MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000416691
Querying Taster for transcript #2: ENST00000455146
MT speed 0 s - this script 3.985543 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
COG6	polymorphism_automatic	1.18295254030176e-05	simple_aae		affected		C32S	single base exchange	rs3812883		show file
COG6	polymorphism_automatic	1.18295254030176e-05	simple_aae		affected		C32S	single base exchange	rs3812883		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999988170474597 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:40229957T>AN/A show variant in all transcripts IGV

HGNC symbol

COG6

Ensembl transcript ID

ENST00000416691

Genbank transcript ID

NM_001145079

UniProt peptide

Q9Y2V7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.94T>A
cDNA.194T>A
g.194T>A

AA changes

C32S Score: 112 explain score(s)

position(s) of altered AA
if AA alteration in CDS

frameshift

known variant

Reference ID: rs3812883

database	homozygous (A/A)	heterozygous	allele carriers
1000G	618	1189	1807
ExAC	9890	12987	22877

regulatory features

H4K5ac, Histone, Histone 4 Lysine 5 Acetylation
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
Gabp, Transcription Factor, Gabp TF binding
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
H2AZ, Histone, Histone 2A variant Z
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
CTCF, Transcription Factor, CCCTC-binding factor
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
EBF, Transcription Factor, EBF Transcription Factor Binding
ZEB1, Transcription Factor, ZEB1 Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.074	0.972
	0.934	0.974
(flanking)	-0.079	0.97

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor increased	194	wt: 0.43 / mu: 0.95	wt: CGACCTGCAACCCGC mu: CGACCAGCAACCCGC	ACCT\|gcaa
Donor gained	189	0.53	mu: GGCGACGACCAGCAA	CGAC\|gacc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

not conserved

ENSPTRG00000005805

Mmulatta

not conserved

ENSMMUG00000004486

Fcatus

no alignment

ENSFCAG00000003420

n/a

Mmusculus

not conserved

ENSMUSG00000027742

Ggallus

no alignment

ENSGALG00000017035

n/a

Trubripes

not conserved

ENSTRUG00000014316

Drerio

not conserved

ENSDARG00000012336

Dmelanogaster

no alignment

FBgn0033401

n/a

Celegans

not conserved

K07C11.9

Xtropicalis

not conserved

ENSXETG00000016035

TPAAVQS

protein features

start (aa)	end (aa)	feature	details
158	158	CONFLICT	S -> F (in Ref. 2; CAH10495).	might get lost (downstream of altered splice site)
379	379	CONFLICT	N -> S (in Ref. 2; CAH10495).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1848 / 1848

position (AA) of stopcodon in wt / mu AA sequence

616 / 616

position of stopcodon in wt / mu cDNA

1948 / 1948

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

101 / 101

chromosome

strand

last intron/exon boundary

1927

theoretical NMD boundary in CDS

1776

length of CDS

1848

coding sequence (CDS) position

cDNA position
(for ins/del: last normal base / first normal base)

194

gDNA position
(for ins/del: last normal base / first normal base)

194

chromosomal position
(for ins/del: last normal base / first normal base)

40229957

original gDNA sequence snippet

GCGGGACCTCGGCGACGACCTGCAACCCGCTGTCGCGCAAG

altered gDNA sequence snippet

GCGGGACCTCGGCGACGACCAGCAACCCGCTGTCGCGCAAG

original cDNA sequence snippet

GCGGGACCTCGGCGACGACCTGCAACCCGCTGTCGCGCAAG

altered cDNA sequence snippet

GCGGGACCTCGGCGACGACCAGCAACCCGCTGTCGCGCAAG

wildtype AA sequence

MAEGSGEVVA VSATGAANGL NNGAGGTSAT TCNPLSRKLH KILETRLDND KEMLEALKAL
STFFVENSLR TRRNLRGDIE RKSLAINEEF VSIFKEVKEE LESISEDVQA MSNCCQDMTS
RLQAAKEQTQ DLIVKTTKLQ SESQKLEIRA QVADAFLSKF QLTSDEMSLL RGTREGPITE
DFFKALGRVK QIHNDVKVLL RTNQQTAGLE IMEQMALLQE TAYERLYRWA QSECRTLTQE
SCDVSPVLTQ AMEALQDRPV LYKYTLDEFG TARRSTVVRG FIDALTRGGP GGTPRPIEMH
SHDPLRYVGD MLAWLHQATA SEKEHLEALL KHVTTQGVEE NIQEVVGHIT EGVCRPLKVR
IEQVIVAEPG AVLLYKISNL LKFYHHTISG IVGNSATALL TTIEEMHLLS KKIFFNSLSL
HASKLMDKVE LPPPDLGPSS ALNQTLMLLR EVLASHDSSV VPLDARQADF VQVLSCVLDP
LLQMCTVSAS NLGTADMATF MVNSLYMMKT TLALFEFTDR RLEMLQFQIE AHLDTLINEQ
ASYVLTRVGL SYIYNTVQQH KPEQGSLANM PNLDSVTLKA AMVQFDRYLS APDNLLIPQL
NFLLSATVKR PPNGP*

mutated AA sequence

MAEGSGEVVA VSATGAANGL NNGAGGTSAT TSNPLSRKLH KILETRLDND KEMLEALKAL
STFFVENSLR TRRNLRGDIE RKSLAINEEF VSIFKEVKEE LESISEDVQA MSNCCQDMTS
RLQAAKEQTQ DLIVKTTKLQ SESQKLEIRA QVADAFLSKF QLTSDEMSLL RGTREGPITE
DFFKALGRVK QIHNDVKVLL RTNQQTAGLE IMEQMALLQE TAYERLYRWA QSECRTLTQE
SCDVSPVLTQ AMEALQDRPV LYKYTLDEFG TARRSTVVRG FIDALTRGGP GGTPRPIEMH
SHDPLRYVGD MLAWLHQATA SEKEHLEALL KHVTTQGVEE NIQEVVGHIT EGVCRPLKVR
IEQVIVAEPG AVLLYKISNL LKFYHHTISG IVGNSATALL TTIEEMHLLS KKIFFNSLSL
HASKLMDKVE LPPPDLGPSS ALNQTLMLLR EVLASHDSSV VPLDARQADF VQVLSCVLDP
LLQMCTVSAS NLGTADMATF MVNSLYMMKT TLALFEFTDR RLEMLQFQIE AHLDTLINEQ
ASYVLTRVGL SYIYNTVQQH KPEQGSLANM PNLDSVTLKA AMVQFDRYLS APDNLLIPQL
NFLLSATVKR PPNGP*

speed

1.22 s

All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999988170474597 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:40229957T>AN/A show variant in all transcripts IGV

HGNC symbol

COG6

Ensembl transcript ID

ENST00000455146

Genbank transcript ID

NM_020751

UniProt peptide

Q9Y2V7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.94T>A
cDNA.144T>A
g.194T>A

AA changes

C32S Score: 112 explain score(s)

position(s) of altered AA
if AA alteration in CDS

frameshift

known variant

Reference ID: rs3812883

database	homozygous (A/A)	heterozygous	allele carriers
1000G	618	1189	1807
ExAC	9890	12987	22877

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.074	0.972
	0.934	0.974
(flanking)	-0.079	0.97

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor increased	194	wt: 0.43 / mu: 0.95	wt: CGACCTGCAACCCGC mu: CGACCAGCAACCCGC	ACCT\|gcaa
Donor gained	189	0.53	mu: GGCGACGACCAGCAA	CGAC\|gacc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

not conserved

ENSPTRG00000005805

Mmulatta

not conserved

ENSMMUG00000004486

Fcatus

no alignment

ENSFCAG00000003420

n/a

Mmusculus

not conserved

ENSMUSG00000027742

Ggallus

no alignment

ENSGALG00000017035

n/a

Trubripes

not conserved

ENSTRUG00000014316

Drerio

not conserved

ENSDARG00000012336

Dmelanogaster

no alignment

FBgn0033401

n/a

Celegans

not conserved

K07C11.9

Xtropicalis

not conserved

ENSXETG00000016035

TPAAVQS

protein features

start (aa)	end (aa)	feature	details
158	158	CONFLICT	S -> F (in Ref. 2; CAH10495).	might get lost (downstream of altered splice site)
379	379	CONFLICT	N -> S (in Ref. 2; CAH10495).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1974 / 1974

position (AA) of stopcodon in wt / mu AA sequence

658 / 658

position of stopcodon in wt / mu cDNA

2024 / 2024

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

51 / 51

chromosome

strand

last intron/exon boundary

1877

theoretical NMD boundary in CDS

1776

length of CDS

1974

coding sequence (CDS) position

cDNA position
(for ins/del: last normal base / first normal base)

144

gDNA position
(for ins/del: last normal base / first normal base)

194

chromosomal position
(for ins/del: last normal base / first normal base)

40229957

original gDNA sequence snippet

GCGGGACCTCGGCGACGACCTGCAACCCGCTGTCGCGCAAG

altered gDNA sequence snippet

GCGGGACCTCGGCGACGACCAGCAACCCGCTGTCGCGCAAG

original cDNA sequence snippet

GCGGGACCTCGGCGACGACCTGCAACCCGCTGTCGCGCAAG

altered cDNA sequence snippet

GCGGGACCTCGGCGACGACCAGCAACCCGCTGTCGCGCAAG

wildtype AA sequence

mutated AA sequence

speed

0.33 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems