COL4A1 Q1334H - GET-Evidence

Curation:
Currentness:

COL4A1 Q1334H

(COL4A1 Gln1334His)


Short summary

This common variant has been associated with arterial stiffness and, in Japanese, a small increased risk of myocardial infarction (MI, a.k.a. heart attack). This last observation supported a dominant effect for this variant and, assuming a lifetime risk of 15% for MI, we estimate carriers have an additional risk of 0.5-3%.

Variant evidence
Computational

This collagen gene is associated with angiopathy, but amino acid change is not disruptive and polyphen 2 predicts a benign effect.

Functional -
Case/Control 5

Very high significance

See Yamada Y et al. 2008 (18077766).

Familial
 
Clinical importance
Severity 4

Myocardial infarction can be fatal

Treatability 4

Standard treatments exist to treat cardiovascular disease

Penetrance 2

0.5-3% attributable increased risk

 

Impact

Low clinical importance, Likely pathogenic

(The "low clinical importance, likely" qualifier is assigned automatically based on the above evidence and importance scores.)

Inheritance pattern

dominant

Summary of published research, and additional commentary

 

Allele frequency

  • G @ chr13:110818598: 32.5% (3493/10758) in EVS
  • G @ chr13:109616598: 30.5% (39/128) in GET-Evidence
  • Frequency shown in summary reports: 32.5% (3493/10758)

Publications
 

Blacher J, Asmar R, Djane S, London GM, Safar ME. Aortic pulse wave velocity as a marker of cardiovascular risk in hypertensive patients. Hypertension. 1999 May;33(5):1111-7. PubMed PMID: 10334796.

This paper is used to try to help interpret the phenotype risk for PWV findings in Tarasov et al. Using figure 1, it looks like there’s about .0325 (3.25%) increased risk of cardiovascular disease per meter/second PWV.

Yamada Y, Kato K, Oguri M, Fujimaki T, Yokoi K, Matsuo H, Watanabe S, Metoki N, Yoshida H, Satoh K, Ichihara S, Aoyagi Y, Yasunaga A, Park H, Tanaka M, Nozawa Y. Genetic risk for myocardial infarction determined by polymorphisms of candidate genes in a Japanese population. J Med Genet. 2008 Apr;45(4):216-21. Epub 2007 Dec 12. PubMed PMID: 18077766.

This association study looked for associations between 40 variants and myocardial infarction, including this variant. The case/control genotype counts are: case var/var: 76, case var/+: 481, case /: 771, cont var/var: 148, cont var/+: 864, cont /: 1093.

These numbers are highly significant when applying Fisher’s Exact test to a dominant hypothesis (p = 3.2e-7) and counting number of alleles in each group (p = 3.1e-6), but not under a recessive hypothesis (p = 0.30). Thus, we treat this as having a dominant effect. Assuming a lifetime risk of MI of 15%, we estimate from these numbers that this variant is associated with an attributable increased risk of 3% (18% total risk).

Tarasov KV, Sanna S, Scuteri A, Strait JB, Orrù M, Parsa A, Lin PI, Maschio A, Lai S, Piras MG, Masala M, Tanaka T, Post W, O'Connell JR, Schlessinger D, Cao A, Nagaraja R, Mitchell BD, Abecasis GR, Shuldiner AR, Uda M, Lakatta EG, Najjar SS. COL4A1 is associated with arterial stiffness by genome-wide association scan. Circ Cardiovasc Genet. 2009 Apr;2(2):151-8. Epub 2009 Feb 18. PubMed PMID: 20031579; PubMed Central PMCID: PMC2801872.

This variant is associated with an effect of 16 cm/s PWV.

Based on Blacher et al, this is .5% increased risk of cardiovascular disease. This is much smaller than the effect implied by Yamada et al, but our estimation of the effect size in that case was also based upon some assumptions on the prevalence of MI. In addition, the Yamada et al. report may overestimate the variant’s effect due to publication bias.

Genomes
 

hu011C57 - CGI sample GS01669-DNA_B05 from PGP sample 86486261
het G @ chr13:110818598

 

hu034DB1 - CGI sample GS00253-DNA_A02_200_37
het G @ chr13:110818598

 

hu0D879F - CGI sample GS00253-DNA_G01_200_37
hom G @ chr13:110818598

 

 

hu241DEA - CGI sample GS01175-DNA_D05 from PGP sample 1205491
het G @ chr13:110818598

 

hu2D6140 - CGI sample GS01173-DNA_F06 from PGP sample 64191565
hom G @ chr13:110818598

 

hu342A08 - CGI sample GS01175-DNA_B05 from PGP sample 83494370
het G @ chr13:110818598

 

 

hu38168C - CGI sample GS01173-DNA_H06 from PGP sample 91708424
het G @ chr13:110818598

 

 

hu3CAB43 - CGI sample GS01175-DNA_D03 from PGP sample 27486199
het G @ chr13:110818598

 

hu72A81D - CGI sample GS01173-DNA_C02 from PGP sample 10366372
het G @ chr13:110818598

 

hu92C40A - CGI sample GS01175-DNA_G03 from PGP sample 92527586
het G @ chr13:110818598

 

hu9385BA - CGI sample GS00253-DNA_E01_200_37
het G @ chr13:110818598

 

huA0E089 - CGI sample GS01175-DNA_B04 from PGP sample 88590671
het G @ chr13:110818598

 

huAE6220 - CGI sample GS00253-DNA_H01_200_37
het G @ chr13:110818598

 

huBEDA0B - CGI sample GS00253-DNA_C01_200_37
het G @ chr13:110818598

 

huC30901 - CGI sample GS00253-DNA_B01_200_37
hom G @ chr13:110818598

 

huD37D14 - CGI sample GS01175-DNA_A04 from PGP sample 13272228
het G @ chr13:110818598

 

huD81F3D - CGI sample GS01173-DNA_D06 from PGP sample 69488604
hom G @ chr13:110818598

 

huFAF983 - CGI sample GS01175-DNA_F02 from PGP sample 95788191
het G @ chr13:110818598

 

huFFAD87 - CGI sample GS01669-DNA_H05 from PGP sample 10971581
het G @ chr13:110818598

 

GS10851 - var-GS10851-1100-36-ASM
het G @ chr13:109616599

 

GS12004 - var-GS12004-1100-36-ASM
hom G @ chr13:109616599

 

GS18504 - var-GS18504-1100-36-ASM
het G @ chr13:109616599

 

GS18517 - var-GS18517-1100-36-ASM
het G @ chr13:109616599

 

GS18558 - var-GS18558-1100-36-ASM
het G @ chr13:109616599

 

GS18947 - var-GS18947-1100-36-ASM
het G @ chr13:109616599

 

GS19020 - var-GS19020-1100-36-ASM
het G @ chr13:109616599

 

GS19025 - var-GS19025-1100-36-ASM
het G @ chr13:109616599

 

GS19129 - var-GS19129-1100-36-ASM
het G @ chr13:109616599

 

GS19239 - var-GS19239-1100-36-ASM
het G @ chr13:109616599

 

GS19648 - var-GS19648-1100-36-ASM
hom G @ chr13:109616599

 

GS19649 - var-GS19649-1100-36-ASM
het G @ chr13:109616599

 

GS19670 - var-GS19670-1100-36-ASM
het G @ chr13:109616599

 

GS19701 - var-GS19701-1100-36-ASM
het G @ chr13:109616599

 

GS19703 - var-GS19703-1100-36-ASM
het G @ chr13:109616599

 

GS19704 - var-GS19704-1100-36-ASM
het G @ chr13:109616599

 

GS19735 - var-GS19735-1100-36-ASM
het G @ chr13:109616599

 

GS20502 - var-GS20502-1100-36-ASM
het G @ chr13:109616599

 

Other external references
 

    dbSNP
  • rs3742207
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    GeneTests
  • GeneTests records for the COL4A1 gene
    Autosomal Dominant Type 1 Porencephaly
    Brain Small Vessel Disease with Hemorrhage
    COL4A1-Related Disorders
    Hereditary Angiopathy with Nephropathy, Aneurysms, and Muscle Cr
    www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/COL4A1
    GWAS
  • Arterial stiffness (rs3742207-C)
    Tarasov 1-Apr-09 in Circ Cardiovasc Genet
    OR or beta: 21 [11.79-30.21] cm/s increase
    Risk allele frequency: 0.44
    p-value: 5.00E-08
    Initial sample: 4,221 Sardinian individuals
    Replication sample: 1,828 Sardinian individuals, 813 Old-Order Amish individuals
    www.ncbi.nlm.nih.gov/pubmed/20031579
    PharmGKB
  • [Cardiovascular Diseases]
    This SNP was identified in a GWAS performed for 4221 Sardinian individuals as being significantly associated with Carotid-femoral pulse wave velocity, which is a measure of arterial stiffness. The association was replicated in a second Sardinian cohort (1857 subjects) and then in a cohort of 813 Old-Order Amish of Lancaster, PA. Risk or phenotype-associated allele: C allele. Phenotype: increased Pulse Wave Velocity. Significance metric(s): P value: overall p = 5.16 x 10(-8). Type of association: CO; GN.
    www.ncbi.nlm.nih.gov/pubmed/20031579
  • [Myocardial Infarction]
    This variant is significantly associated with myocardial infarction in Japanese population.
    www.ncbi.nlm.nih.gov/pubmed/18077766
    PolyPhen-2
  • Score: 0.16 (benign)
    Web search results (17 hits -- see all)
  • 刘志诚教授针刺治疗单纯性肥胖症经验介绍
    刘志诚是南京中医药大学第二临床医学院教授,博士研究生导师,享受国务院政府津贴,江苏省名中西医结合专家。20多年来,先后主持了卫生部和国家自然科学基金会以及国家教育部博导基金会等 ... COL4A1基因Q1334H多态性与中国男性骨密度显著相关性研究. 葛根素对大鼠视网膜缺血再灌注损伤中肿瘤坏死因子-α表达的影响及意义. 胃 ...
    www.chemdrug.com/databases/7_1_tsnrixrfrejhnrwn.html
  • 胡黄连苷Ⅱ在谷氨酸诱导的PC12细胞损伤中的保护作用
    目的:以谷氨酸为工具药建立氧化应激模型,观察胡黄连苷Ⅱ的保护作用并初步探讨其作用机制。方法:分别用不同浓度的胡黄连苷Ⅱ和10mmol/L的谷氨酸处理PC12细胞,通过MTT法检测 ... COL4A1基因Q1334H多态性与中国男性骨密度显著相关性研究. 葛根素对大鼠视网膜缺血再灌注损伤中肿瘤坏死因子-α表达的影响及意义. 胃 ...
    www.chemdrug.com/databases/7_2_wbrqtmlmkomxttjb.html
  • polymorphism 在 内分泌腺及全身性疾病 分类中 的双语句对查询结果 --cnki翻译助手
    polymorphism 在 内分泌腺及全身性疾病 分类中 的双语句对查询结果:||双语例句|英文例句|相关文摘 ... found between the Q1334H polymorphism of the COL4A1 gene and lower femoral neck BMD (p=0.0074) ...
    dict.cnki.net/...&style=E065&tjType=sentence
  • 中国现代医学杂志.China Journal of Modern Medicine(2007年3期)-万方数据知识服务平台
    首页学术期刊学位论文学术会议中外专利中外标准科技成果法律法规专题. 首页 > 学术期刊 > 医药卫生 > 医药卫生总论 > 中国现代医学杂志 > ... COL4A1基因Q1334H多态性与中国男性骨密度显著相关性研究 吴涤,洪秀梅,杨天鹏,李志平,臧桐华,WU Di,HONG Xiu-mei,YANG Tian ...
    c.wanfangdata.com.cn/periodical/zgxdyxzz/2007-3.aspx
  • 期刊各卷期文章清單
    Synthesis and Characterization of Hydroxyapatite Nanoparticles for ... COL4A1基因Q1334H多态性与中国男性骨密度显著相关性研究. 吴涤;洪秀梅;杨天鹏;李志平;臧桐华. 269-271. 5. 论著. 小鼠肝细胞胰岛素与EGF信号转导磷蛋白质组的动力 ...
    ceps.com.tw/ec/...&jnltype=45&newIssueIID=45340&jnliid=2498
  • 中国现代医学杂志 - China Journal of Modern Medicine -2007年 第03期目录- 维普中文期刊
    COL4A1基因Q1334H多态性与中国男性骨密度显著相关性研究. 吴涤 洪秀梅 杨天鹏 李志平 臧桐华 (269) 小鼠肝细胞胰岛素与EGF信号转导磷蛋白质组的动力学行为对比分析. 刘友平 李洪 丁慧荣 何涛 张春燕 (272) 葛根素对大鼠视网膜缺血再灌注损伤中肿瘤坏死因子-α表达的影响及意义. 游志鹏 赵成 (275) ...
    www.cqvip.com/qk/98531X/200703/index.shtml
  • author:杨天鹏 - CNKI知识搜索
    COL4A1基因Q1334H多态性与中国男性骨密度显著相关性研究. 吴涤 洪秀梅 杨天鹏 李志平 臧桐华 中国现代医学杂志 2007年 第03期 ...
    search.cnki.com.cn/search.aspx?...&cluster=all&val=&p=0

Other in silico analyses
 

  • NBLOSUM100 score = –1
  • GET-Evidence autoscore = 4

Edit history
 

Gene search

"GENE" or "GENE A123C":

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