Table 1 Genes with sentinel variants enriched more than fourfold in either UKB or FG datasets
From: Genetic associations of protein-coding variants in human disease
Gene | rs ID (amino acid change) | Chr | A0/A1 | A1 frequency (UKB; FG (%)) | log2 FE (FG/UKB) | OMIM gene–phenotype relationships | CWAS gene–phenotype relationships |
|---|---|---|---|---|---|---|---|
CHEK2 | rs17879961 (I200T) rs555607708a (T410fs) | 22 | A/G AG/– | 0.04%; 2.99% 0.24%; 0.64% | 6.25 1.42 | Cancer (breast, prostate, colorectal, osteosarcoma); Li–Fraumeni syndrome | rs17879961:G, benign meningeal neoplasm rs555607708:del (2.8× FG enriched), cancer (breast, thyroid, colorectal (benign)); uterine leiomyoma; ovarian cysts; PCOS |
DBH | rs77273740 (R79W) | 9 | C/T | 0.10%; 4.95% | 5.69 | Orthostatic hypotension | Hypertension (IA) |
PITX2 | rs143452464 (P41S) | 4 | G/A | 0.02%; 1.01% | 5.42 | Anterior segment dysgenesis; Axenfeld–Rieger syndrome; ring dermoid of cornea | Arrythmia and AF |
SLC24A5 | rs1426654 (T111A) | 15 | A/G | 0.09%; 1.13% | 3.67 | Skin, hair, eye pigmentation (dark); oculocutaneous albinism | Non-epithelial cancer of skin (other) (IA) |
CFHR5 | rs565457964 (E163fs) | 1 | C/CAA | 0.32%; 3.96% | 3.66 | Nephropathy due to CFHR5 deficiency | Degeneration of macula and posterior pole of retina (IA) |
ANKH | rs146886108 (R187Q) | 5 | C/T | 0.72%; 0.07% | -3.28 | Chondrocalcinosis; craniometaphyseal dysplasia | Type 2 diabetes mellitus (IA) |
ALDH16A1 | rs150414818 (P527R) | 19 | C/G | 0.10%; 0.95% | 3.23 | – | Gout |
LRRK1 | rs41531245 (T967M) | 15 | C/T | 0.09%; 0.76% | 3.15 | – | Contracture of palmar fascia; fasciitis; umbilical hernia |
CFI | rs141853578 (G119R) | 4 | C/T | 0.11%; 0.01% | −3.10 | Atypical haemolytic uremic syndrome; age-related macular degeneration; CFI deficiency | Retinal disorders (other) |
FLG | rs61816761 (R501*) rs138381300a (S761fs) | 1 | G/A CACTG/− | 2.45%; 0.29% 2.45%; 1.35% | −3.10 −0.85 | Atopic dermatitis; ichthyosis vulgaris | rs61816761:A, dermatitis (other) rs138381300:del (1.8× UKB enriched), asthma; non-epithelial cancer of skin (other) |
SOS2 | rs72681869 (P191R) | 14 | G/C | 1.09%; 0.15% | −2.84 | Noonan syndrome | Hypertension (IA) |
XPA | rs144725456 (H244R) | 9 | T/C | 0.01%; 0.06% | 2.61 | Xeroderma pigmentosum | Non-epithelial cancer of skin (other) |
CDC25A | rs146179438 (Q24H) | 3 | C/A | 1.52%; 8.72% | 2.52 | − | Kidney and urinary stones (IA) |
F10 | rs61753266 (E142K) | 13 | G/A | 0.33%; 1.83% | 2.46 | Factor X deficiency | PE and pulmonary heart disease (inverse association) |
TNXB | rs61745355 (G2848R) rs10947230a (R2704H) rs11507521 (T302A) | 6 | C/T C/T T/C | 2.22%; 11.86% 5.96%; 14.75% 13.29%; 9.17% | 2.42 2.31 −0.54 | Ehlers–Danlos syndrome; vesicoureteral reflux | rs61745355:T, lymphoma rs10947230:T, lichen planus rs1150752:C, chronic hepatitis; other inflammatory liver diseases; atherosclerosis |
SLC39A8 | rs13107325 (A391T) | 4 | C/T | 7.40%; 1.46% | −2.35 | Congenital disorder of glycosylation | Shoulder lesions |
CLPTM1 | rs150484293 (L140F) | 19 | C/T | 0.35%; 0.07% | −2.33 | − | Dementia |
ELL2 | rs141299831 (S18L) | 5 | G/A | 0.02%; 0.12% | 2.29 | − | Benign neoplasm of other and ill-defined parts of digestive system |
CASP7 | rs141266925 (F214L) | 10 | T/C | 0.31%; 1.5% | 2.29 | − | Cataracts |
BRCA1 | rs80357906 (Q1777fs) | 17 | T/TG | 0.001%; 0.01% | 2.21 | Cancer (breast, ovarian, pancreatic); Fanconi anaemia | Breast cancer |
SCN5A | rs45620037 (T220I) | 3 | G/A | 0.11%; 0.49% | 2.20 | Sudden infant death syndrome; dilated cardiomyopathy; arrythmiab | Arrythmia and AF |
CACNA1D | rs1250342280 (F1943del) | 3 | CCTT/C | 0.60%; 0.14% | −2.09 | Primary aldosteronism, seizures, and neurologic abnormalities; sinoatrial node dysfunction and deafness | Hypertension |
WNT10A | rs121908120 (F228I) | 2 | T/A | 2.72%; 0.65% | −2.06 | Odontoonychodermal dysplasia; Schopf–Schulz–Passarge syndrome; selective tooth agenesis | Follicular cysts of skin and subcutaneous tissue (IA) |
