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: ENST00000312962
Querying Taster for transcript #2: ENST00000361821
MT speed 2.33 s - this script 4.649807 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
KRI1	polymorphism_automatic	7.69195818151047e-12	simple_aae		affected		T5A	single base exchange	rs3218222		show file
KRI1	polymorphism_automatic	0.00464091164134905	without_aae		affected			single base exchange	rs3218222		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999992308 (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)

chr19:10676681T>CN/A show variant in all transcripts IGV

HGNC symbol

KRI1

Ensembl transcript ID

ENST00000312962

Genbank transcript ID

NM_023008

UniProt peptide

Q8N9T8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.13A>G
cDNA.33A>G
g.33A>G

AA changes

T5A Score: 58 explain score(s)

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

frameshift

known variant

Reference ID: rs3218222

database	homozygous (C/C)	heterozygous	allele carriers
1000G	990	1046	2036
ExAC	1951	2521	4472

regulatory features

ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
Max, Transcription Factor, Max TF binding
Gabp, Transcription Factor, Gabp TF binding
HDAC3, Transcription Factor, HDAC3 Transcription Factor Binding
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
E2F4, Transcription Factor, E2F4 Transcription Factor Binding
Tcf12, Transcription Factor, Tcf12 Transcription Factor Binding
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Cmyc, Transcription Factor, Cmyc TF binding
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
HDAC1, Transcription Factor, HDAC1 Transcription Factor Binding
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
CTCF, Transcription Factor, CCCTC-binding factor
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
CBP, Transcription Factor, CBP Transcription Factor Binding
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
Nrf1, Transcription Factor, Nrf1 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.467	0.251
	0.503	0.129
(flanking)	-0.315	0.008

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	24	wt: 0.23 / mu: 0.28	wt: CAATGGGCCACAGAA mu: CAATGGGCCACAGAG	ATGG\|gcca
Donor gained	32	0.62	mu: CACAGAGCCGCCATG	CAGA\|gccg
Donor gained	27	0.55	mu: TGGGCCACAGAGCCG	GGCC\|acag

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

no homologue

Mmulatta

not conserved

ENSMMUG00000011951

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000035047

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000075380

n/a

Dmelanogaster

no alignment

FBgn0036254

n/a

Celegans

no alignment

F54C9.9

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
97	97	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
99	99	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
100	100	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
101	101	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
103	103	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
104	429	COMPBIAS	Glu-rich.	might get lost (downstream of altered splice site)
142	142	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
147	147	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
156	156	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
171	171	CONFLICT	R -> W (in Ref. 1; BAC04240).	might get lost (downstream of altered splice site)
177	177	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
258	258	CONFLICT	E -> G (in Ref. 1; BAB14357).	might get lost (downstream of altered splice site)
285	285	CONFLICT	D -> G (in Ref. 1; BAB14357).	might get lost (downstream of altered splice site)
286	286	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
287	287	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
322	322	CONFLICT	S -> N (in Ref. 1; BAC04240).	might get lost (downstream of altered splice site)
351	351	CONFLICT	K -> E (in Ref. 1; BAC04240).	might get lost (downstream of altered splice site)
562	562	CONFLICT	K -> E (in Ref. 1; BAB15278).	might get lost (downstream of altered splice site)
633	633	CONFLICT	E -> G (in Ref. 1; BAB15278).	might get lost (downstream of altered splice site)
634	634	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
645	645	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2130 / 2130

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

710 / 710

position of stopcodon in wt / mu cDNA

2150 / 2150

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

21 / 21

chromosome

strand

-1

last intron/exon boundary

1820

theoretical NMD boundary in CDS

1749

length of CDS

2130

coding sequence (CDS) position

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

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

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

10676681

original gDNA sequence snippet

CGTGCGCAATGGGCCACAGAACCGCCATGCCGGAACCGCGC

altered gDNA sequence snippet

CGTGCGCAATGGGCCACAGAGCCGCCATGCCGGAACCGCGC

original cDNA sequence snippet

CGTGCGCAATGGGCCACAGAACCGCCATGCCGGAACCGCGC

altered cDNA sequence snippet

CGTGCGCAATGGGCCACAGAGCCGCCATGCCGGAACCGCGC

wildtype AA sequence

MGHRTAMPEP RGSSQLRVNA AFAARYNRYR EREELQRLKD RYGDRDSSSD SSSESDSSDE
RVEFDPQQER DFYKTLSLLK KKDPRIYQKD ATFYNRTASS SDSEEDPEAL EKQKKVRPMY
LKDYERKVIL EKAGKYVDEE NSDGETSNHR LQETSSQSYV EEQKQLKESF RAFVEDSEDE
DGAGEGGSSL LQKRAKTRQE KAQEEADYIE WLKGQKEIRN PDSLKELTHL KEYWNDPELD
EGERFLRDYI LNKRYEEEEE EEEDEEEMEE EEGVHGPPVQ LAVDDSSDEG ELFLKKQEDF
EQKYNFRFEE PDSASVKTYP RSIASSVRRK DERRKEKREE TRERKKREKA KKQEELKQLK
NLKRKEILAK LEKLRKVTGN EMLGLEEGDL EDDFDPAQHD QLMQKCFGDE YYGAVEEEKP
QFEEEEGLED DWNWDTWDGP EQEGDWSQQE LHCEDPNFNM DADYDPSQPR KKKREAPLTG
KKKRKSPFAA AVGQEKPVFE PGDKTFEEYL DEYYRLDYED IIDDLPCRFK YRTVVPCDFG
LSTEEILAAD DKELNRWCSL KKTCMYRSEQ EELRDKRAYS QKAQNSWKKR QVFKSLCREE
AETPAEATGK PQRDEAGPQR QLPALDGSLM GPESPPAQEE EAPVSPHKKP APQKRRRAKK
ARLLGPTVML GGCEFSRQRL QAFGLNPKRL HFRQLGRQRR KQQGPKNSS*

mutated AA sequence

MGHRAAMPEP RGSSQLRVNA AFAARYNRYR EREELQRLKD RYGDRDSSSD SSSESDSSDE
RVEFDPQQER DFYKTLSLLK KKDPRIYQKD ATFYNRTASS SDSEEDPEAL EKQKKVRPMY
LKDYERKVIL EKAGKYVDEE NSDGETSNHR LQETSSQSYV EEQKQLKESF RAFVEDSEDE
DGAGEGGSSL LQKRAKTRQE KAQEEADYIE WLKGQKEIRN PDSLKELTHL KEYWNDPELD
EGERFLRDYI LNKRYEEEEE EEEDEEEMEE EEGVHGPPVQ LAVDDSSDEG ELFLKKQEDF
EQKYNFRFEE PDSASVKTYP RSIASSVRRK DERRKEKREE TRERKKREKA KKQEELKQLK
NLKRKEILAK LEKLRKVTGN EMLGLEEGDL EDDFDPAQHD QLMQKCFGDE YYGAVEEEKP
QFEEEEGLED DWNWDTWDGP EQEGDWSQQE LHCEDPNFNM DADYDPSQPR KKKREAPLTG
KKKRKSPFAA AVGQEKPVFE PGDKTFEEYL DEYYRLDYED IIDDLPCRFK YRTVVPCDFG
LSTEEILAAD DKELNRWCSL KKTCMYRSEQ EELRDKRAYS QKAQNSWKKR QVFKSLCREE
AETPAEATGK PQRDEAGPQR QLPALDGSLM GPESPPAQEE EAPVSPHKKP APQKRRRAKK
ARLLGPTVML GGCEFSRQRL QAFGLNPKRL HFRQLGRQRR KQQGPKNSS*

speed

1.32 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: 0.995359088358651 (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)

chr19:10676681T>CN/A show variant in all transcripts IGV

HGNC symbol

KRI1

Ensembl transcript ID

ENST00000361821

Genbank transcript ID

N/A

UniProt peptide

Q8N9T8

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.16A>G
g.33A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs3218222

database	homozygous (C/C)	heterozygous	allele carriers
1000G	990	1046	2036
ExAC	1951	2521	4472

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.467	0.251
	0.503	0.129
(flanking)	-0.315	0.008

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

splice sites

splice site change before start ATG (at aa -40) | splice site change before start ATG (at aa -39) | splice site change before start ATG (at aa -37) |

effect	gDNA position	score	detection sequence	exon-intron border
Donor increased	24	wt: 0.23 / mu: 0.28	wt: CAATGGGCCACAGAA mu: CAATGGGCCACAGAG	ATGG\|gcca
Donor gained	32	0.62	mu: CACAGAGCCGCCATG	CAGA\|gccg
Donor gained	27	0.55	mu: TGGGCCACAGAGCCG	GGCC\|acag

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
97	97	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
99	99	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
100	100	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
101	101	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
103	103	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
104	429	COMPBIAS	Glu-rich.	might get lost (downstream of altered splice site)
142	142	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
147	147	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
156	156	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
171	171	CONFLICT	R -> W (in Ref. 1; BAC04240).	might get lost (downstream of altered splice site)
177	177	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
258	258	CONFLICT	E -> G (in Ref. 1; BAB14357).	might get lost (downstream of altered splice site)
285	285	CONFLICT	D -> G (in Ref. 1; BAB14357).	might get lost (downstream of altered splice site)
286	286	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
287	287	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
322	322	CONFLICT	S -> N (in Ref. 1; BAC04240).	might get lost (downstream of altered splice site)
351	351	CONFLICT	K -> E (in Ref. 1; BAC04240).	might get lost (downstream of altered splice site)
562	562	CONFLICT	K -> E (in Ref. 1; BAB15278).	might get lost (downstream of altered splice site)
633	633	CONFLICT	E -> G (in Ref. 1; BAB15278).	might get lost (downstream of altered splice site)
634	634	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
645	645	MOD_RES	Phosphoserine.	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

131 / 131

chromosome

strand

-1

last intron/exon boundary

1918

theoretical NMD boundary in CDS

1737

length of CDS

2118

coding sequence (CDS) position

N/A

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

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

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

10676681

original gDNA sequence snippet

CGTGCGCAATGGGCCACAGAACCGCCATGCCGGAACCGCGC

altered gDNA sequence snippet

CGTGCGCAATGGGCCACAGAGCCGCCATGCCGGAACCGCGC

original cDNA sequence snippet

GCAATGGGCCACAGAACCGCCATGCCGGAACCGCGC

altered cDNA sequence snippet

GCAATGGGCCACAGAGCCGCCATGCCGGAACCGCGC

wildtype AA sequence

MRAGACARRP VGKWGVEWPR RLTWGGASRL CPAVKDRYGD RDSSSDSSSE SDSSDERVEF
DPQQERDFYK TLSLLKKKDP RIYQKDATFY NRTASSSDSE EDPEALEKQK KVRPMYLKDY
ERKVILEKAG KYVDEENSDG ETSNHRLQET SSQSYVEEQK QLKESFRAFV EDSEDEDGAG
EGGSSLLQKR AKTRQEKAQE EADYIEWLKG QKEIRNPDSL KELTHLKEYW NDPELDEGER
FLRDYILNKR YEEEEEEEED EEEMEEEEGV HGPPVQLAVD DSSDEGELFL KKQEDFEQKY
NFRFEEPDSA SVKTYPRSIA SSVRRKDERR KEKREETRER KKREKAKKQE ELKQLKNLKR
KEILAKLEKL RKVTGNEMLG LEEGDLEDDF DPAQHDQLMQ KCFGDEYYGA VEEEKPQFEE
EEGLEDDWNW DTWDGPEQEG DWSQQELHCE DPNFNMDADY DPSQPRKKKR EAPLTGKKKR
KSPFAAAVGQ EKPVFEPGDK TFEEYLDEYY RLDYEDIIDD LPCRFKYRTV VPCDFGLSTE
EILAADDKEL NRWCSLKKTC MYRSEQEELR DKRAYSQKAQ NSWKKRQVFK SLCREEAETP
AEATGKPQRD EAGPQRQLPA LDGSLMGPES PPAQEEEAPV SPHKKPAPQK RRRAKKARLL
GPTVMLGGCE FSRQRLQAFG LNPKRLHFRQ LGRQRRKQQG PKNSS*

mutated AA sequence

N/A

speed

1.01 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems