Genes of related-Non-synonymous SNPs

The most frequent type of variation  found in human genome  are Single Nucleotide Polymorphism (SNP's).SNP's occur both in coding as well as non-coding regions but the Non-Synonymous SNP's in coding region have the higest impact on phenotype.We tested the non-synonymous SNPs for their possible effect on function and structure of proteins using Polyphen.Among the 4436 SNP's , 3477 (78%) were predicted as benign(no effect) while 602 (14%) were predicted as possibly damaging and 357(7.3 %) as probably damaging.These predictions were similar to Watson non-synonymous SNP analysis.Predictions were also made  using SIFT  (Seperating Intolerant From Tolerant) .Among 2589 SNP's sampled ,2092 (80%) were predicted to be tolerated while 477 (18%) as deleterious.

            

Comparison of Polyphen results of Watson genome project and Korean genome project.

Genome Project	Sampling	Probably damaging	Possibly damaging	Bening (No effect)
Korean Genome	4436	357 (8 %)	602 (14 %)	3477 (78 %)
Watson Genome	3898	7.3 %	13 %	74 %

 

Input file : Maq's SNP result

Known SNP -> dbsnp129 -> non-syn, sequence -> polyphen, SIFT, Mutatome -> TGFbeta related genes, Albumin

Novel SNP -> UCSC hg18 -> non-syn, sequence -> polyphen, SIFT, Mutatome -> TGFbeta related genes, Albumin

