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.
rs5742905
Current Build 156
Released September 21, 2022
- Organism
- Homo sapiens
- Position
-
chr21:43063074 (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
- A>G
- Variation Type
- SNV Single Nucleotide Variation
- Frequency
-
G=0.006061 (1177/194203, ALFA)G=0.00025 (20/78612, PAGE_STUDY)G=0.00006 (1/16760, 8.3KJPN) (+ 7 more)
- Clinical Significance
- Reported in ClinVar
- Gene : Consequence
- CBS : Missense Variant
- Publications
- 44 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: 20230706150541
| Population | Group | Sample Size | Ref Allele | Alt Allele |
|---|---|---|---|---|
| Total | Global | 210177 | A=0.994300 | G=0.005700 |
| European | Sub | 178852 | A=0.994515 | G=0.005485 |
| African | Sub | 9385 | A=0.9812 | G=0.0188 |
| African Others | Sub | 352 | A=0.969 | G=0.031 |
| African American | Sub | 9033 | A=0.9817 | G=0.0183 |
| Asian | Sub | 6616 | A=1.0000 | G=0.0000 |
| East Asian | Sub | 4736 | A=1.0000 | G=0.0000 |
| Other Asian | Sub | 1880 | A=1.0000 | G=0.0000 |
| Latin American 1 | Sub | 482 | A=0.998 | G=0.002 |
| Latin American 2 | Sub | 1126 | A=0.9964 | G=0.0036 |
| South Asian | Sub | 294 | A=1.000 | G=0.000 |
| Other | Sub | 13422 | A=0.99732 | G=0.00268 |
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 |
|---|---|---|---|---|---|
| Allele Frequency Aggregator | Total | Global | 194203 | A=0.993939 | G=0.006061 |
| Allele Frequency Aggregator | European | Sub | 168960 | A=0.994295 | G=0.005705 |
| Allele Frequency Aggregator | Other | Sub | 12016 | A=0.99717 | G=0.00283 |
| Allele Frequency Aggregator | Asian | Sub | 6616 | A=1.0000 | G=0.0000 |
| Allele Frequency Aggregator | African | Sub | 4709 | A=0.9630 | G=0.0370 |
| Allele Frequency Aggregator | Latin American 2 | Sub | 1126 | A=0.9964 | G=0.0036 |
| Allele Frequency Aggregator | Latin American 1 | Sub | 482 | A=0.998 | G=0.002 |
| Allele Frequency Aggregator | South Asian | Sub | 294 | A=1.000 | G=0.000 |
| The PAGE Study | Global | Study-wide | 78612 | A=0.99975 | G=0.00025 |
| The PAGE Study | AfricanAmerican | Sub | 32444 | A=0.99975 | G=0.00025 |
| The PAGE Study | Mexican | Sub | 10808 | A=0.99991 | G=0.00009 |
| The PAGE Study | Asian | Sub | 8318 | A=0.9998 | G=0.0002 |
| The PAGE Study | PuertoRican | Sub | 7912 | A=1.0000 | G=0.0000 |
| The PAGE Study | NativeHawaiian | Sub | 4528 | A=1.0000 | G=0.0000 |
| The PAGE Study | Cuban | Sub | 4230 | A=0.9995 | G=0.0005 |
| The PAGE Study | Dominican | Sub | 3826 | A=0.9992 | G=0.0008 |
| The PAGE Study | CentralAmerican | Sub | 2448 | A=1.0000 | G=0.0000 |
| The PAGE Study | SouthAmerican | Sub | 1982 | A=1.0000 | G=0.0000 |
| The PAGE Study | NativeAmerican | Sub | 1260 | A=0.9968 | G=0.0032 |
| The PAGE Study | SouthAsian | Sub | 856 | A=1.000 | G=0.000 |
| 8.3KJPN | JAPANESE | Study-wide | 16760 | A=0.99994 | G=0.00006 |
| 1000Genomes | Global | Study-wide | 5008 | A=0.9998 | G=0.0002 |
| 1000Genomes | African | Sub | 1322 | A=1.0000 | G=0.0000 |
| 1000Genomes | East Asian | Sub | 1008 | A=1.0000 | G=0.0000 |
| 1000Genomes | Europe | Sub | 1006 | A=0.9990 | G=0.0010 |
| 1000Genomes | South Asian | Sub | 978 | A=1.000 | G=0.000 |
| 1000Genomes | American | Sub | 694 | A=1.000 | G=0.000 |
| KOREAN population from KRGDB | KOREAN | Study-wide | 2922 | A=0.9966 | G=0.0034 |
| Genome of the Netherlands Release 5 | Genome of the Netherlands | Study-wide | 998 | A=0.989 | G=0.011 |
| HapMap | Global | Study-wide | 304 | A=1.000 | G=0.000 |
| HapMap | African | Sub | 116 | A=1.000 | G=0.000 |
| HapMap | American | Sub | 112 | A=1.000 | G=0.000 |
| HapMap | Asian | Sub | 76 | A=1.00 | G=0.00 |
| Qatari | Global | Study-wide | 216 | A=0.931 | G=0.069 |
| SGDP_PRJ | Global | Study-wide | 56 | A=0.50 | G=0.50 |
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 21 | NC_000021.9:g.43063074A>G |
| GRCh37.p13 chr 21 | NC_000021.8:g.44483184A>G |
| CBS RefSeqGene (LRG_777) | NG_008938.1:g.17857T>C |
Gene: CBS, cystathionine beta-synthase
(minus strand)
| Molecule type | Change | Amino acid[Codon] | SO Term |
|---|---|---|---|
| CBS transcript variant 5 | NM_001321072.1:c.518T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform 2 | NP_001308001.1:p.Ile173Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant 3 | NM_001178009.3:c.833T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform 1 | NP_001171480.1:p.Ile278Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant 1 | NM_000071.3:c.833T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform 1 | NP_000062.1:p.Ile278Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant 4 | NM_001320298.2:c.833T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform 1 | NP_001307227.1:p.Ile278Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant 2 | NM_001178008.3:c.833T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform 1 | NP_001171479.1:p.Ile278Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant X22 | XM_011529783.2:c.518T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform X6 | XP_011528085.1:p.Ile173Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant X5 | XM_011529777.2:c.833T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform X3 | XP_011528079.1:p.Ile278Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant X1 | XM_047441017.1:c.884T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform X1 | XP_047296973.1:p.Ile295Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant X2 | XM_011529774.3:c.884T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform X1 | XP_011528076.1:p.Ile295Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant X3 | XM_047441018.1:c.884T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform X2 | XP_047296974.1:p.Ile295Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant X4 | XM_047441019.1:c.884T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform X2 | XP_047296975.1:p.Ile295Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant X6 | XM_047441020.1:c.833T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform X3 | XP_047296976.1:p.Ile278Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant X7 | XM_047441021.1:c.833T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform X3 | XP_047296977.1:p.Ile278Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant X8 | XM_047441022.1:c.833T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform X3 | XP_047296978.1:p.Ile278Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant X9 | XM_047441023.1:c.833T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform X3 | XP_047296979.1:p.Ile278Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant X10 | XM_047441024.1:c.833T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform X3 | XP_047296980.1:p.Ile278Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant X11 | XM_047441025.1:c.833T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform X3 | XP_047296981.1:p.Ile278Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant X12 | XM_047441026.1:c.833T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform X4 | XP_047296982.1:p.Ile278Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant X13 | XM_047441027.1:c.833T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform X4 | XP_047296983.1:p.Ile278Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant X14 | XM_047441028.1:c.833T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform X4 | XP_047296984.1:p.Ile278Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant X15 | XM_017028491.3:c.833T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform X4 | XP_016883980.1:p.Ile278Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant X16 | XM_047441029.1:c.833T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform X4 | XP_047296985.1:p.Ile278Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant X17 | XM_047441030.1:c.833T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform X4 | XP_047296986.1:p.Ile278Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant X18 | XM_047441031.1:c.833T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform X4 | XP_047296987.1:p.Ile278Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant X19 | XM_047441032.1:c.626T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform X5 | XP_047296988.1:p.Ile209Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant X23 | XM_047441033.1:c.518T>C | I [ATT] > T [ACT] | Coding Sequence Variant |
| cystathionine beta-synthase isoform X7 | XP_047296989.1:p.Ile173Thr | I (Ile) > T (Thr) | Missense Variant |
| CBS transcript variant X20 | XR_001754915.2:n.1204T>C | N/A | Non Coding Transcript Variant |
| CBS transcript variant X21 | XR_007067793.1:n.983T>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: G (allele ID:
15159
)
| ClinVar Accession | Disease Names | Clinical Significance |
|---|---|---|
| RCV000000141.7 | Homocystinuria, pyridoxine-responsive | Pathogenic |
| RCV000000142.8 | HYPERHOMOCYSTEINEMIA, THROMBOTIC, CBS-RELATED | Pathogenic |
| RCV000078111.31 | not provided | Pathogenic |
| RCV000173640.29 | Classic homocystinuria | Pathogenic |
| RCV000249462.4 | Cardiovascular phenotype | Pathogenic |
| RCV000781197.3 | Homocystinuria | Pathogenic |
| RCV001252178.2 | Intellectual disability | Uncertain-Significance |
| RCV002276525.1 | Connective tissue disorder | Benign |
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 | A= | G |
|---|---|---|
| GRCh38.p14 chr 21 | NC_000021.9:g.43063074= | NC_000021.9:g.43063074A>G |
| GRCh37.p13 chr 21 | NC_000021.8:g.44483184= | NC_000021.8:g.44483184A>G |
| CBS RefSeqGene (LRG_777) | NG_008938.1:g.17857= | NG_008938.1:g.17857T>C |
| CBS transcript variant 2 | NM_001178008.3:c.833= | NM_001178008.3:c.833T>C |
| CBS transcript variant 2 | NM_001178008.2:c.833= | NM_001178008.2:c.833T>C |
| CBS transcript variant 2 | NM_001178008.1:c.833= | NM_001178008.1:c.833T>C |
| CBS transcript variant 1 | NM_000071.3:c.833= | NM_000071.3:c.833T>C |
| CBS transcript variant 1 | NM_000071.2:c.833= | NM_000071.2:c.833T>C |
| CBS transcript variant 3 | NM_001178009.3:c.833= | NM_001178009.3:c.833T>C |
| CBS transcript variant 3 | NM_001178009.2:c.833= | NM_001178009.2:c.833T>C |
| CBS transcript variant 3 | NM_001178009.1:c.833= | NM_001178009.1:c.833T>C |
| CBS transcript variant 4 | NM_001320298.2:c.833= | NM_001320298.2:c.833T>C |
| CBS transcript variant 4 | NM_001320298.1:c.833= | NM_001320298.1:c.833T>C |
| CBS transcript variant 5 | NM_001321072.1:c.518= | NM_001321072.1:c.518T>C |
| CBS transcript variant X2 | XM_011529774.3:c.884= | XM_011529774.3:c.884T>C |
| CBS transcript variant X1 | XM_011529774.2:c.884= | XM_011529774.2:c.884T>C |
| CBS transcript variant X2 | XM_011529774.1:c.884= | XM_011529774.1:c.884T>C |
| CBS transcript variant X15 | XM_017028491.3:c.833= | XM_017028491.3:c.833T>C |
| CBS transcript variant X3 | XM_017028491.2:c.833= | XM_017028491.2:c.833T>C |
| CBS transcript variant X10 | XM_017028491.1:c.833= | XM_017028491.1:c.833T>C |
| CBS transcript variant X22 | XM_011529783.2:c.518= | XM_011529783.2:c.518T>C |
| CBS transcript variant X10 | XM_011529783.1:c.518= | XM_011529783.1:c.518T>C |
| CBS transcript variant X5 | XM_011529777.2:c.833= | XM_011529777.2:c.833T>C |
| CBS transcript variant X5 | XM_011529777.1:c.833= | XM_011529777.1:c.833T>C |
| CBS transcript variant X20 | XR_001754915.2:n.1204= | XR_001754915.2:n.1204T>C |
| CBS transcript variant X5 | XR_001754915.1:n.1204= | XR_001754915.1:n.1204T>C |
| CBS transcript variant X19 | XM_047441032.1:c.626= | XM_047441032.1:c.626T>C |
| CBS transcript variant X8 | XM_047441022.1:c.833= | XM_047441022.1:c.833T>C |
| CBS transcript variant X12 | XM_047441026.1:c.833= | XM_047441026.1:c.833T>C |
