MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000269081
Querying Taster for transcript #2: ENST00000416101
Querying Taster for transcript #3: ENST00000432313
MT speed 0 s - this script 4.208291 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ABCA10	polymorphism_automatic	2.85604873084822e-12	simple_aae				P203S	single base exchange	rs9909216		show file
ABCA10	polymorphism_automatic	2.85604873084822e-12	simple_aae				P203S	single base exchange	rs9909216		show file
ABCA10	polymorphism_automatic	2.85604873084822e-12	simple_aae				P203S	single base exchange	rs9909216		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999997144 (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)

chr17:67212423G>AN/A show variant in all transcripts IGV

HGNC symbol

ABCA10

Ensembl transcript ID

ENST00000269081

Genbank transcript ID

NM_080282

UniProt peptide

Q8WWZ4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.607C>T
cDNA.1517C>T
g.28565C>T

AA changes

P203S Score: 74 explain score(s)

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

203

frameshift

known variant

Reference ID: rs9909216

database	homozygous (A/A)	heterozygous	allele carriers
1000G	901	1106	2007
ExAC	24065	-15363	8702

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.928	0.018
	1.184	0.017
(flanking)	-0.188	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
Donor marginally increased	28563	wt: 0.2295 / mu: 0.2319 (marginal change - not scored)	wt: ATCAATCCCAATTGT mu: ATCAATCTCAATTGT	CAAT\|ccca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

203

mutated

not conserved

203

Ptroglodytes

no homologue

Mmulatta

no alignment

ENSMMUG00000018604

n/a

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

not conserved

ENSGALG00000021399

291

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0031170

340

KINWSE

Celegans

not conserved

Y39D8C.1

386

MHF

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
185	205	TRANSMEM	Helical; (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4632 / 4632

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

1544 / 1544

position of stopcodon in wt / mu cDNA

5542 / 5542

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

911 / 911

chromosome

strand

-1

last intron/exon boundary

5444

theoretical NMD boundary in CDS

4483

length of CDS

4632

coding sequence (CDS) position

607

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

1517

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

28565

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

67212423

original gDNA sequence snippet

CTCTGGTCATAACATCAATCCCAATTGTATTTCATACTGGC

altered gDNA sequence snippet

CTCTGGTCATAACATCAATCTCAATTGTATTTCATACTGGC

original cDNA sequence snippet

CTCTGGTCATAACATCAATCCCAATTGTATTTCATACTGGC

altered cDNA sequence snippet

CTCTGGTCATAACATCAATCTCAATTGTATTTCATACTGGC

wildtype AA sequence

MNKMALASFM KGRTVIGTPD EETMDIELPK KYHEMVGVIF SDTFSYRLKF NWGYRIPVIK
EHSEYTEHCW AMHGEIFCYL AKYWLKGFVA FQAAINAAII EVTTNHSVME ELTSVIGINM
KIPPFISKGE IMNEWFHFTC LVSFSSFIYF ASLNVARERG KFKKLMTVMG LRESAFWLSW
GLTYICFIFI MSIFMALVIT SIPIVFHTGF MVIFTLYSLY GLSLIALAFL MSVLIRKPML
AGLAGFLFTV FWGCLGFTVL YRQLPLSLGW VLSLLSPFAF TAGMAQITHL DNYLSGVIFP
DPSGDSYKMI ATFFILAFDT LFYLIFTLYF ERVLPDKDGH GDSPLFFLKS SFWSKHQNTH
HEIFENEINP EHSSDDSFEP VSPEFHGKEA IRIRNVIKEY NGKTGKVEAL QGIFFDIYEG
QITAILGHNG AGKSTLLNIL SGLSVSTEGS ATIYNTQLSE ITDMEEIRKN IGFCPQFNFQ
FDFLTVRENL RVFAKIKGIQ PKEVEQEVKR IIMELDMQSI QDIIAKKLSG GQKRKLTLGI
AILGDPQVLL LDEPTAGLDP FSRHRVWSLL KEHKVDRLIL FSTQFMDEAD ILADRKVFLS
NGKLKCAGSS LFLKRKWGIG YHLSLHRNEM CDTEKITSLI KQHIPDAKLT TESEEKLVYS
LPLEKTNKFP DLYSDLDKCS DQGIRNYAVS VTSLNEVFLN LEGKSAIDEP DFDIGKQEKI
HVTRNTGDES EMEQVLCSLP ETRKAVSSAA LWRRQIYAVA TLRFLKLRRE RRALLCLLLV
LGIAFIPIIL EKIMYKVTRE THCWEFSPSM YFLSLEQIPK TPLTSLLIVN NTGSNIEDLV
HSLKCQDIVL EIDDFRNRNG SDDPSYNGAI IVSGDQKDYR FSVACNTKKL NCFPVLMGIV
SNALMGIFNF TELIQMESTS FSRDDIVLDL GFIDGSIFLL LITNCVSPFI GMSSISDYKK
NVQSQLWISG LWPSAYWCGQ ALVDIPLYFL ILFSIHLIYY FIFLGFQLSW ELMFVLVVCI
IGCAVSLIFL TYVLSFIFRK WRKNNGFWSF GFFIILICVS TIMVSTQYEK LNLILCMIFI
PSFTLLGYVM LLIQLDFMRN LDSLDNRINE VNKTILLTTL IPYLQSVIFL FVIRCLEMKY
GNEIMNKDPV FRISPRSRET HPNPEEPEEE DEDVQAERVQ AANALTAPNL EEEPVITASC
LHKEYYETKK SCFSTRKKKI AIRNVSFCVK KGEVLGLLGH NGAGKSTSIK MITGCTKPTA
GVVVLQGSRA SVRQQHDNSL KFLGYCPQEN SLWPKLTMKE HLELYAAVKG LGKEDAALSI
SRLVEALKLQ EQLKAPVKTL SEGIKRKLCF VLSILGNPSV VLLDEPFTGM DPEGQQQMWQ
ILQATVKNKE RGTLLTTHYM SEAEAVCDRM AMMVSGTLRC IGSIQHLKNK FGRDYLLEIK
MKEPTQVEAL HTEILKLFPQ AAWQERYSSL MAYKLPVEDV HPLSRAFFKL EAMKQTFNLE
EYSLSQATLE QVFLELCKEQ ELGNVDDKID TTVEWKLLPQ EDP*

mutated AA sequence

MNKMALASFM KGRTVIGTPD EETMDIELPK KYHEMVGVIF SDTFSYRLKF NWGYRIPVIK
EHSEYTEHCW AMHGEIFCYL AKYWLKGFVA FQAAINAAII EVTTNHSVME ELTSVIGINM
KIPPFISKGE IMNEWFHFTC LVSFSSFIYF ASLNVARERG KFKKLMTVMG LRESAFWLSW
GLTYICFIFI MSIFMALVIT SISIVFHTGF MVIFTLYSLY GLSLIALAFL MSVLIRKPML
AGLAGFLFTV FWGCLGFTVL YRQLPLSLGW VLSLLSPFAF TAGMAQITHL DNYLSGVIFP
DPSGDSYKMI ATFFILAFDT LFYLIFTLYF ERVLPDKDGH GDSPLFFLKS SFWSKHQNTH
HEIFENEINP EHSSDDSFEP VSPEFHGKEA IRIRNVIKEY NGKTGKVEAL QGIFFDIYEG
QITAILGHNG AGKSTLLNIL SGLSVSTEGS ATIYNTQLSE ITDMEEIRKN IGFCPQFNFQ
FDFLTVRENL RVFAKIKGIQ PKEVEQEVKR IIMELDMQSI QDIIAKKLSG GQKRKLTLGI
AILGDPQVLL LDEPTAGLDP FSRHRVWSLL KEHKVDRLIL FSTQFMDEAD ILADRKVFLS
NGKLKCAGSS LFLKRKWGIG YHLSLHRNEM CDTEKITSLI KQHIPDAKLT TESEEKLVYS
LPLEKTNKFP DLYSDLDKCS DQGIRNYAVS VTSLNEVFLN LEGKSAIDEP DFDIGKQEKI
HVTRNTGDES EMEQVLCSLP ETRKAVSSAA LWRRQIYAVA TLRFLKLRRE RRALLCLLLV
LGIAFIPIIL EKIMYKVTRE THCWEFSPSM YFLSLEQIPK TPLTSLLIVN NTGSNIEDLV
HSLKCQDIVL EIDDFRNRNG SDDPSYNGAI IVSGDQKDYR FSVACNTKKL NCFPVLMGIV
SNALMGIFNF TELIQMESTS FSRDDIVLDL GFIDGSIFLL LITNCVSPFI GMSSISDYKK
NVQSQLWISG LWPSAYWCGQ ALVDIPLYFL ILFSIHLIYY FIFLGFQLSW ELMFVLVVCI
IGCAVSLIFL TYVLSFIFRK WRKNNGFWSF GFFIILICVS TIMVSTQYEK LNLILCMIFI
PSFTLLGYVM LLIQLDFMRN LDSLDNRINE VNKTILLTTL IPYLQSVIFL FVIRCLEMKY
GNEIMNKDPV FRISPRSRET HPNPEEPEEE DEDVQAERVQ AANALTAPNL EEEPVITASC
LHKEYYETKK SCFSTRKKKI AIRNVSFCVK KGEVLGLLGH NGAGKSTSIK MITGCTKPTA
GVVVLQGSRA SVRQQHDNSL KFLGYCPQEN SLWPKLTMKE HLELYAAVKG LGKEDAALSI
SRLVEALKLQ EQLKAPVKTL SEGIKRKLCF VLSILGNPSV VLLDEPFTGM DPEGQQQMWQ
ILQATVKNKE RGTLLTTHYM SEAEAVCDRM AMMVSGTLRC IGSIQHLKNK FGRDYLLEIK
MKEPTQVEAL HTEILKLFPQ AAWQERYSSL MAYKLPVEDV HPLSRAFFKL EAMKQTFNLE
EYSLSQATLE QVFLELCKEQ ELGNVDDKID TTVEWKLLPQ EDP*