 TOTAL : 2676726

-------------------

VALID : 2325941

UTR-3: 16286

UTR-5: 3303

SPLICE-3: 24

SPLICE-5: 39

INTRON: 863387

CDS-SYNON: 9330

CDS-NONSYNON: 0

NONSENSE: 197

MISSENSE: 9124

FRAMESHIFT: 27

-------------------

UNVALID : 350785

UTR-3: 1499

UTR-5: 527

SPLICE-3: 1

SPLICE-5: 7

INTRON: 122138

CDS-SYNON: 707

CDS-NONSYNON: 0

NONSENSE: 28

MISSENSE: 794

FRAMESHIFT: 16

SNP classification data

5-UTR, 3-UTR, Intron, Synonymous, Non-synonymous

unknown

untranslated-3

intron

near-gene-3,near-gene-5

near-gene-3

cds-reference,missense

coding-synon,cds-reference

untranslated-5

near-gene-5

intron,cds-reference,missense

near-gene-5,untranslated-5

intron,near-gene-5

intron,near-gene-3

near-gene-5,untranslated-3

near-gene-3,untranslated-3

cds-reference,missense,untranslated-3

coding-synon,cds-reference,untranslated-3

cds-reference,nonsense

coding-synon,cds-reference,nonsense,missense

coding-synon,cds-reference,missense

coding-synon,cds-reference,untranslated-5

intron,near-gene-3,near-gene-5

cds-reference,missense,untranslated-3,untranslated-5

cds-reference,missense,untranslated-5

near-gene-3,untranslated-5

cds-reference,near-gene-3,missense,untranslated-5

coding-synon,cds-reference,near-gene-3,untranslated-5

intron,untranslated-5

coding-synon,cds-reference,near-gene-3

cds-reference,near-gene-5,missense

cds-reference,near-gene-3,missense

cds-reference,near-gene-3,frameshift

coding-synon,cds-reference,near-gene-5

cds-reference,frameshift

cds-reference,nonsense,missense

intron,splice-5

coding-synon,intron,cds-reference

intron,near-gene-5,untranslated-5

coding-synon,cds-reference,near-gene-5,missense

intron,cds-reference,near-gene-3,missense

intron,near-gene-3,untranslated-5

coding-synon,intron,cds-reference,near-gene-5

intron,cds-reference,near-gene-5,frameshift

intron,cds-reference,near-gene-5,missense

coding-synon,intron,cds-reference,untranslated-5

intron,cds-reference,nonsense

intron,untranslated-3

intron,untranslated-5,splice-3

near-gene-3,near-gene-5,untranslated-3

cds-reference,near-gene-3,near-gene-5,missense,untranslated-3

intron,near-gene-3,untranslated-3

coding-synon,cds-reference,near-gene-5,untranslated-5

intron,splice-3

coding-synon,intron,cds-reference,missense

coding-synon,cds-reference,missense,untranslated-5

intron,cds-reference,missense,untranslated-5

intron,near-gene-3,splice-3

coding-synon,cds-reference,missense,frameshift

near-gene-3,near-gene-5,untranslated-5

untranslated-3,untranslated-5

intron,cds-reference,frameshift

cds-reference,missense,splice-3

splice-5

coding-synon,intron,cds-reference,near-gene-3

cds-reference,near-gene-5,frameshift

intron,cds-reference,near-gene-5,missense,untranslated-3

coding-synon,cds-reference,near-gene-5,missense,untranslated-3

splice-3

cds-reference,near-gene-3,nonsense

cds-reference,frameshift,untranslated-3

cds-reference,near-gene-5,nonsense

cds-reference,frameshift,untranslated-5

intron,near-gene-5,splice-3

coding-synon,cds-reference,nonsense

intron,cds-reference,missense,untranslated-3

near-gene-3,splice-5

coding-synon,cds-reference,missense,untranslated-3

cds-reference,near-gene-3,missense,untranslated-3

intron,cds-reference,nonsense,missense

near-gene-3,near-gene-5,untranslated-3,untranslated-5

near-gene-5,untranslated-3,untranslated-5

intron,near-gene-5,untranslated-3

intron,cds-reference,near-gene-5,missense,untranslated-5

coding-synon,cds-reference,near-gene-3,near-gene-5

cds-reference,near-gene-3,near-gene-5,missense

intron,cds-reference,near-gene-3,near-gene-5,missense

coding-synon,cds-reference,near-gene-3,missense

coding-synon,intron,cds-reference,near-gene-3,missense

intron,cds-reference,near-gene-3,nonsense

cds-reference,near-gene-3,near-gene-5,frameshift

coding-synon,cds-reference,frameshift

splice-3,splice-5

near-gene-3,untranslated-3,untranslated-5

cds-reference,near-gene-5,missense,untranslated-5

coding-synon,intron,cds-reference,splice-3

cds-reference,near-gene-3,nonsense,missense

coding-synon,intron,cds-reference,untranslated-3

cds-reference,nonsense,untranslated-3

cds-reference,nonsense,untranslated-5

cds-reference,missense,frameshift

untranslated-5,splice-5

intron,cds-reference,near-gene-5,frameshift,untranslated-5

coding-synon,cds-reference,near-gene-3,untranslated-3

cds-reference,near-gene-5,missense,untranslated-3

coding-synon,cds-reference,near-gene-5,untranslated-3

coding-synon,intron,cds-reference,near-gene-3,near-gene-5

coding-synon,intron,cds-reference,near-gene-5,untranslated-5

cds-reference,near-gene-3,frameshift,untranslated-3

intron,near-gene-3,near-gene-5,splice-3

intron,near-gene-5,splice-5

coding-synon,intron,cds-reference,near-gene-3,splice-3

intron,cds-reference,missense,splice-3

intron,near-gene-5,untranslated-5,splice-3

untranslated-3,splice-5

coding-synon,cds-reference,near-gene-3,frameshift

intron,untranslated-3,untranslated-5

coding-synon,cds-reference,near-gene-5,missense,frameshift

coding-synon,cds-reference,splice-3

cds-reference,near-gene-3,nonsense,untranslated-5

cds-reference,near-gene-3,frameshift,untranslated-5

intron,cds-reference,frameshift,untranslated-3

intron,near-gene-3,near-gene-5,untranslated-5

intron,cds-reference,near-gene-3,missense,untranslated-5

untranslated-3,splice-3

coding-synon,cds-reference,frameshift,untranslated-3

intron,cds-reference,near-gene-3,frameshift