| CBS transcript variant X16 | XM_047441029.1:c.833= | XM_047441029.1:c.833T>C |
| CBS transcript variant X11 | XM_047441025.1:c.833= | XM_047441025.1:c.833T>C |
| CBS transcript variant X9 | XM_047441023.1:c.833= | XM_047441023.1:c.833T>C |
| CBS transcript variant X13 | XM_047441027.1:c.833= | XM_047441027.1:c.833T>C |
| CBS transcript variant X14 | XM_047441028.1:c.833= | XM_047441028.1:c.833T>C |
| CBS transcript variant X18 | XM_047441031.1:c.833= | XM_047441031.1:c.833T>C |
| CBS transcript variant X1 | XM_047441017.1:c.884= | XM_047441017.1:c.884T>C |
| CBS transcript variant X3 | XM_047441018.1:c.884= | XM_047441018.1:c.884T>C |
| CBS transcript variant X10 | XM_047441024.1:c.833= | XM_047441024.1:c.833T>C |
| CBS transcript variant X7 | XM_047441021.1:c.833= | XM_047441021.1:c.833T>C |
| CBS transcript variant X4 | XM_047441019.1:c.884= | XM_047441019.1:c.884T>C |
| CBS transcript variant X23 | XM_047441033.1:c.518= | XM_047441033.1:c.518T>C |
| CBS transcript variant X17 | XM_047441030.1:c.833= | XM_047441030.1:c.833T>C |
| CBS transcript variant X6 | XM_047441020.1:c.833= | XM_047441020.1:c.833T>C |
| CBS transcript variant X21 | XR_007067793.1:n.983= | XR_007067793.1:n.983T>C |
| cystathionine beta-synthase isoform 1 | NP_001171479.1:p.Ile278= | NP_001171479.1:p.Ile278Thr |
| cystathionine beta-synthase isoform 1 | NP_000062.1:p.Ile278= | NP_000062.1:p.Ile278Thr |
| cystathionine beta-synthase isoform 1 | NP_001171480.1:p.Ile278= | NP_001171480.1:p.Ile278Thr |
| cystathionine beta-synthase isoform 1 | NP_001307227.1:p.Ile278= | NP_001307227.1:p.Ile278Thr |
| cystathionine beta-synthase isoform 2 | NP_001308001.1:p.Ile173= | NP_001308001.1:p.Ile173Thr |
| cystathionine beta-synthase isoform X1 | XP_011528076.1:p.Ile295= | XP_011528076.1:p.Ile295Thr |
| cystathionine beta-synthase isoform X4 | XP_016883980.1:p.Ile278= | XP_016883980.1:p.Ile278Thr |
| cystathionine beta-synthase isoform X6 | XP_011528085.1:p.Ile173= | XP_011528085.1:p.Ile173Thr |
| cystathionine beta-synthase isoform X3 | XP_011528079.1:p.Ile278= | XP_011528079.1:p.Ile278Thr |
| cystathionine beta-synthase isoform X5 | XP_047296988.1:p.Ile209= | XP_047296988.1:p.Ile209Thr |
| cystathionine beta-synthase isoform X3 | XP_047296978.1:p.Ile278= | XP_047296978.1:p.Ile278Thr |
| cystathionine beta-synthase isoform X4 | XP_047296982.1:p.Ile278= | XP_047296982.1:p.Ile278Thr |
| cystathionine beta-synthase isoform X4 | XP_047296985.1:p.Ile278= | XP_047296985.1:p.Ile278Thr |
| cystathionine beta-synthase isoform X3 | XP_047296981.1:p.Ile278= | XP_047296981.1:p.Ile278Thr |
| cystathionine beta-synthase isoform X3 | XP_047296979.1:p.Ile278= | XP_047296979.1:p.Ile278Thr |
| cystathionine beta-synthase isoform X4 | XP_047296983.1:p.Ile278= | XP_047296983.1:p.Ile278Thr |
| cystathionine beta-synthase isoform X4 | XP_047296984.1:p.Ile278= | XP_047296984.1:p.Ile278Thr |
| cystathionine beta-synthase isoform X4 | XP_047296987.1:p.Ile278= | XP_047296987.1:p.Ile278Thr |
| cystathionine beta-synthase isoform X1 | XP_047296973.1:p.Ile295= | XP_047296973.1:p.Ile295Thr |
| cystathionine beta-synthase isoform X2 | XP_047296974.1:p.Ile295= | XP_047296974.1:p.Ile295Thr |
| cystathionine beta-synthase isoform X3 | XP_047296980.1:p.Ile278= | XP_047296980.1:p.Ile278Thr |
| cystathionine beta-synthase isoform X3 | XP_047296977.1:p.Ile278= | XP_047296977.1:p.Ile278Thr |
| cystathionine beta-synthase isoform X2 | XP_047296975.1:p.Ile295= | XP_047296975.1:p.Ile295Thr |
| cystathionine beta-synthase isoform X7 | XP_047296989.1:p.Ile173= | XP_047296989.1:p.Ile173Thr |
| cystathionine beta-synthase isoform X4 | XP_047296986.1:p.Ile278= | XP_047296986.1:p.Ile278Thr |
| cystathionine beta-synthase isoform X3 | XP_047296976.1:p.Ile278= | XP_047296976.1:p.Ile278Thr |
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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#.
