rs4523957

This is a upstream gene variant variant in the SMG6 gene.

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GWAS Catalog Trait Associations (3)

Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.

osteoarthritis, knee, total knee arthroplasty

Hatzikotoulas K et al. “Translational genomics of osteoarthritis in 1,962,069 individuals.” Nature 641(8065):1217-1224 (2025)
Allele T
OR 0.93
p 2.0e-20
N 1,006,624
Large GWAS
multi-ancestry

schizophrenia

“Biological insights from 108 schizophrenia-associated genetic loci.” Nature 511(7510):421-7 (2014)
Allele T
OR 1.07
p 3.0e-10
N 83,550
Large GWAS
multi-ancestry
Goes FS et al. “Genome-wide association study of schizophrenia in Ashkenazi Jews.” American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics : the Official Publication of the International Society of Psychiatric Genetics 168(8):649-59 (2015)
Allele T
OR 1.07
p 1.0e-9
N 151,161
Large GWAS
Other
Ikeda M et al. “Genome-Wide Association Study Detected Novel Susceptibility Genes for Schizophrenia and Shared Trans-Populations/Diseases Genetic Effect.” Schizophrenia Bulletin 45(4):824-834 (2019)
Allele T
OR 1.07
p 1.0e-9
N 122,624
Large GWAS
multi-ancestry
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Research that mentions this SNP (2)

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Common variants in QPCT gene confer risk of schizophrenia in the Han Chinese population
MethodsRaja Amjad Waheed Khan et al.(2016)· American Journal of Medical Genetics Part B: Neuropsychiatric Genetics

This paper presents CalPen, a web-based tool for calculating penetrance (disease likelihood given a mutation) in complex genetic disorders. The authors validated CalPen against published penetrance calculations for schizophrenia-associated copy number variants (CNVs) and single nucleotide polymorphisms (SNPs). They analyzed 15 CNVs in 39,059 schizophrenia patients and 55,084 controls (average penetrance 7%, ranging from ~1.4% for 15q11.2 deletions to ~20% for 22q11.21 CNVs) and 145 SNPs in 45,405 patients and 122,761 controls (average penetrance 0.7%, with rs1801028 showing the highest at 1.6%).

Traits studied:Schizophrenia
PubMedDOIMetascience Observatory
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Genetic Variants Associated With Cardiac Structure and Function
Meta-analysisN=16,706Ramachandran S. Vasan et al.(2009)· JAMA

Meta-analysis of genome-wide association studies in 12,612 individuals from the EchoGen consortium identified 16 genetic loci associated with echocardiographic traits in stage 1, with 5 loci replicating in stage 2: rs89107 and rs11153768 (6q22) associated with left ventricular diastolic dimensions (explaining <1% variance), and rs17470137, rs4026608, rs10770612, rs893817 (5q23, 12q14, 12p12, 15q24 loci) associated with aortic root size (explaining 1-3% variance).

Traits studied:Aortic root sizeLeft atrial sizeLeft ventricular diastolic internal dimensionsLeft ventricular massLeft ventricular systolic dysfunctionLeft ventricular wall thickness
PubMedDOIMetascience Observatory

About SMG6

This gene encodes a component of the telomerase ribonucleoprotein complex responsible for the replication and maintenance of chromosome ends. The encoded protein also plays a role in the nonsense-mediated mRNA decay (NMD) pathway, providing the endonuclease activity near the premature translation termination codon that is needed to initiate NMD. Alternatively spliced transcript variants encoding distinct protein isoforms have been described. [provided by RefSeq, Feb 2014]

View all SMG6 variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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