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 1 transcript(s)...
Querying Taster for transcript #1: ENST00000389916
MT speed 0.79 s - this script 2.860525 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
KIF19	polymorphism_automatic	0.014703210972051	simple_aae		affected		R807H	single base exchange	rs2271535		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.985296789027949 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:72350412G>AN/A show variant in all transcripts IGV

HGNC symbol

KIF19

Ensembl transcript ID

ENST00000389916

Genbank transcript ID

NM_153209

UniProt peptide

Q2TAC6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2420G>A
cDNA.2558G>A
g.28064G>A

AA changes

R807H Score: 29 explain score(s)

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

807

frameshift

known variant

Reference ID: rs2271535

database	homozygous (A/A)	heterozygous	allele carriers
1000G	355	1008	1363
ExAC	11202	10363	21565

regulatory features

CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Rad21, Transcription Factor, Rad21 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.025	0.841
	0.242	0.853
(flanking)	1.253	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	28066	wt: 0.51 / mu: 0.59	wt: AGCGCAGCAGCCTGT mu: AGCACAGCAGCCTGT	CGCA\|gcag
Donor marginally increased	28056	wt: 0.7637 / mu: 0.7937 (marginal change - not scored)	wt: CCCGCGACAGAGCGC mu: CCCGCGACAGAGCAC	CGCG\|acag

distance from splice site

112

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

807

mutated

not conserved

807

Ptroglodytes

no homologue

Mmulatta

no alignment

ENSMMUG00000020975

n/a

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000010021

806

Ggallus

no homologue

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000053026

825

LPPPPSP

Dmelanogaster

no alignment

FBgn0038205

n/a

Celegans

no alignment

F22F4.3

n/a

Xtropicalis

all identical

ENSXETG00000012830

809

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2997 / 2997

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

999 / 999

position of stopcodon in wt / mu cDNA

3135 / 3135

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

139 / 139

chromosome

strand

last intron/exon boundary

3005

theoretical NMD boundary in CDS

2816

length of CDS

2997

coding sequence (CDS) position

2420

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

2558

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

28064

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

72350412

original gDNA sequence snippet

GCTGGCACCCGCGACAGAGCGCAGCAGCCTGTCCCTGCACT

altered gDNA sequence snippet

GCTGGCACCCGCGACAGAGCACAGCAGCCTGTCCCTGCACT

original cDNA sequence snippet

GCTGGCACCCGCGACAGAGCGCAGCAGCCTGTCCCTGCACT

altered cDNA sequence snippet

GCTGGCACCCGCGACAGAGCACAGCAGCCTGTCCCTGCACT

wildtype AA sequence

MKDSGDSKDQ QLMVALRVRP ISVAELEEGA TLIAHKVDEQ MVVLMDPMED PDDILRAHRS
REKSYLFDVA FDFTATQEMV YQATTKSLIE GVISGYNATV FAYGPTGCGK TYTMLGTDQE
PGIYVQTLND LFRAIEETSN DMEYEVSMSY LEIYNEMIRD LLNPSLGYLE LREDSKGVIQ
VAGITEVSTI NAKEIMQLLM KGNRQRTQEP TAANQTSSRS HAVLQVTVRQ RSRVKNILQE
VRQGRLFMID LAGSERASQT QNRGQRMKEG AHINRSLLAL GNCINALSDK GSNKYINYRD
SKLTRLLKDS LGGNSRTVMI AHISPASSAF EESRNTLTYA GRAKNIKTRV KQNLLNVSYH
IAQYTSIIAD LRGEIQRLKR KIDEQTGRGQ ARGRQDRGDI RHIQAEVQLH SGQGEKAGMG
QLREQLASAF QEQMDVRRRL LELENRAMEV QIDTSRHLLT IAGWKHEKSR RALKWREEQR
KECYAKDDSE KDSDTGDDQP DILEPPEVAA ARESIAALVD EQKQLRKQKL ALEQRCRELR
ARGRRLEETL PRRIGSEEQR EVLSLLCRVH ELEVENTEMQ SHALLRDGAL RHRHEAVRRL
EQHRSLCDEI IQGQRQIIDD YNLAVPQRLE ELYEVYLREL EEGSLEQATI MDQVASRALQ
DSSLPKITPA GTSLTPDSDL ESVKTLSSDA QHLQNSALPP LSTESEGHHV FKAGTGAWQA
KSSSVPTPPP IQLGSLVTQE APAQDSLGSW INSSPDSSEN LSEIPLSHKE RKEILTGTKC
IWVKAARRRS RALGTEGRHL LAPATERSSL SLHSLSEGDD ARPPGPLACK RPPSPTLQHA
ASEDNLSSST GEAPSRAVGH HGDGPRPWLR GQKKSLGKKR EESLEAKRRK RRSRSFEVTG
QGLSHPKTHL LGPHQAERIS DHRMPVCRHP APGIRHLGKV TLPLAKVKLP PSQNTGPGDS
SPLAVPPNPG GGSRRATRGP RLPHGTSTHG KDGCSRHN*

mutated AA sequence

MKDSGDSKDQ QLMVALRVRP ISVAELEEGA TLIAHKVDEQ MVVLMDPMED PDDILRAHRS
REKSYLFDVA FDFTATQEMV YQATTKSLIE GVISGYNATV FAYGPTGCGK TYTMLGTDQE
PGIYVQTLND LFRAIEETSN DMEYEVSMSY LEIYNEMIRD LLNPSLGYLE LREDSKGVIQ
VAGITEVSTI NAKEIMQLLM KGNRQRTQEP TAANQTSSRS HAVLQVTVRQ RSRVKNILQE
VRQGRLFMID LAGSERASQT QNRGQRMKEG AHINRSLLAL GNCINALSDK GSNKYINYRD
SKLTRLLKDS LGGNSRTVMI AHISPASSAF EESRNTLTYA GRAKNIKTRV KQNLLNVSYH
IAQYTSIIAD LRGEIQRLKR KIDEQTGRGQ ARGRQDRGDI RHIQAEVQLH SGQGEKAGMG
QLREQLASAF QEQMDVRRRL LELENRAMEV QIDTSRHLLT IAGWKHEKSR RALKWREEQR
KECYAKDDSE KDSDTGDDQP DILEPPEVAA ARESIAALVD EQKQLRKQKL ALEQRCRELR
ARGRRLEETL PRRIGSEEQR EVLSLLCRVH ELEVENTEMQ SHALLRDGAL RHRHEAVRRL
EQHRSLCDEI IQGQRQIIDD YNLAVPQRLE ELYEVYLREL EEGSLEQATI MDQVASRALQ
DSSLPKITPA GTSLTPDSDL ESVKTLSSDA QHLQNSALPP LSTESEGHHV FKAGTGAWQA
KSSSVPTPPP IQLGSLVTQE APAQDSLGSW INSSPDSSEN LSEIPLSHKE RKEILTGTKC
IWVKAARRRS RALGTEGRHL LAPATEHSSL SLHSLSEGDD ARPPGPLACK RPPSPTLQHA
ASEDNLSSST GEAPSRAVGH HGDGPRPWLR GQKKSLGKKR EESLEAKRRK RRSRSFEVTG
QGLSHPKTHL LGPHQAERIS DHRMPVCRHP APGIRHLGKV TLPLAKVKLP PSQNTGPGDS
SPLAVPPNPG GGSRRATRGP RLPHGTSTHG KDGCSRHN*

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

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

Problems