy phenotypes involving central vision loss. Alapati A et al. 2014 Investigative ophthalmology & visual science
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.post774+babeb33