Loss-of-function gene variant identified that is associated with lower non-HDL-c and CAD risk

Variant ASGR1 Associated with a Reduced Risk of Coronary Artery Disease 

Literature - Nioi P et al., N Engl J Med 2016

P. Nioi, Sigurdsson A, Thorleifsson G, et al.
N Engl J Med 2016;374:2131-2141


Non-HDL-c, encompassing all cholesterol-containing proatherogenic lipoproteins, has been shown to be a better predictor of CV risk than LDL-c. Non-HDL-c is calculated by subtracting HDL-c levels from total cholesterol, and included LDL-c, VLDL, IDL, lipoprotein(a) and chylomicron [1].
Genetic studies have discovered sequence variants that affect both cholesterol and the risk of coronary artery disease, thereby providing targets for the development of drugs to treat dyslipidaemia [2-6].
This study aimed to search for new variants that affect non-HDL-c levels, by interrogating whole genomes in samples obtained from a cohort of 2636 Icelanders. Variants that were found in these genomes were then imputed into the genomes of about 398,000 Icelanders, of whom 119,1146 had information on serum non-HDL-c levels. Icelandic data were corrected for familial relatedness.

Main results

  • Seven correlated noncoding single-nucleotide polymorphisms (SNPs) were identified on chromosome 17p13.1 that have an association with non-HDL-c levels.
  • The strongest association was seen with the minor allele of rs186021206 located 7.3 kb downstream from ASGR1, which encodes a subunit of the asialoglycoprotein receptor. This allele was associated with a decreases of non-HDL-c by 12.9 mg/dL (95%CI: 8.7 – 17.1 [0.33 mmol/L, 95%CI: 0.22-0.44], P=1.4x10-9).
  • Separate sequencing of a CG-enriched region of intron 4 of ASGR1 of 738 revealed a 12-bp deletion (del12). Del12 was seen in 1 in 120 heterozygous Icelandic carriers.
  • Del12 was more strongly associated with lower non-HDL-c levels than were any of the seven SNPs: 13.6 mg/dL (95%CI: 9,4-177 [0.35 mmol/L, 95%CI: 0.24-0.46], P=2.5x10-10) lower in heterozygous carriers than in noncarriers of del12.
  • After adjustment for the presence of del12, none of the seven SNPs remained significantly associated with the non-HDL-c level.
  • The association between del12 and lipid levels were also examined in samples from The Netherlands and Denmark, and similar effect sizes for the relation with non-HDL-c were observed. When combining all data, del12 was found to be associated with decreases of non-HDL-c by 15.3 mg/dL (95%CI: 11,7-18.9 [0.40 mmol/L, 95%CI: 0.30-0.49], P=1.0x10-16).
  • Functional analyses revealed that del12 altered splicing in carriers, resulting in a truncated ASGR1 protein that is degraded.
  • The association of del12 with non-HDL-c was found to be independent of both alkaline phosphatase and vitamin B12 levels, both of which were increased. The increase of alkaline phosphatase levels (almost 50%) was unlikely to reflect liver disease, since del12 was not related to other measures of liver function that commonly accompany changes in alkaline phosphatase levels during liver disease.
  • The effect of the del12 variant on the risk of coronary artery disease was assessed in 33,090 case patients and 236,254 controls from Iceland and in 9434 case patients and 13,160 controls from the United States. Carriers of del12 showed a lower risk of coronary artery disease in all data sets, yielding a combined odds ratio of 0.66 (95%CI: 0.55-0.79, P=4.0x10-6). Icelandic del12 carriers had a life span 1.5 years longer than that of noncarriers (95%CI: 0.2-2.8, P=0.02).
  • Another loss-of-function ASGR1 variant (p.W158X, 1 in 1850 persons) was identified in an extended Icelandic dataset, which was also associated with a lower non-HDL-c level (-24.9 mg/dL, 95%CI: -40.6 t -9.3, P=1.8x10-3) but no significantly lower risk of coronary artery disease was seen (OR: 0.65, 95%CI: 0.26-1.40, P=0.24).


Two loss-of-function variants have been identified of ASGR1 that are associated with lower levels of non-HDL-c levels. ASGR1 is a lectin that plays a role in the homeostasis of circulating glycoproteins, by mediating the endocytosis and degradation of a variety of desialylated glycoproteins. This study showed that the ASGR1 del12 variant has a larger effect on the risk of coronary artery disease than is predicted based on its effect on levels of non-HDL-c. This suggests that the atheroprotective effects of del12 go beyond the lowering of serum cholesterol levels.

Editorial comment [8]

Nioi et al. identified and confirmed in various cohorts that a del12 mutation in the ASGR1 gene was associated with a 34% lower risk of coronary artery disease. “This reduction in coronary risk is considerably larger than that associated with other genetic variants (e.g. PCSK9 mutation) and yet has a relatively lesser effect on non-HDL-cholesterol, which suggests that del12 protects against atherosclerosis through mechanisms independent of those governing non-HDL cholesterol levels.One such mechanism could be reduced inflammation2 owing to the lower triglyceride levels observed by Nioi and colleagues.” (…) “On the basis of studies in mice, the authors speculate that ASGPR [asialoglycoprotein receptor] may interact with the asialylated form of the LDL receptor and facilitate LDL-receptor recycling through endocytosis by the plasma membrane of hepatocytes, thereby affecting LDL cholesterol levels.”
Thus, the identification of ASGR1 as a link between the sialylation pathway, plasma levels of non-HDL cholesterol and coronary artery disease may provide a path to the development of future therapies for the prevention of coronary artery disease, but the mechanism via which loss-of-function of ASGR1 cause CV risk reduction need to be determined.

Find this article online at NEJM


1. Rana JS, Boekholdt SM, Kastelein JJ, Shah PK. The role of non-HDL cholesterol in risk stratification for coronary artery disease. Curr Atheroscler Rep 2012; 14:130-4.
2. Cohen J, Pertsemlidis A, Kotowski IK, et al. Low LDL cholesterol in individuals of African descent resulting from frequent nonsense mutations in PCSK9. Nat Genet 2005; 37: 161-5.
3. Abifadel M, Varret M, Rabès JP, et al. Mutations in PCSK9 cause autosomal dominant hypercholesterolemia. Nat Genet 2003; 34: 154-6.
4. Haddad L, Day IN, Hunt S, et al. Evidence for a third genetic locus causing familial hypercholesterolemia: a non-LDLR, non-APOB kindred. J Lipid Res 1999; 40: 1113-22.
5. Timms KM, Wagner S, Samuels ME, et al. A mutation in PCSK9 causing autosomal-dominant hypercholesterolemia in a Utah pedigree. Hum Genet 2004; 114:349-53.
6. Varret M, Rabès JP, Saint-Jore B, et al. A third major locus for autosomal dominant hypercholesterolemia maps to 1p34.1-p32. Am J Hum Genet 1999; 64: 1378-87.
7. Hunt SC, Hopkins PN, Bulka K, et al. Genetic localization to chromosome 1p32 of the third locus for familial hypercholesterolemia in a Utah kindred. Arterioscler Thromb Vasc Biol 2000; 20: 1089-93.
8. Tybjærg-Hansen A. The Sialylation Pathway and Coronary Artery Disease. N Engl J Med 2016;374:2169-2171.

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