intron,near-gene-3,near-gene-5,untranslated-3

intron,near-gene-3,splice-5

intron,cds-reference,missense,splice-5

coding-synon,cds-reference,nonsense,untranslated-3

coding-synon,cds-reference,missense,splice-5

cds-reference,nonsense,missense,frameshift

cds-reference,nonsense,frameshift

near-gene-5,splice-3

cds-reference,missense,splice-5

intron,cds-reference,frameshift,splice-5

cds-reference,near-gene-3,nonsense,untranslated-3

near-gene-3,splice-3

cds-reference,near-gene-3,near-gene-5,missense,untranslated-5

cds-reference,near-gene-3,near-gene-5,nonsense,untranslated-5

coding-synon,intron,cds-reference,near-gene-5,splice-3

cds-reference,near-gene-5,frameshift,untranslated-3

intron,cds-reference,missense,frameshift

cds-reference,near-gene-5,frameshift,untranslated-5

coding-synon,intron,cds-reference,splice-5

coding-synon,cds-reference,near-gene-3,nonsense,missense

coding-synon,cds-reference,near-gene-3,nonsense

cds-reference,near-gene-3,near-gene-5,nonsense

cds-reference,near-gene-5,nonsense,missense

coding-synon,cds-reference,near-gene-3,missense,untranslated-5

coding-synon,cds-reference,near-gene-3,near-gene-5,missense

intron,cds-reference,near-gene-3,near-gene-5,frameshift

coding-synon,intron,cds-reference,near-gene-3,untranslated-3

intron,near-gene-3,untranslated-3,untranslated-5

coding-synon,cds-reference,near-gene-5,missense,untranslated-5

near-gene-5,untranslated-5,splice-5

coding-synon,cds-reference,near-gene-5,nonsense

cds-reference,nonsense,missense,untranslated-3

near-gene-5,splice-5

intron,cds-reference,near-gene-3,missense,untranslated-3

intron,cds-reference,near-gene-5,nonsense

intron,near-gene-5,untranslated-3,untranslated-5

coding-synon,intron,cds-reference,nonsense

intron,untranslated-5,splice-5

coding-synon,cds-reference,untranslated-3,untranslated-5

intron,cds-reference,nonsense,untranslated-3

coding-synon,intron,cds-reference,frameshift

intron,cds-reference,nonsense,splice-5

coding-synon,intron,cds-reference,untranslated-5,splice-3

coding-synon,intron,cds-reference,near-gene-5,nonsense

intron,untranslated-3,splice-3

intron,cds-reference,near-gene-3,near-gene-5,nonsense

coding-synon,intron,cds-reference,near-gene-3,near-gene-5,missense

intron,cds-reference,near-gene-3,near-gene-5,nonsense,missense

intron,cds-reference,near-gene-5,nonsense,untranslated-3

coding-synon,intron,cds-reference,near-gene-5,untranslated-3

coding-synon,intron,cds-reference,missense,untranslated-3

coding-synon,intron,cds-reference,nonsense,untranslated-3

cds-reference,near-gene-3,nonsense,missense,untranslated-3

coding-synon,cds-reference,splice-5

coding-synon,cds-reference,near-gene-3,near-gene-5,untranslated-3

cds-reference,near-gene-3,near-gene-5,frameshift,untranslated-3

cds-reference,near-gene-3,missense,splice-3

near-gene-3,untranslated-3,splice-5

intron,cds-reference,near-gene-5,nonsense,missense

intron,untranslated-3,splice-5

intron,cds-reference,frameshift,splice-3

cds-reference,near-gene-3,missense,frameshift

intron,cds-reference,frameshift,untranslated-5

coding-synon,intron,cds-reference,near-gene-3,untranslated-5

coding-synon,cds-reference,near-gene-3,missense,untranslated-3

cds-reference,near-gene-5,nonsense,untranslated-5

coding-synon,cds-reference,near-gene-5,nonsense,missense

coding-synon,cds-reference,near-gene-5,frameshift

coding-synon,intron,cds-reference,near-gene-5,missense

coding-synon,cds-reference,near-gene-5,nonsense,untranslated-3

intron,near-gene-3,untranslated-5,splice-3

cds-reference,nonsense,missense,untranslated-5

intron,cds-reference,near-gene-3,frameshift,untranslated-3

intron,cds-reference,nonsense,untranslated-5

coding-synon,cds-reference,near-gene-5,untranslated-3,untranslated-5

cds-reference,near-gene-5,missense,untranslated-3,untranslated-5

coding-synon,intron,cds-reference,missense,untranslated-5

coding-synon,intron,cds-reference,near-gene-3,nonsense,untranslated-3

coding-synon,intron,cds-reference,near-gene-3,missense,untranslated-3

cds-reference,near-gene-5,missense,splice-3

intron,cds-reference,near-gene-3,nonsense,untranslated-3

coding-synon,intron,cds-reference,near-gene-5,frameshift

coding-synon,cds-reference,untranslated-3,splice-5

untranslated-3,splice-3,splice-5

coding-synon,intron,cds-reference,missense,frameshift

coding-synon,intron,cds-reference,near-gene-3,frameshift

cds-reference,frameshift,untranslated-3,untranslated-5

untranslated-5,splice-3

coding-synon,cds-reference,near-gene-3,near-gene-5,missense,untranslated-3

cds-reference,nonsense,splice-5

coding-synon,cds-reference,nonsense,missense,frameshift

coding-synon,cds-reference,nonsense,frameshift

cds-reference,near-gene-3,frameshift,splice-3

cds-reference,frameshift,splice-3

cds-reference,missense,frameshift,splice-3

intron,cds-reference,nonsense,missense,frameshift

coding-synon,intron,cds-reference,nonsense,missense

cds-reference,missense,frameshift,untranslated-3

near-gene-5,untranslated-3,splice-5

near-gene-3,splice-3,splice-5

intron,near-gene-3,untranslated-3,splice-5

intron,near-gene-3,near-gene-5,splice-5

coding-synon,intron,cds-reference,near-gene-5,untranslated-3,untranslated-5

intron,cds-reference,near-gene-5,nonsense,missense,untranslated-5

coding-synon,intron,cds-reference,near-gene-5,untranslated-5,splice-5

intron,cds-reference,near-gene-5,missense,untranslated-3,untranslated-5