MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000462901
Querying Taster for transcript #2: ENST00000309495
MT speed 1.63 s - this script 3.667123 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ZNF654	polymorphism_automatic	0.020389156050504	simple_aae		affected		I294T	single base exchange	rs7653652		show file
CGGBP1	polymorphism_automatic	0.999999999278333	without_aae		affected			single base exchange	rs7653652		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.979610843949496 (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)

chr3:88189341T>CN/A show variant in all transcripts IGV

HGNC symbol

ZNF654

Ensembl transcript ID

ENST00000309495

Genbank transcript ID

NM_018293

UniProt peptide

Q8IZM8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.881T>C
cDNA.1088T>C
g.1088T>C

AA changes

I294T Score: 89 explain score(s)

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

294

frameshift

known variant

Reference ID: rs7653652
Allele 'C' was neither found in ExAC nor 1000G.

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.358	0.951
	1.491	0.966
(flanking)	-0.026	0.964

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	1085	wt: 0.44 / mu: 0.68	wt: TCACAGGATATTTCA mu: TCACAGGACATTTCA	ACAG\|gata

distance from splice site

858

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

294

mutated

not conserved

294

Ptroglodytes

all identical

ENSPTRG00000030181

294

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000047141

292

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000079350

1396

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
268	292	ZN_FING	C2H2-type 4.	might get lost (downstream of altered splice site)
294	294	CONFLICT	I -> T (in Ref. 1; AAN40504 and 2; BAA91946).	lost
297	321	ZN_FING	C2H2-type 5.	might get lost (downstream of altered splice site)
548	548	CONFLICT	K -> E (in Ref. 2; BAB15007).	might get lost (downstream of altered splice site)
576	576	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
580	580	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1746 / 1746

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

582 / 582

position of stopcodon in wt / mu cDNA

1953 / 1953

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

208 / 208

chromosome

strand

last intron/exon boundary

1946

theoretical NMD boundary in CDS

1688

length of CDS

1746

coding sequence (CDS) position

881

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

1088

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

1088

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

88189341

original gDNA sequence snippet

GCACACAAAAAGTCACAGGATATTTCAGGCTCAGTGTAGTT

altered gDNA sequence snippet

GCACACAAAAAGTCACAGGACATTTCAGGCTCAGTGTAGTT

original cDNA sequence snippet

GCACACAAAAAGTCACAGGATATTTCAGGCTCAGTGTAGTT

altered cDNA sequence snippet

GCACACAAAAAGTCACAGGACATTTCAGGCTCAGTGTAGTT

wildtype AA sequence

MLCNKEFLGG HIVRHAQAHQ KKGSFACVIC GRKFRNRGLM QKHLKNHVKK IQRQQIAAAQ
QDDQEVTALE EINCSSSSIS FENGNSDSKD LEVETLTASS EGNKEVIPEH VAEFIEIPIS
VPEDVIENVI ENGSPNNSLN NVFKPLTECG DDYEEEEDEE GDYEEDDYDL NQETSVIHKI
NGTVCHPKDI YATDQEGNFK CPALGCVRIF KRIGFLNKHA MTVHPTDLNV RQTVMKWSKG
KCKFCQRQFE DSQHFIDHLN RHSYPNVYFC LHFNCNESFK LPFQLAQHTK SHRIFQAQCS
FPECHELFED LPLLYEHEAQ HYLSKTPESS AQPSETILWD VQTDSNPNQE KDSSSNEKQT
ISLPVSTSKS RKESTEPKTC IESMEKKTDS LVQNGNERSD DTVSNISLID QKMPDIEPNS
ENNCSSSDIV NGHSEIEQTP LVSSDPALKI DTNRIRTENG SILPSVVPQE HNTLPVSQAP
SKPNLTSEHT SYGLILTKPY VRPLPPSYLD ERYLSMPKRR KFLTDRVDAC SDQDNVYKKS
VKRLRCGKCL TTYCNAEALE AHLAQKKCQT LFGFDSDDES A*

mutated AA sequence

MLCNKEFLGG HIVRHAQAHQ KKGSFACVIC GRKFRNRGLM QKHLKNHVKK IQRQQIAAAQ
QDDQEVTALE EINCSSSSIS FENGNSDSKD LEVETLTASS EGNKEVIPEH VAEFIEIPIS
VPEDVIENVI ENGSPNNSLN NVFKPLTECG DDYEEEEDEE GDYEEDDYDL NQETSVIHKI
NGTVCHPKDI YATDQEGNFK CPALGCVRIF KRIGFLNKHA MTVHPTDLNV RQTVMKWSKG
KCKFCQRQFE DSQHFIDHLN RHSYPNVYFC LHFNCNESFK LPFQLAQHTK SHRTFQAQCS
FPECHELFED LPLLYEHEAQ HYLSKTPESS AQPSETILWD VQTDSNPNQE KDSSSNEKQT
ISLPVSTSKS RKESTEPKTC IESMEKKTDS LVQNGNERSD DTVSNISLID QKMPDIEPNS
ENNCSSSDIV NGHSEIEQTP LVSSDPALKI DTNRIRTENG SILPSVVPQE HNTLPVSQAP
SKPNLTSEHT SYGLILTKPY VRPLPPSYLD ERYLSMPKRR KFLTDRVDAC SDQDNVYKKS
VKRLRCGKCL TTYCNAEALE AHLAQKKCQT LFGFDSDDES A*

speed

0.79 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: without_aae, prob: 7.21666691293583e-10 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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)

chr3:88189341T>CN/A show variant in all transcripts IGV

HGNC symbol

CGGBP1

Ensembl transcript ID

ENST00000462901

Genbank transcript ID

N/A

UniProt peptide

Q9UFW8

alteration type

single base exchange

alteration region

intron

DNA changes

g.9695A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs7653652
Allele 'C' was neither found in ExAC nor 1000G.

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.358	0.951
	1.491	0.966
(flanking)	-0.026	0.964

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

splice sites

splice site change before start ATG (at aa -75) |

effect	gDNA position	score	detection sequence	exon-intron border
Donor increased	9689	wt: 0.76 / mu: 0.99	wt: GAGCCTGAAATATCC mu: GAGCCTGAAATGTCC	GCCT\|gaaa

distance from splice site

779

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
80	84	MOTIF	Nuclear localization signal (Potential).	might get lost (downstream of altered splice site)
164	164	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
165	165	CONFLICT	Q -> R (in Ref. 2; CAB55894).	might get lost (downstream of altered splice site)

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

513 / 513

chromosome

strand

-1

last intron/exon boundary

490

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

504

coding sequence (CDS) position

N/A

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

N/A

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

9695

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

88189341

original gDNA sequence snippet

AACTACACTGAGCCTGAAATATCCTGTGACTTTTTGTGTGC

altered gDNA sequence snippet

AACTACACTGAGCCTGAAATGTCCTGTGACTTTTTGTGTGC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MERFVVTAPP ARNRSKTALY VTPLDRVTEF GGELHEDGGK LFCTSCNVVL NHVRKSAISD
HLKSKTHTKR KAEFEEQNVR KKQRPLTASL QCNSTAQTEK VSVIQDFVKM CLEANIPLEK
ADHPAVRAFL SRHVKNGGSI PKSDQLRRAY LPDGYENENQ LLNSQDC*

mutated AA sequence

N/A

speed

0.84 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems