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Table 1 Some clear, consistent common disease associations.

From: Functional single nucleotide polymorphism-based association studies

Gene

Disease

Presumed

causative

variant

Functional effect

Approximate frequency

(in ethnic population of

first positive study)

Frequency information

For other populationsa

PTPN22

Rheumatoid

arthritis [3–13]

R620W

nsSNP

9-10% (Caucasian)[3–13]

0% in n = 1,600 Japanese;

0% in n = 60 Africans [3, 14]

-

Type 1

diabetes [7, 9, 15–20]

-

-

-

-

CFH

(factorH)

Macular

degeneration [21–26]

Y402H

nsSNP

30 40%

(Caucasians)[21–26]

Unknown

FV

(factor5)

Deep venous

thrombosis [27–34]

R506W

nsSNP

3 7% (Caucasians)[35]

0% in n = 800 from Africa,

South-East Asia, Australasia and the

Americas (Native) [35, 36]

F2

(prothrombin)

Deep venous

thrombosis [34, 37–40]

G20210A

3' utr mRNA

cleavage site [41]

1 3% (Caucasians)[42]

0% in Asians;0% in Africans [36, 40, 42]

CARD15

(NOD2)

Crohn's

disease [43–46]

1007fs

Frame shift causing

truncated protein

~2% (Caucasians)

0% in [Q3] n = 888 Asians; 0% in n = 640 Gambians [47–49]

-

-

R702W

nsSNP

~4% (Caucasians)

< 0.1% in 888 Asians; 0% in 640 Gambians [47–49]

-

-

G908R

nsSNP

~1% (Caucasians)

< 0.1% in n = 888 Asians; 0% in n = 640 Gambians [47–49]

-

-

Several very

rare variants

nsSNPs

< 1% (Caucasians)

Unknown

CHEK2

Breast cancer [50–56]

1100delC

Frame shift causing

truncated protein

0.5-1.5% (Caucasians)[50–56]

Unknown

APOE

Alzheimer's

disease [57–60]

C112R

nsSNP

~15% (Caucasians)[57–61]

25 40% in Africans; 8% in Asians [62–65]

KCNJ11

Type 2 diabetes [66, 67]

E23K

nsSNP

~40% (Caucasians)[68]

Unknown

CCR5

HIV infection [69–73]

Delta32

Frame shift causing truncated protein

8 10% (Caucasians)[69–73]

Absent in Africans and Asians; 2 5% in the Middle East, India, Europe [74]

HLA-

various genes

Many autoimmune

diseases

Varied

Largely

nsSNPs/haplotypes

Varied

Varied; many show striking population frequency differences

  1. Abbreviations: nsSNP = non-synonymous single nucleotide polymorphisms; utr = untranslated regions.
  2. a With the exception of HLA and APOE, none of the presumed causative variants have been shown to be present above 1 per cent in multiple major ethnic populations. While the 112R allele of APOE (which defines APOE*4 from the major allele, APOE*3) is seen in African, Asians and Caucasians, this variant is not associated with Alzheimer's disease in African populations [63].
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Human Genomics

ISSN: 1479-7364