speed

0.85 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: 0.999999999997144 (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)

chr17:67212423G>AN/A show variant in all transcripts IGV

HGNC symbol

ABCA10

Ensembl transcript ID

ENST00000416101

Genbank transcript ID

N/A

UniProt peptide

Q8WWZ4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.607C>T
cDNA.1486C>T
g.28565C>T

AA changes

P203S Score: 74 explain score(s)

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

203

frameshift

known variant

Reference ID: rs9909216

database	homozygous (A/A)	heterozygous	allele carriers
1000G	901	1106	2007
ExAC	24065	-15363	8702

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.928	0.018
	1.184	0.017
(flanking)	-0.188	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
Donor marginally increased	28563	wt: 0.2295 / mu: 0.2319 (marginal change - not scored)	wt: ATCAATCCCAATTGT mu: ATCAATCTCAATTGT	CAAT\|ccca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

203

mutated

not conserved

203

Ptroglodytes

no homologue

Mmulatta

no alignment

ENSMMUG00000018604

n/a

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

not conserved

ENSGALG00000021399

291

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0031170

340

KINWSE

Celegans

not conserved

Y39D8C.1

386

MHF

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
185	205	TRANSMEM	Helical; (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1401 / 1401

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

467 / 467

position of stopcodon in wt / mu cDNA

2280 / 2280

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

880 / 880

chromosome

strand

-1

last intron/exon boundary

5237

theoretical NMD boundary in CDS

4307

length of CDS

1401

coding sequence (CDS) position

607

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

1486

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

28565

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

67212423

original gDNA sequence snippet

CTCTGGTCATAACATCAATCCCAATTGTATTTCATACTGGC

altered gDNA sequence snippet

CTCTGGTCATAACATCAATCTCAATTGTATTTCATACTGGC

original cDNA sequence snippet

CTCTGGTCATAACATCAATCCCAATTGTATTTCATACTGGC

altered cDNA sequence snippet

CTCTGGTCATAACATCAATCTCAATTGTATTTCATACTGGC

wildtype AA sequence

mutated AA sequence

speed

1.25 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999997144 (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)

chr17:67212423G>AN/A show variant in all transcripts IGV

HGNC symbol

ABCA10

Ensembl transcript ID

ENST00000432313

Genbank transcript ID

N/A

UniProt peptide

Q8WWZ4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.607C>T
cDNA.1486C>T
g.28565C>T

AA changes

P203S Score: 74 explain score(s)

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

203

frameshift

known variant

Reference ID: rs9909216

database	homozygous (A/A)	heterozygous	allele carriers
1000G	901	1106	2007
ExAC	24065	-15363	8702

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.928	0.018
	1.184	0.017
(flanking)	-0.188	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
Donor marginally increased	28563	wt: 0.2295 / mu: 0.2319 (marginal change - not scored)	wt: ATCAATCCCAATTGT mu: ATCAATCTCAATTGT	CAAT\|ccca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

203

mutated

not conserved

203

Ptroglodytes

no homologue

Mmulatta

no alignment

ENSMMUG00000018604

n/a

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

not conserved

ENSGALG00000021399

291

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0031170

340

VKINWS

Celegans

not conserved

Y39D8C.1

386

MHF

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
185	205	TRANSMEM	Helical; (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1359 / 1359

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

453 / 453

position of stopcodon in wt / mu cDNA

2238 / 2238

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

880 / 880

chromosome

strand

-1

last intron/exon boundary

2114

theoretical NMD boundary in CDS

1184

length of CDS

1359

coding sequence (CDS) position

607

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

1486

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

28565

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

67212423

original gDNA sequence snippet

CTCTGGTCATAACATCAATCCCAATTGTATTTCATACTGGC

altered gDNA sequence snippet

CTCTGGTCATAACATCAATCTCAATTGTATTTCATACTGGC

original cDNA sequence snippet

CTCTGGTCATAACATCAATCCCAATTGTATTTCATACTGGC

altered cDNA sequence snippet

CTCTGGTCATAACATCAATCTCAATTGTATTTCATACTGGC

wildtype AA sequence

mutated AA sequence

speed

0.97 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems