rs143383
| Orientation | minus |
| Stabilized | minus |
| Geno | Mag | Summary |
|---|---|---|
| (C;C) | 0 | normal risk for osteoarthritis |
| (C;T) | 1.2 | 1.1x increased risk for osteoarthritis |
| (T;T) | 1.8 | 1.3x increased risk for osteoarthritis |
| Reference | GRCh38 38.1/141 |
| Chromosome | 20 |
| Position | 35438203 |
| Gene | GDF5 |
| is a | snp |
| is | mentioned by |
| dbSNP | rs143383 |
| dbSNP (classic) | rs143383 |
| ClinGen | rs143383 |
| ebi | rs143383 |
| HLI | rs143383 |
| Exac | rs143383 |
| Gnomad | rs143383 |
| Varsome | rs143383 |
| LitVar | rs143383 |
| Map | rs143383 |
| PheGenI | rs143383 |
| Biobank | rs143383 |
| 1000 genomes | rs143383 |
| hgdp | rs143383 |
| ensembl | rs143383 |
| geneview | rs143383 |
| scholar | rs143383 |
| rs143383 | |
| pharmgkb | rs143383 |
| gwascentral | rs143383 |
| openSNP | rs143383 |
| 23andMe | rs143383 |
| SNPshot | rs143383 |
| SNPdbe | rs143383 |
| MSV3d | rs143383 |
| GWAS Ctlg | rs143383 |
| GMAF | 0.4646 |
| Max Magnitude | 1.8 |
| ? | (C;C) (C;T) (T;T) | 28 |
|---|---|---|
|
| ||
This SNP is associated with osteoarthritis (OA). It is located in the five prime untranslated region (5′UTR) of the gene encoding growth differentiation factor 5 (GDF5), a chondrogenic protein active from the embryonic stage onwards. GDF5 is also known as cartilage-derived morphogenetic protein 1 or BMP14.
The risk allele T (+ 104T/C;rs143383) causes reduction of the GDF5 promoter sequence activity. Reduction of GDF5 in human cartilage of patients with OA by up to 27% has been observed [1]. This effect is influenced by a second SNP ( rs143384 , C/T ) in the same area. The C alleles of both SNPs form CpG dinucleotides. Demethylation of both SNP's increases GDF5 expression.[2] [PMID 21642387] "Expression of the osteoarthritis-associated gene GDF5 is modulated epigenetically by DNA methylation." Thus the authors conclude that epigenetic manipulation offers options in developing therapies for OA.
[PMID 17384641] rs143383 showed significant association with hip osteoarthritis in two independent Japanese populations. It also showed association with knee osteoarthritis in Japanese and Chinese populations.
[PMID 17676627] is *not* a risk factor for osteoarthritis in Greek Caucasians
A subsequent study showed that the same risk allele, rs143383(T), was (somewhat) associated with osteoarthritis in European populations. The odds ratio was 1.10 for the allele, 1.28 for carrier status (p=0.03, p=0.004, respectively). The (T) allele appears to make less GDF5 protein, which eventually renders an individual somewhat more susceptible to osteoarthritis.[PMID 17616513]
A meta-analysis combining data from 11,000+ individuals as well as both European and Asian populations found strong evidence (p < 0.0004) confirming increased risk for osteoarthritis from the rs143383(T) allele. The best model is a dominant one, and the odds ratio reported is 1.21 in general and 1.48 for the dominant model.[PMID 18299287]
Another meta-analysis of 14 studies concluded that rs143383 did indeed show significant association with osteoarthritis, at least for knee osteoarthritis, and probably for hand and hip (but to a lesser degree). The effect size wasn't large, though (odds ratio 1.15, CI: 1.09-1.22, p = 9.4 x 10e-7).[PMID 19479880
]
A haplotype of rs143383 and rs6060369 can be defined, which also links osteoarthritis to height since rs6060369 was linked to height in a study ultimately involving over 28,000 individuals.[PMID 18193045]
The Medpage article on this finding notes that rs143383 was previously shown to be associated with increased risk for osteoarthritis and in this recent study [PMID 18193045] it was significantly associated with shorter height in the initial scans, at p=2.70x10e-5.
Note that the authors of [PMID 18193045] refer to rs143383 in the opposite orientation compared to it's entry in dbSNP.
[PMID 18947434] A study of 338 Han Chinese children affected by congenital dysplasia of the hip revealed that rs143383(T) alleles conferred a 1.4x increased risk for the disorder, particularly in females (odds ratio 1.43, CI: 1.11 - 1.85, p = 0.0078).
[PMID 19029166] A study of 6,365 elderly Caucasian men and women observed significant association between rs143383 and osteoarthritis, height, bone size and fracture risk in women.
[PMID 19565498] Functional analysis of the osteoarthritis susceptibility-associated GDF5 regulatory polymorphism
[PMID 20499385] Different risk factors are involved in clinically severe large joint osteoarthritis according to the presence of hand interphalangeal nodes
[PMID 20633687] Evidence of association between GDF5 polymorphisms and congenital dislocation of the hip in a Caucasian population
[PMID 21128259] GDF5 SNP rs143383 is associated with lumbar disc disease in northern European women
[PMID 21542882] Knee osteoarthritis, lumbar-disc degeneration and developmental dysplasia of the hip - an emerging genetic overlap
[PMID 22284607] Genetic association analysis of GDF5 and ADAM12 for knee osteoarthritis.
[PMID 18245884] [Genomic approaches to bone and joint diseases. Current status of genetic study of osteoarthritis].
[PMID 18471798] Genome-wide association scan identifies a prostaglandin-endoperoxide synthase 2 variant involved in risk of knee osteoarthritis.
[PMID 19054821] Association of the DVWA and GDF5 polymorphisms with osteoarthritis in UK populations.
[PMID 19343178] Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size.
[PMID 20237151] Field synopsis and synthesis of genetic association studies in osteoarthritis: the CUMAGAS-OSTEO information system.
[PMID 20360039] Components of the transforming growth factor-beta family and the pathogenesis of human Achilles tendon pathology--a genetic association study.
[PMID 20870806] The GDF5 rs143383 polymorphism is associated with osteoarthritis of the knee with genome-wide statistical significance.
[PMID 21154330] [Association of genetic and mechanical factors with age of onset of knee osteoarthritis].
[PMID 21281725] Deep sequencing of GDF5 reveals the absence of rare variants at this important osteoarthritis susceptibility locus.
[PMID 21360499] GDF5 single-nucleotide polymorphism rs143383 is associated with lumbar disc degeneration in Northern European women.
[PMID 22615457] Genetic contribution to radiographic severity in osteoarthritis of the knee.
[PMID 23090674] The GDF5 Gene and Anterior Cruciate Ligament Rupture
[PMID 23825960] The Identification of Trans-acting Factors That Regulate the Expression of GDF5 via the Osteoarthritis Susceptibility SNP rs143383
[PMID 24003854] The genetics of common degenerative skeletal disorders: osteoarthritis and degenerative disc disease
[PMID 24105021] A SNP in the 5'UTR of GDF5 is associated with susceptibility to symptomatic lumbar disc herniation in the Chinese Han population
[PMID 24227118] The GDF5 SNP is Associated with Meniscus Injury and Function Recovery in Male Chinese Soldiers
[PMID 22929025] A rare variant in the osteoarthritis-associated locus GDF5 is functional and reveals a site that can be manipulated to modulate GDF5 expression.
[PMID 22956599] Evaluation of the genetic overlap between osteoarthritis with body mass index and height using genome-wide association scan data.
[PMID 23357225] Association study of candidate genes for the progression of hand osteoarthritis.
[PMID 24861163] CpG methylation regulates allelic expression of GDF5 by modulating binding of SP1 and SP3 repressor proteins to the osteoarthritis susceptibility SNP rs143383
| ClinVar | |
|---|---|
| Risk | Rs143383(C;C) |
| Alt | Rs143383(C;C) |
| Reference | Rs143383(T;T) |
| Significance | Other |
| Disease | Osteoarthritis of hip Fibular hypoplasia and complex brachydactyly Chondrodysplasia Acromesomelic Dysplasia Symphalangism-brachydactyly syndrome Brachydactyly |
| Variation | info |
| Gene | GDF5 |
| CLNDBN | Osteoarthritis of hip Fibular hypoplasia and complex brachydactyly Chondrodysplasia Acromesomelic Dysplasia Symphalangism-brachydactyly syndrome Brachydactyly |
| Reversed | 1 |
| HGVS | NC_000020.10:g.34025983A>G |
| CLNSRC | OMIM Allelic Variant |
| CLNACC | RCV000008898.3, RCV000285133.1, RCV000290932.1, RCV000344695.1, RCV000350530.1, RCV000385268.1, |
[PMID 25894512] A comprehensive meta-analysis of association between genetic variants of GDF5 and osteoarthritis of the knee, hip and hand
[PMID 29056119] Polymorphisms in the Growth Differentiation Factor 5 (GDF 5) Gene in Knee Osteoarthritis.
[PMID 29797005] Genetic Influence in Developmental Dysplasia of the Hip in Saudi Arabian Children Due to GDF5 Polymorphism.
[PMID 30044130] Association Between the SNP rs143383 + 104T/C in the GDF5 Gene and the Risk of Knee Osteoarthritis in a Population from Northern Mexico-A Case-Control Study.
[PMID 30186416] Association between GDF5 single nucleotide polymorphism rs143383 and lumbar disc degeneration.
[PMID 32185351] Genetic Association Between Growth Differentiation Factor 5 Single Nucleotide Polymorphism and Primary Knee Osteoarthritis in a Group of Egyptian Patients: A Pilot Study.