67 SubSNP,
9 Frequency,
8 ClinVar
submissions
| No | Submitter | Submission ID | Date (Build) |
|---|---|---|---|
| 1 | O_LEUT | ss7986638 | Apr 21, 2003 (114) |
| 2 | SC_SNP | ss18806698 | Feb 28, 2004 (126) |
| 3 | HGSV | ss84217964 | Dec 15, 2007 (130) |
| 4 | CORNELL | ss86271783 | Mar 23, 2008 (129) |
| 5 | ILLUMINA | ss161109702 | Dec 01, 2009 (131) |
| 6 | OMICIA | ss169689463 | Aug 28, 2012 (137) |
| 7 | ILLUMINA | ss244303299 | Jul 04, 2010 (132) |
| 8 | OMIM-CURATED-RECORDS | ss288288985 | Dec 21, 2010 (133) |
| 9 | NHLBI-ESP | ss342533557 | May 09, 2011 (134) |
| 10 | ILLUMINA | ss482077511 | May 04, 2012 (137) |
| 11 | ILLUMINA | ss483026637 | Sep 08, 2015 (146) |
| 12 | ILLUMINA | ss485814964 | May 04, 2012 (137) |
| 13 | ILLUMINA | ss485827558 | May 04, 2012 (137) |
| 14 | EXOME_CHIP | ss491566437 | May 04, 2012 (137) |
| 15 | CLINSEQ_SNP | ss491816878 | May 04, 2012 (137) |
| 16 | ILLUMINA | ss536005763 | Sep 08, 2015 (146) |
| 17 | ILLUMINA | ss780758897 | Aug 21, 2014 (142) |
| 18 | ILLUMINA | ss783353325 | Sep 08, 2015 (146) |
| 19 | ILLUMINA | ss783437632 | Aug 21, 2014 (142) |
| 20 | ILLUMINA | ss832615391 | Sep 08, 2015 (146) |
| 21 | EVA-GONL | ss995164678 | Aug 21, 2014 (142) |
| 22 | 1000GENOMES | ss1366456380 | Aug 21, 2014 (142) |
| 23 | ILLUMINA | ss1752410613 | Sep 08, 2015 (146) |
| 24 | ILLUMINA | ss1752410614 | Sep 08, 2015 (146) |
| 25 | HAMMER_LAB | ss1809708663 | Sep 08, 2015 (146) |
| 26 | ILLUMINA | ss1917952016 | Feb 12, 2016 (147) |
| 27 | WEILL_CORNELL_DGM | ss1938715311 | Feb 12, 2016 (147) |
| 28 | ILLUMINA | ss1946570952 | Feb 12, 2016 (147) |
| 29 | ILLUMINA | ss1959958010 | Feb 12, 2016 (147) |
| 30 | ILLUMINA | ss2094810879 | Dec 20, 2016 (150) |
| 31 | ILLUMINA | ss2633855647 | Nov 08, 2017 (151) |
| 32 | AFFY | ss2985230517 | Nov 08, 2017 (151) |
| 33 | ILLUMINA | ss3022164118 | Nov 08, 2017 (151) |
| 34 | CSHL | ss3352741272 | Nov 08, 2017 (151) |
| 35 | ILLUMINA | ss3628492750 | Oct 12, 2018 (152) |
| 36 | ILLUMINA | ss3628492751 | Oct 12, 2018 (152) |
| 37 | ILLUMINA | ss3633267131 | Oct 12, 2018 (152) |
| 38 | ILLUMINA | ss3633982218 | Oct 12, 2018 (152) |
| 39 | ILLUMINA | ss3634857511 | Oct 12, 2018 (152) |
| 40 | ILLUMINA | ss3634857512 | Oct 12, 2018 (152) |
| 41 | ILLUMINA | ss3635666908 | Oct 12, 2018 (152) |
| 42 | ILLUMINA | ss3636553485 | Oct 12, 2018 (152) |
| 43 | ILLUMINA | ss3637419084 | Oct 12, 2018 (152) |
| 44 | ILLUMINA | ss3640564811 | Oct 12, 2018 (152) |
| 45 | ILLUMINA | ss3640564812 | Oct 12, 2018 (152) |
| 46 | ILLUMINA | ss3644794076 | Oct 12, 2018 (152) |
| 47 | ILLUMINA | ss3652625022 | Oct 12, 2018 (152) |
| 48 | ILLUMINA | ss3653998419 | Oct 12, 2018 (152) |
| 49 | ILLUMINA | ss3744499053 | Jul 13, 2019 (153) |
| 50 | ILLUMINA | ss3745157362 | Jul 13, 2019 (153) |
| 51 | ILLUMINA | ss3745157363 | Jul 13, 2019 (153) |
| 52 | EVA | ss3759162282 | Jul 13, 2019 (153) |
| 53 | PAGE_CC | ss3772077649 | Jul 13, 2019 (153) |
| 54 | ILLUMINA | ss3772653391 | Jul 13, 2019 (153) |
| 55 | ILLUMINA | ss3772653392 | Jul 13, 2019 (153) |
| 56 | EVA | ss3825410407 | Apr 27, 2020 (154) |
| 57 | SGDP_PRJ | ss3890096619 | Apr 27, 2020 (154) |
| 58 | KRGDB | ss3940442732 | Apr 27, 2020 (154) |
| 59 | TOMMO_GENOMICS | ss5231719640 | Apr 26, 2021 (155) |
| 60 | EVA | ss5316042514 | Oct 16, 2022 (156) |
| 61 | SANFORD_IMAGENETICS | ss5624498133 | Oct 16, 2022 (156) |
| 62 | EVA | ss5839102153 | Oct 16, 2022 (156) |
| 63 | EVA | ss5847514833 | Oct 16, 2022 (156) |
| 64 | EVA | ss5847936370 | Oct 16, 2022 (156) |
| 65 | EVA | ss5959000424 | Oct 16, 2022 (156) |
| 66 | EVA | ss5979630937 | Oct 16, 2022 (156) |
| 67 | EVA | ss5981319903 | Oct 16, 2022 (156) |
| 68 | 1000Genomes | NC_000021.8 - 44483184 | Oct 12, 2018 (152) |
| 69 | Genome of the Netherlands Release 5 | NC_000021.8 - 44483184 | Apr 27, 2020 (154) |
| 70 | HapMap | NC_000021.9 - 43063074 | Apr 27, 2020 (154) |
| 71 | KOREAN population from KRGDB | NC_000021.8 - 44483184 | Apr 27, 2020 (154) |
| 72 | The PAGE Study | NC_000021.9 - 43063074 | Jul 13, 2019 (153) |
| 73 | Qatari | NC_000021.8 - 44483184 | Apr 27, 2020 (154) |
| 74 | SGDP_PRJ | NC_000021.8 - 44483184 | Apr 27, 2020 (154) |
| 75 | 8.3KJPN | NC_000021.8 - 44483184 | Apr 26, 2021 (155) |
| 76 | ALFA | NC_000021.9 - 43063074 | Apr 26, 2021 (155) |
| 77 | ClinVar | RCV000000141.7 | Oct 16, 2022 (156) |
| 78 | ClinVar | RCV000000142.8 | Oct 16, 2022 (156) |
| 79 | ClinVar | RCV000078111.31 | Oct 16, 2022 (156) |
| 80 | ClinVar | RCV000173640.29 | Oct 16, 2022 (156) |
| 81 | ClinVar | RCV000249462.4 | Oct 16, 2022 (156) |
| 82 | ClinVar | RCV000781197.3 | Oct 16, 2022 (156) |
| 83 | ClinVar | RCV001252178.2 | Oct 16, 2022 (156) |
| 84 | ClinVar | RCV002276525.1 | Oct 16, 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).
| Associated ID | History Updated (Build) |
|---|---|
| rs12329790 | Mar 11, 2006 (126) |
| rs59005818 | May 25, 2008 (130) |
| rs117019516 | Aug 16, 2010 (132) |
Added to this RefSNP Cluster:
| Submission IDs | Observation SPDI | Canonical SPDI | Source RSIDs |
|---|---|---|---|
| ss84217964, ss161109702, ss244303299, ss485827558, ss491816878 | NC_000021.7:43356252:A:G | NC_000021.9:43063073:A:G | (self) |
| 79982677, 19721108, 47620126, 20757233, 42113599, 89688947, ss342533557, ss482077511, ss483026637, ss485814964, ss491566437, ss536005763, ss780758897, ss783353325, ss783437632, ss832615391, ss995164678, ss1366456380, ss1752410613, ss1752410614, ss1809708663, ss1917952016, ss1938715311, ss1946570952, ss1959958010, ss2094810879, ss2633855647, ss2985230517, ss3022164118, ss3352741272, ss3628492750, ss3628492751, ss3633267131, ss3633982218, ss3634857511, ss3634857512, ss3635666908, ss3636553485, ss3637419084, ss3640564811, ss3640564812, ss3644794076, ss3652625022, ss3653998419, ss3744499053, ss3745157362, ss3745157363, ss3759162282, ss3772653391, ss3772653392, ss3825410407, ss3890096619, ss3940442732, ss5231719640, ss5316042514, ss5624498133, ss5839102153, ss5847514833, ss5847936370, ss5959000424, ss5979630937, ss5981319903 | NC_000021.8:44483183:A:G | NC_000021.9:43063073:A:G | (self) |
| RCV000000141.7, RCV000000142.8, RCV000078111.31, RCV000173640.29, RCV000249462.4, RCV000781197.3, RCV001252178.2, RCV002276525.1, 2218428, 1299118, 832690776, ss169689463, ss288288985, ss3772077649 | NC_000021.9:43063073:A:G | NC_000021.9:43063073:A:G | (self) |
| ss7986638, ss86271783 | NT_011515.12:1477624:A:G | NC_000021.9:43063073:A:G | (self) |
| ss18806698 | NT_030188.3:1232509:A:G | NC_000021.9:43063073:A:G | (self) |
Help
Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.
44
citations for rs5742905
| PMID | Title | Author | Year | Journal |
|---|---|---|---|---|
| 1301198 | Screening for mutations by expressing patient cDNA segments in E. coli: homocystinuria due to cystathionine beta-synthase deficiency. | Kozich V et al. | 1992 | Human mutation |
| 7506602 | Molecular basis of cystathionine beta-synthase deficiency in pyridoxine responsive and nonresponsive homocystinuria. | Hu FL et al. | 1993 | Human molecular genetics |
| 7611293 | A missense mutation (I278T) in the cystathionine beta-synthase gene prevalent in pyridoxine-responsive homocystinuria and associated with mild clinical phenotype. | Shih VE et al. | 1995 | American journal of human genetics |
| 7762555 | The molecular basis of homocystinuria due to cystathionine beta-synthase deficiency in Italian families, and report of four novel mutations. | Sebastio G et al. | 1995 | American journal of human genetics |
| 8755636 | Defective cystathionine beta-synthase regulation by S-adenosylmethionine in a partially pyridoxine responsive homocystinuria patient. | Kluijtmans LA et al. | 1996 | The Journal of clinical investigation |
| 8940271 | High prevalence of a mutation in the cystathionine beta-synthase gene. | Tsai MY et al. | 1996 | American journal of human genetics |
| 10328723 | Prevalence of congenital homocystinuria in Denmark. | Gaustadnes M et al. | 1999 | The New England journal of medicine |
| 10338090 | Cystathionine beta-synthase mutations in homocystinuria. | Kraus JP et al. | 1999 | Human mutation |
| 10364517 | The molecular basis of cystathionine beta-synthase deficiency in Dutch patients with homocystinuria: effect of CBS genotype on biochemical and clinical phenotype and on response to treatment. | Kluijtmans LA et al. | 1999 | American journal of human genetics |
| 10807759 | Familial thrombophilia associated with homozygosity for the cystathionine beta-synthase 833T-->C mutation. | Gaustadnes M et al. | 2000 | Arteriosclerosis, thrombosis, and vascular biology |
| 11748855 | Cystathionine beta-synthase deficiency in Central Europe: discrepancy between biochemical and molecular genetic screening for homocystinuric alleles. | Sokolová J et al. | 2001 | Human mutation |
| 14722927 | The molecular basis of cystathionine beta-synthase (CBS) deficiency in UK and US patients with homocystinuria. | Moat SJ et al. | 2004 | Human mutation |
| 15748616 | Detection and allele-frequencies of the 833T>C, 844ins68 and a novel mutation in the cystathionine beta-synthase gene. | Griffioen PH et al. | 2005 | Clinica chimica acta; international journal of clinical chemistry |
| 15972722 | Expression of mutant human cystathionine beta-synthase rescues neonatal lethality but not homocystinuria in a mouse model. | Wang L et al. | 2005 | Human molecular genetics |
| 17072863 | Diversity of cystathionine beta-synthase haplotypes bearing the most common homocystinuria mutation c.833T>C: a possible role for gene conversion. | Vyletal P et al. | 2007 | Human mutation |
| 19112534 | Lack of association of polymorphisms in homocysteine metabolism genes with pseudoexfoliation syndrome and glaucoma. | Fan BJ et al. | 2008 | Molecular vision |
| 19330901 | Association of 77 polymorphisms in 52 candidate genes with blood pressure progression and incident hypertension: the Women's Genome Health Study. | Conen D et al. | 2009 | Journal of hypertension |
| 19493349 | 118 SNPs of folate-related genes and risks of spina bifida and conotruncal heart defects. | Shaw GM et al. | 2009 | BMC medical genetics |
| 19559392 | A candidate gene association study of 77 polymorphisms in migraine. | Schürks M et al. | 2009 | The journal of pain |
| 19683694 | Genetic association study of putative functional single nucleotide polymorphisms of genes in folate metabolism and spina bifida. | Martinez CA et al. | 2009 | American journal of obstetrics and gynecology |
| 19819175 | A revisit to the natural history of homocystinuria due to cystathionine beta-synthase deficiency. | Skovby F et al. | 2010 | Molecular genetics and metabolism |
| 20301697 | Homocystinuria Caused by Cystathionine Beta-Synthase Deficiency. | Sacharow SJ et al. | 1993 | GeneReviews(®) |
| 20419766 | Epidemiologic and genetic aspects of spina bifida and other neural tube defects. | Au KS et al. | 2010 | Developmental disabilities research reviews |
