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. Author manuscript; available in PMC: 2016 Jan 1.
Published in final edited form as: Nat Genet. 2015 May 18;47(7):717–726. doi: 10.1038/ng.3304

Table 1. Summary of conditions for which pathogenic genes were identified (class A, B or C).

Disease Project category Result class Genea Coding consequence Inheritance (Zygosity)b Variant
Acquired essential
thrombocytosis 		1.1 C THPO splicing D (het) NM_001177598: c.13+1G>C
Asplenia 2.2 C RPSAc splicing D (het) NM_002295.4:c.-34+5G>C
Cerebellar ataxia 1.2 B SPTBN2 nonsense AR (hom) NM_006946:c.1881G>A:p.C627*
Common variable
immunodeficiency disorder 		3 C d missense d d
Congenital dyserythropoietic
anaemia, type 1 		1.2 A C15ORF41 missense AR (hom) NM_001130010:c.533T>A:p.L178Q
Congenital myasthenic syndrome 3 B ALG2 missense AR (hom) NM_033087:c.203T>G:p.V68G
Craniosynostosis 2.1 A ZIC1 nonsense DN (het) NM_003412.3: c.1163C>A: p.S388*
2.1 B HUWE1 missense DN (het) NM_031407.6: c.329G>A:p.R110Q
Erythrocytosis 1.1 A EPO noncoding D (het) NM_000799.2:c.-136G>A
1.1 A EPO noncoding D (het) NM_000799.2:c.-136G>A
3 C BPGM missense D (het) NM_001724:c.269G>A:p.R90H
Familial hypoparathyroidism 1.3 C SOX3 noncoding XL (hemi) deletion of chrX:139,502,946-139,504,327,
1.5kb downstream of SOX3
1.1 C CASR missense D (het) NM_000388:c.2299G>C:p.E767Q
Familial juvenile hyperuricaemic
nephropathy 		1.4 C UMOD missense D (het) NM_001008389:c.410G>A:p.C137Y
Familial tubulo-interstitial
nephropathy 		1.1 C UMOD missense (inframe insertion/deletion) D (het) NM_001008389:c.279_289del:p.93_97del;
NM_001008389:c.278_279insCCGCCTCC:p.V9 3fs
Hypertrophic cardiomyopathy (sarcomere gene-negative) 1.1 C MYBPC3 nonsense e NM_000256:c.1303C>T:p.Q435*
Inflammatory bowel
syndrome/colitis 		4 A d missense d d
Interstitial nephritis 1.4 C MUC1c - D (het) d
Long QT syndrome 1.1 C KCNQ1 missense D (het) NM_000218:c.1195_1196insC:p.A399fs
Mental retardation 2.1 C GRIA3 missense XL (hemi) a
Ohtahara syndrome and other
early-onset epilepsies 		2.1 A PIGQ splicing SR (hom) NM_004204:c.690-2A>G
2.1 B KCNT1 missense UPID (hom) NM_020822: c. 2896G>A:p.A966T
2.1 C KCNQ2 missense DN (het) NM_004518:c.827C>T:p.T276I
2.1 C SCN2A missense DN (het) NM_001040143:c.5558A>G:p.H1853R
Multiple adenoma 1.1 A POLD1 missense D (het) NM_002691:c.1433G>A:p.S478N
1.1 A POLD1 missense D (het) NM_002691:c.1433G>A:p.S478N
4 A POLE missense D (het) NM_006231:c.1270C>G:p.L424V
4 C MSH6 missense and nonsense CR (het; het) NM_000179:c.2315G>A:p.R772Q
4 C BMPR1A frameshift AR (hom) NM_004329.2:c.142_143insT:p.Thr49Asnfs*2 2
4 C APC splicing D (het) NM_001127511:c.251-2A>G
Saethre-Chotzen syndrome
(TWIST1 negative) 		3 A TCF12 nonsense DN (het) NM_207037.1:c.1283T>G; p.L428*
3 A TCF12 splicing DN (het) NM_207037.1:c.1035+3G>C
2.1 A CDC45 synonymous (splicing) and missense CR (het; het) NM_001178010.2:c.318C>T;p.V106=;
NM_001178010.2:c.773A>G;p.D258G
a

Each line represents a separate case or family, so if the same gene is reported on two lines, this signifies that the gene is thought to be pathogenic in both cases. Some genes have two mutations in the same affected individual, likely representing compound heterozygous inheritance, which is indicated in the Inheritance column.

b

D(het): dominant - affected individual/s heterozygous; AR (hom): autosomal recessive – affected individual/s homozygous; DN (het) :de novo – affected individual/s heterozygous; XL (hemi): X-linked recessive – affected male/s hemizygous, affected female/s homozygous; UPD (hom): uniparental isodisomy–affected individual homozygous; CR (het; het): compound recessive – affected individual /s heterozygous for two different variants in the same gene

c

Causal variant discovered independently of WGS500.

d

Details will be reported in an independent publication.

e

Form of inheritance not clear. See Supplementary Table 8.