Table 2

Diseases associated with genes containing nsSNPs

General Category

# Associated Deleterious SNPs

Gene names

Diseases


Apoptosis

8

CYCS;

Huntington's disease

DNA damage

Alzheimer's disease

TNFRSF10D;

Thrombocytopenia

Bipolar

Rheumatoid arthritis

CASP7; MAP3K1;

Diabetes mellitus type I

Renal cell carcinoma

Myeloproliferative disorders

PRKCZ; MPL;

TNFRSF19

Leukemia

Diabetes mellitus type II

Amyotrophic lateral Sclerosis

Pancreatitis

Carcinoma (multiple types)

Multiple sclerosis


Cell cycle

20

BRCA2; POLD2;

Spontaneous abortion

Genomic instability

Drug toxicity

CDC14A; CDT1;

CHAF1A; WRN;

Endometriosis

Anemia

Li-Fraumeni Syndrome

IPO5; KIF23; TTK;

Aneuploidy

Amyotrophic lateral Sclerosis

Diabetes mellitus type I

MSH2; CASC5;

PRKCZ; CASP7;

Carcinoma (multiple types)

Diabetes mellitus type II

Werner Syndrome

SERPINB13;

LATS1

Male infertility

Rheumatoid arthritis

osteoporosis


Development

11

NCOA6; PABPN1;

Carcinoma (multiple types)

Endometriosis

Asthma

LTF; MAP3K1;

TLL1; YAP1; SPEN;

Deglutition disorders

Male infertility

Coronary disease

IL18R1

Oculopharyngeal Muscular dystrophy

Li-Fraumeni Syndrome

Idiopathic pulmonary fibrosis


DNA repair

9

BRCA2; CHAF1A;

Genomic instability

Werner Syndrome

Fanconi anemia

FANCM; RAD51L1;

Carcinoma (multiple types)

Diabetes mellitus type I

Drug toxicity

WRN; MSH2


Inflammation

22

CYCS; SOCS6;

Huntington's disease

Severe combined Immunodeficiency

Stomach ulcer

BDKRB1; HPRT1;

IL18R1; IL7R;

Thrombocytopenia

Multiple sclerosis

Ataxia

MAP3K1; 1L27RA;

Asthma

Rheumatoid arthritis

Leukemia

PRKCZ; OAS2;

Diabetes mellitus type I

Myeloproliferative disorders

Sarcoidosis

CD53; LAMA3;

LAMA4; IL174A;

Diabetic nephropathies

Crohn's disease

Carcinoma (multiple types)

HABP2; KLKB1

Autosomal dominant polycystic kidney

Sjogren's syndrome

Gout

Rhinitis

Nasal polyps

Telangiectasis

Lesch-Nyhan syndrome

Arteriosclerosis

Genome instability


Metabolism

4

P2RX2; LTF;

Anoxia

Encephalitis

Rheumatoid arthritis

ACACB; PRKCZ

Carcinoma (multiple types)

Diabetes mellitus type II

Glomberulonephritis


Nervous System

17

CDK5RAP2;

Microcephaly

Lipodystrophy

Rheumatoid arthritis

P2RX2;

Anoxia

Mucolipidoses

Fragile X Syndrome

ST8S1A2; HTR1F;

Schizophrenia

Pain

Liver cirrhosis

SCN10A; SLC28A2;

Parkinson's disease

Asthma

Diabetes mellitus type I

MCOLN1; DLGAP4;

Glioma

Acquired immunodeficiency

SYT8; ATP2B3;

MAP1A; LAMA4;

MAP3K1; AHNAK;

AFF2; CASP7


Protein folding

4

CHAF1A; GRPEL1;

Aneurysm

Pulmonary fibrosis

Diabetes mellitus type I

HSPA4; EEF1A2;

Carcinoma (multiple types)

Graft vs. host disease

Paralysis


Reproduction

13

SPDY1; CENPI;

Gastrointestinal diseases

Hyperaldosteronism

Genomic instability

BRCA2; NCOA4;

RBAK; CASC5;

Carcinoma (multiple types)

Diabetes mellitus type II

Oligospermia

PRKCZ; MAP3K1

anemia


Signal transduction

19

BRCA2; CASP7;

Spontaneous abortion

Arteriosclerosis

Dilated cardiomyopathy

NCOA6;IL7R;

CYCS; BAMBI;

Carcinoma (multiple types)

Hypertension

Asthma

KLKB1; IL17RA;

MAP3K1; DSG2;

Huntington's disease

Severe combined immunodeficiency

Sarcoidosis

PRKCZ; IFI44;

IL18R1; HABP2;

Thrombocytopenia

Multiple sclerosis

Diabetes mellitus type I

Rheumatoid arthritis

Alzheimer's disease

Arrhythmogenic right ventricular dysplasia


Transcription

8

NCOA6; BRCA2;

Retinoblastoma

Oculopharyngeal muscular dystrophies

Rheumatoid arthritis

MAP3K1; TAF3;

PABPN1

Spontaneous abortion

Aneuploidy

Deglutition disorders

Carcinoma (multiple types)

Infertility


Transport

11

KCNH3; LTF;

Anemia

Genomic instability

Liver cirrhosis

MSH2;NCOA4;

Alzheimer's disease

Crohn's disease

Obesity

PPARGC1B;

Epilepsy

Diabetes mellitus type II

Barrett esophagus

ZNF217;

Carcinoma (multiple types)

Gastritis

progeria

ME2;P2RX2;ANK3;

LATS1; MAT2A


A list of genes containing probably or possibly damaging nsSNPs as predicted by PolyPhen-2 was submitted for network analysis in GeneGo. Characterization of the genes containing nsSNPs is achieved by listing the general cellular process (column 1), the total number of deleterious nsSNPs in the genes that GeneGo annotated (column 2), the genes associated with the cellular process (column 3), and the specific diseases that have been associated by GeneGo with the genes in question (columns 4-6).

Fawcett et al. BMC Genomics 2011 12:311   doi:10.1186/1471-2164-12-311

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