| 21254358 | Nonsyndromic cleft lip and palate: CRISPLD genes and the folate gene pathway connection. | Chiquet BT et al. | 2011 | Birth defects research. Part A, Clinical and molecular teratology |
| 21254359 | Folate pathway and nonsyndromic cleft lip and palate. | Blanton SH et al. | 2011 | Birth defects research. Part A, Clinical and molecular teratology |
| 21302343 | The ATXN1 and TRIM31 genes are related to intelligence in an ADHD background: evidence from a large collaborative study totaling 4,963 subjects. | Rizzi TS et al. | 2011 | American journal of medical genetics. Part B, Neuropsychiatric genetics |
| 21567207 | Tetra primer ARMS-PCR relates folate/homocysteine pathway genes and ACE gene polymorphism with coronary artery disease. | Masud R et al. | 2011 | Molecular and cellular biochemistry |
| 21615938 | Genetic polymorphisms in folate pathway enzymes, DRD4 and GSTM1 are related to temporomandibular disorder. | Aneiros-Guerrero A et al. | 2011 | BMC medical genetics |
| 21957013 | Genetic studies of the cystathionine beta-synthase gene and myelomeningocele. | Tilley MM et al. | 2012 | Birth defects research. Part A, Clinical and molecular teratology |
| 22833659 | Gender and single nucleotide polymorphisms in MTHFR, BHMT, SPTLC1, CRBP2, CETP, and SCARB1 are significant predictors of plasma homocysteine normalized by RBC folate in healthy adults. | Clifford AJ et al. | 2012 | The Journal of nutrition |
| 23592311 | Correction of cystathionine β-synthase deficiency in mice by treatment with proteasome inhibitors. | Gupta S et al. | 2013 | Human mutation |
| 23656756 | Single nucleotide polymorphisms in CETP, SLC46A1, SLC19A1, CD36, BCMO1, APOA5, and ABCA1 are significant predictors of plasma HDL in healthy adults. | Clifford AJ et al. | 2013 | Lipids in health and disease |
| 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 |
| 24033266 | A systematic approach to assessing the clinical significance of genetic variants. | Duzkale H et al. | 2013 | Clinical genetics |
| 24524080 | The effect of multiple single nucleotide polymorphisms in the folic acid pathway genes on homocysteine metabolism. | Liang S et al. | 2014 | BioMed research international |
| 26791477 | The effects of genes implicated in cardiovascular disease on blood pressure response to treatment among treatment-naive hypertensive African Americans in the GenHAT study. | Do AN et al. | 2016 | Journal of human hypertension |
| 28250422 | Components of the folate metabolic pathway and ADHD core traits: an exploration in eastern Indian probands. | Saha T et al. | 2017 | Journal of human genetics |
| 28514598 | The communal relation of MTHFR, MTR, ACE gene polymorphisms and hyperhomocysteinemia as conceivable risk of coronary artery disease. | Masud R et al. | 2017 | Applied physiology, nutrition, and metabolism = Physiologie appliquee, nutrition et metabolisme |
| 29413960 | Total sulfane sulfur bioavailability reflects ethnic and gender disparities in cardiovascular disease. | Rajpal S et al. | 2018 | Redox biology |
| 29574679 | In silico characterization of functional single nucleotide polymorphisms of folate pathway genes. | Vohra M et al. | 2018 | Annals of human genetics |
| 30380942 | Association of Cystathionine β-Synthase Gene Polymorphisms With Preeclampsia. | de León Bautista MP et al. | 2018 | Clinical and applied thrombosis/hemostasis |
| 33013017 | Association of Genetic Variants with Hyperhomocysteinemia in Indian Patients with Thrombosis. | Paradkar MU et al. | 2020 | Indian journal of clinical biochemistry |
| 33719952 | Molecular Evaluation of Exon 8 Cystathionine rs5742905T T>C Gene Polymorphism and Determination of its Frequency, Distribution Pattern, and Association with Susceptibility to Coronary Artery Disease in the North Indian Population. | Sumi MP et al. | 2021 | Cardiovascular & hematological disorders drug targets |
| 35264229 | Association of MTHFR rs1801133 and homocysteine with Legg-Calvé-Perthes disease in Mexican patients. | Buendía-Pazarán JG et al. | 2022 | Orphanet journal of rare diseases |
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
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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.
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.