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: ENST00000273859
Querying Taster for transcript #2: ENST00000504445
MT speed 0 s - this script 3.392392 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ATP10D	polymorphism_automatic	3.37759820112637e-11	simple_aae				T43I	single base exchange	rs33995001		show file
ATP10D	polymorphism_automatic	3.37759820112637e-11	simple_aae				T43I	single base exchange	rs33995001		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999966224 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:47514685C>TN/A show variant in all transcripts IGV

HGNC symbol

ATP10D

Ensembl transcript ID

ENST00000273859

Genbank transcript ID

NM_020453

UniProt peptide

Q9P241

alteration type

single base exchange

alteration region

CDS

DNA changes

c.128C>T
cDNA.397C>T
g.27381C>T

AA changes

T43I Score: 89 explain score(s)

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

frameshift

known variant

Reference ID: rs33995001

database	homozygous (T/T)	heterozygous	allele carriers
1000G	287	953	1240
ExAC	9686	13395	23081

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.314	0
	0.307	0
(flanking)	0.27	0.001

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
Acc marginally increased	27387	wt: 0.3620 / mu: 0.3834 (marginal change - not scored)	wt: CAAGTCCTCTCAGACCCCTAAACTGTCAGGAAGGCACCGGA mu: CAAGTCCTCTCAGATCCCTAAACTGTCAGGAAGGCACCGGA	ctaa\|ACTG
Donor marginally increased	27383	wt: 0.7489 / mu: 0.7562 (marginal change - not scored)	wt: AGACCCCTAAACTGT mu: AGATCCCTAAACTGT	ACCC\|ctaa

distance from splice site

163

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000016032

Mmulatta

all identical

ENSMMUG00000021778

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000078887

PQVQ

Dmelanogaster

no alignment

FBgn0032120

n/a

Celegans

all identical

W09D10.2

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
1	97	TOPO_DOM	Cytoplasmic (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4281 / 4281

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

1427 / 1427

position of stopcodon in wt / mu cDNA

4550 / 4550

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

270 / 270

chromosome

strand

last intron/exon boundary

4211

theoretical NMD boundary in CDS

3891

length of CDS

4281

coding sequence (CDS) position

128

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

397

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

27381

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

47514685

original gDNA sequence snippet

TGGGCGCAAGTCCTCTCAGACCCCTAAACTGTCAGGAAGGC

altered gDNA sequence snippet

TGGGCGCAAGTCCTCTCAGATCCCTAAACTGTCAGGAAGGC

original cDNA sequence snippet

TGGGCGCAAGTCCTCTCAGACCCCTAAACTGTCAGGAAGGC

altered cDNA sequence snippet

TGGGCGCAAGTCCTCTCAGATCCCTAAACTGTCAGGAAGGC

wildtype AA sequence

MTEALQWARY HWRRLIRGAT RDDDSGPYNY SSLLACGRKS SQTPKLSGRH RIVVPHIQPF
KDEYEKFSGA YVNNRIRTTK YTLLNFVPRN LFEQFHRAAN LYFLFLVVLN WVPLVEAFQK
EITMLPLVVV LTIIAIKDGL EDYRKYKIDK QINNLITKVY SRKEKKYIDR CWKDVTVGDF
IRLSCNEVIP ADMVLLFSTD PDGICHIETS GLDGESNLKQ RQVVRGYAEQ DSEVDPEKFS
SRIECESPNN DLSRFRGFLE HSNKERVGLS KENLLLRGCT IRNTEAVVGI VVYAGHETKA
MLNNSGPRYK RSKLERRANT DVLWCVMLLV IMCLTGAVGH GIWLSRYEKM HFFNVPEPDG
HIISPLLAGF YMFWTMIILL QVLIPISLYV SIEIVKLGQI YFIQSDVDFY NEKMDSIVQC
RALNIAEDLG QIQYLFSDKT GTLTENKMVF RRCSVAGFDY CHEENARRLE SYQEAVSEDE
DFIDTVSGSL SNMAKPRAPS CRTVHNGPLG NKPSNHLAGS SFTLGSGEGA SEVPHSRQAA
FSSPIETDVV PDTRLLDKFS QITPRLFMPL DETIQNPPME TLYIIDFFIA LAICNTVVVS
APNQPRQKIR HPSLGGLPIK SLEEIKSLFQ RWSVRRSSSP SLNSGKEPSS GVPNAFVSRL
PLFSRMKPAS PVEEEVSQVC ESPQCSSSSA CCTETEKQHG DAGLLNGKAE SLPGQPLACN
LCYEAESPDE AALVYAARAY QCTLRSRTPE QVMVDFAALG PLTFQLLHIL PFDSVRKRMS
VVVRHPLSNQ VVVYTKGADS VIMELLSVAS PDGASLEKQQ MIVREKTQKH LDDYAKQGLR
TLCIAKKVMS DTEYAEWLRN HFLAETSIDN REELLLESAM RLENKLTLLG ATGIEDRLQE
GVPESIEALH KAGIKIWMLT GDKQETAVNI AYACKLLEPD DKLFILNTQS KDACGMLMST
ILKELQKKTQ ALPEQVSLSE DLLQPPVPRD SGLRAGLIIT GKTLEFALQE SLQKQFLELT
SWCQAVVCCR ATPLQKSEVV KLVRSHLQVM TLAIGDGAND VSMIQVADIG IGVSGQEGMQ
AVMASDFAVS QFKHLSKLLL VHGHWCYTRL SNMILYFFYK NVAYVNLLFW YQFFCGFSGT
SMTDYWVLIF FNLLFTSAPP VIYGVLEKDV SAETLMQLPE LYRSGQKSEA YLPHTFWITL
LDAFYQSLVC FFVPYFTYQG SDTDIFAFGN PLNTAALFIV LLHLVIESKS LTWIHLLVII
GSILSYFLFA IVFGAMCVTC NPPSNPYWIM QEHMLDPVFY LVCILTTSIA LLPRFVYRVL
QGSLFPSPIL RAKHFDRLTP EERTKALKKW RGAGKMNQVT SKYANQSAGK SGRRPMPGPS
AVFAMKSASS CAIEQGNLSL CETALDQGYS ETKAFEMAGP SKGKES*

mutated AA sequence

MTEALQWARY HWRRLIRGAT RDDDSGPYNY SSLLACGRKS SQIPKLSGRH RIVVPHIQPF
KDEYEKFSGA YVNNRIRTTK YTLLNFVPRN LFEQFHRAAN LYFLFLVVLN WVPLVEAFQK
EITMLPLVVV LTIIAIKDGL EDYRKYKIDK QINNLITKVY SRKEKKYIDR CWKDVTVGDF
IRLSCNEVIP ADMVLLFSTD PDGICHIETS GLDGESNLKQ RQVVRGYAEQ DSEVDPEKFS
SRIECESPNN DLSRFRGFLE HSNKERVGLS KENLLLRGCT IRNTEAVVGI VVYAGHETKA
MLNNSGPRYK RSKLERRANT DVLWCVMLLV IMCLTGAVGH GIWLSRYEKM HFFNVPEPDG
HIISPLLAGF YMFWTMIILL QVLIPISLYV SIEIVKLGQI YFIQSDVDFY NEKMDSIVQC
RALNIAEDLG QIQYLFSDKT GTLTENKMVF RRCSVAGFDY CHEENARRLE SYQEAVSEDE
DFIDTVSGSL SNMAKPRAPS CRTVHNGPLG NKPSNHLAGS SFTLGSGEGA SEVPHSRQAA
FSSPIETDVV PDTRLLDKFS QITPRLFMPL DETIQNPPME TLYIIDFFIA LAICNTVVVS
APNQPRQKIR HPSLGGLPIK SLEEIKSLFQ RWSVRRSSSP SLNSGKEPSS GVPNAFVSRL
PLFSRMKPAS PVEEEVSQVC ESPQCSSSSA CCTETEKQHG DAGLLNGKAE SLPGQPLACN
LCYEAESPDE AALVYAARAY QCTLRSRTPE QVMVDFAALG PLTFQLLHIL PFDSVRKRMS
VVVRHPLSNQ VVVYTKGADS VIMELLSVAS PDGASLEKQQ MIVREKTQKH LDDYAKQGLR
TLCIAKKVMS DTEYAEWLRN HFLAETSIDN REELLLESAM RLENKLTLLG ATGIEDRLQE
GVPESIEALH KAGIKIWMLT GDKQETAVNI AYACKLLEPD DKLFILNTQS KDACGMLMST
ILKELQKKTQ ALPEQVSLSE DLLQPPVPRD SGLRAGLIIT GKTLEFALQE SLQKQFLELT
SWCQAVVCCR ATPLQKSEVV KLVRSHLQVM TLAIGDGAND VSMIQVADIG IGVSGQEGMQ
AVMASDFAVS QFKHLSKLLL VHGHWCYTRL SNMILYFFYK NVAYVNLLFW YQFFCGFSGT
SMTDYWVLIF FNLLFTSAPP VIYGVLEKDV SAETLMQLPE LYRSGQKSEA YLPHTFWITL
LDAFYQSLVC FFVPYFTYQG SDTDIFAFGN PLNTAALFIV LLHLVIESKS LTWIHLLVII
GSILSYFLFA IVFGAMCVTC NPPSNPYWIM QEHMLDPVFY LVCILTTSIA LLPRFVYRVL
QGSLFPSPIL RAKHFDRLTP EERTKALKKW RGAGKMNQVT SKYANQSAGK SGRRPMPGPS
AVFAMKSASS CAIEQGNLSL CETALDQGYS ETKAFEMAGP SKGKES*

speed

0.73 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: 0.999999999966224 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:47514685C>TN/A show variant in all transcripts IGV

HGNC symbol

ATP10D

Ensembl transcript ID

ENST00000504445

Genbank transcript ID

N/A

UniProt peptide

Q9P241

alteration type

single base exchange

alteration region

CDS

DNA changes

c.128C>T
cDNA.386C>T
g.27381C>T

AA changes

T43I Score: 89 explain score(s)

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

frameshift

known variant

Reference ID: rs33995001

database	homozygous (T/T)	heterozygous	allele carriers
1000G	287	953	1240
ExAC	9686	13395	23081

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.314	0
	0.307	0
(flanking)	0.27	0.001

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
Acc marginally increased	27387	wt: 0.3620 / mu: 0.3834 (marginal change - not scored)	wt: CAAGTCCTCTCAGACCCCTAAACTGTCAGGAAGGCACCGGA mu: CAAGTCCTCTCAGATCCCTAAACTGTCAGGAAGGCACCGGA	ctaa\|ACTG
Donor marginally increased	27383	wt: 0.7489 / mu: 0.7562 (marginal change - not scored)	wt: AGACCCCTAAACTGT mu: AGATCCCTAAACTGT	ACCC\|ctaa

distance from splice site

163

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000016032

Mmulatta

all identical

ENSMMUG00000021778

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000078887

PQVQ

Dmelanogaster

no alignment

FBgn0032120

n/a

Celegans

all identical

W09D10.2

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
1	97	TOPO_DOM	Cytoplasmic (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1608 / 1608

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

536 / 536

position of stopcodon in wt / mu cDNA

1866 / 1866

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

259 / 259

chromosome

strand

last intron/exon boundary

1610

theoretical NMD boundary in CDS

1301

length of CDS

1608

coding sequence (CDS) position

128

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

386

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

27381

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

47514685

original gDNA sequence snippet

TGGGCGCAAGTCCTCTCAGACCCCTAAACTGTCAGGAAGGC

altered gDNA sequence snippet

TGGGCGCAAGTCCTCTCAGATCCCTAAACTGTCAGGAAGGC

original cDNA sequence snippet

TGGGCGCAAGTCCTCTCAGACCCCTAAACTGTCAGGAAGGC

altered cDNA sequence snippet

TGGGCGCAAGTCCTCTCAGATCCCTAAACTGTCAGGAAGGC

wildtype AA sequence

mutated AA sequence

speed

0.67 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems