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: ENST00000389301
Querying Taster for transcript #2: ENST00000568369
MT speed 0 s - this script 3.227583 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FANCA	polymorphism_automatic	2.19824158875781e-14	simple_aae		affected		G809D	single base exchange	rs7195066		show file
FANCA	polymorphism_automatic	2.19824158875781e-14	simple_aae		affected		G809D	single base exchange	rs7195066		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999978 (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)

chr16:89836323C>TN/A show variant in all transcripts IGV

HGNC symbol

FANCA

Ensembl transcript ID

ENST00000389301

Genbank transcript ID

NM_000135

UniProt peptide

O15360

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2426G>A
cDNA.2457G>A
g.46743G>A

AA changes

G809D Score: 94 explain score(s)

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

809

frameshift

known variant

Reference ID: rs7195066

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1235	869	2104
ExAC	16070	627	16697

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.22	0.001
	-0.205	0
(flanking)	-0.122	0

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	46737	wt: 0.6653 / mu: 0.6832 (marginal change - not scored)	wt: GGTGGATGTGGGTCCTCCTGCACCTGGTGCTGGCCTTCCTG mu: GGTGGATGTGGGTCCTCCTGCACCTGATGCTGGCCTTCCTG	ctgc\|ACCT
Donor gained	46739	0.38	mu: CTGCACCTGATGCTG	GCAC\|ctga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

809

mutated

not conserved

809

Ptroglodytes

not conserved

ENSPTRG00000008492

746

Mmulatta

no alignment

ENSMMUG00000029067

n/a

Fcatus

not conserved

ENSFCAG00000003795

807

Mmusculus

not conserved

ENSMUSG00000032815

807

Ggallus

not conserved

ENSGALG00000000516

777

EADFG

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000033926

721

protein features

start (aa)	end (aa)	feature	details
849	849	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
850	850	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
858	858	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1449	1449	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

4368 / 4368

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

1456 / 1456

position of stopcodon in wt / mu cDNA

4399 / 4399

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

32 / 32

chromosome

strand

-1

last intron/exon boundary

4292

theoretical NMD boundary in CDS

4210

length of CDS

4368

coding sequence (CDS) position

2426

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

2457

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

46743

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

89836323

original gDNA sequence snippet

TGTGGGTCCTCCTGCACCTGGTGCTGGCCTTCCTGTCCCTG

altered gDNA sequence snippet

TGTGGGTCCTCCTGCACCTGATGCTGGCCTTCCTGTCCCTG

original cDNA sequence snippet

TGTGGGTCCTCCTGCACCTGGTGCTGGCCTTCCTGTCCCTG

altered cDNA sequence snippet

TGTGGGTCCTCCTGCACCTGATGCTGGCCTTCCTGTCCCTG

wildtype AA sequence

MSDSWVPNSA SGQDPGGRRR AWAELLAGRV KREKYNPERA QKLKESAVRL LRSHQDLNAL
LLEVEGPLCK KLSLSKVIDC DSSEAYANHS SSFIGSALQD QASRLGVPVG ILSAGMVASS
VGQICTAPAE TSHPVLLTVE QRKKLSSLLE FAQYLLAHSM FSRLSFCQEL WKIQSSLLLE
AVWHLHVQGI VSLQELLESH PDMHAVGSWL FRNLCCLCEQ MEASCQHADV ARAMLSDFVQ
MFVLRGFQKN SDLRRTVEPE KMPQVTVDVL QRMLIFALDA LAAGVQEESS THKIVRCWFG
VFSGHTLGSV ISTDPLKRFF SHTLTQILTH SPVLKASDAV QMQREWSFAR THPLLTSLYR
RLFVMLSAEE LVGHLQEVLE TQEVHWQRVL SFVSALVVCF PEAQQLLEDW VARLMAQAFE
SCQLDSMVTA FLVVRQAALE GPSAFLSYAD WFKASFGSTR GYHGCSKKAL VFLFTFLSEL
VPFESPRYLQ VHILHPPLVP GKYRSLLTDY ISLAKTRLAD LKVSIENMGL YEDLSSAGDI
TEPHSQALQD VEKAIMVFEH TGNIPVTVME ASIFRRPYYV SHFLPALLTP RVLPKVPDSR
VAFIESLKRA DKIPPSLYST YCQACSAAEE KPEDAALGVR AEPNSAEEPL GQLTAALGEL
RASMTDPSQR DVISAQVAVI SERLRAVLGH NEDDSSVEIS KIQLSINTPR LEPREHMAVD
LLLTSFCQNL MAASSVAPPE RQGPWAALFV RTMCGRVLPA VLTRLCQLLR HQGPSLSAPH
VLGLAALAVH LGESRSALPE VDVGPPAPGA GLPVPALFDS LLTCRTRDSL FFCLKFCTAA
ISYSLCKFSS QSRDTLCSCL SPGLIKKFQF LMFRLFSEAR QPLSEEDVAS LSWRPLHLPS
ADWQRAALSL WTHRTFREVL KEEDVHLTYQ DWLHLELEIQ PEADALSDTE RQDFHQWAIH
EHFLPESSAS GGCDGDLQAA CTILVNALMD FHQSSRSYDH SENSDLVFGG RTGNEDIISR
LQEMVADLEL QQDLIVPLGH TPSQEHFLFE IFRRRLQALT SGWSVAASLQ RQRELLMYKR
ILLRLPSSVL CGSSFQAEQP ITARCEQFFH LVNSEMRNFC SHGGALTQDI TAHFFRGLLN
ACLRSRDPSL MVDFILAKCQ TKCPLILTSA LVWWPSLEPV LLCRWRRHCQ SPLPRELQKL
QEGRQFASDF LSPEAASPAP NPDWLSAAAL HFAIQQVREE NIRKQLKKLD CEREELLVFL
FFFSLMGLLS SHLTSNSTTD LPKAFHVCAA ILECLEKRKI SWLALFQLTE SDLRLGRLLL
RVAPDQHTRL LPFAFYSLLS YFHEDAAIRE EAFLHVAVDM YLKLVQLFVA GDTSTVSPPA
GRSLELKGQG NPVELITKAR LFLLQLIPRC PKKSFSHVAE LLADRGDCDP EVSAALQSRQ
QAAPDADLSQ EPHLF*

mutated AA sequence

MSDSWVPNSA SGQDPGGRRR AWAELLAGRV KREKYNPERA QKLKESAVRL LRSHQDLNAL
LLEVEGPLCK KLSLSKVIDC DSSEAYANHS SSFIGSALQD QASRLGVPVG ILSAGMVASS
VGQICTAPAE TSHPVLLTVE QRKKLSSLLE FAQYLLAHSM FSRLSFCQEL WKIQSSLLLE
AVWHLHVQGI VSLQELLESH PDMHAVGSWL FRNLCCLCEQ MEASCQHADV ARAMLSDFVQ
MFVLRGFQKN SDLRRTVEPE KMPQVTVDVL QRMLIFALDA LAAGVQEESS THKIVRCWFG
VFSGHTLGSV ISTDPLKRFF SHTLTQILTH SPVLKASDAV QMQREWSFAR THPLLTSLYR
RLFVMLSAEE LVGHLQEVLE TQEVHWQRVL SFVSALVVCF PEAQQLLEDW VARLMAQAFE
SCQLDSMVTA FLVVRQAALE GPSAFLSYAD WFKASFGSTR GYHGCSKKAL VFLFTFLSEL
VPFESPRYLQ VHILHPPLVP GKYRSLLTDY ISLAKTRLAD LKVSIENMGL YEDLSSAGDI
TEPHSQALQD VEKAIMVFEH TGNIPVTVME ASIFRRPYYV SHFLPALLTP RVLPKVPDSR
VAFIESLKRA DKIPPSLYST YCQACSAAEE KPEDAALGVR AEPNSAEEPL GQLTAALGEL
RASMTDPSQR DVISAQVAVI SERLRAVLGH NEDDSSVEIS KIQLSINTPR LEPREHMAVD
LLLTSFCQNL MAASSVAPPE RQGPWAALFV RTMCGRVLPA VLTRLCQLLR HQGPSLSAPH
VLGLAALAVH LGESRSALPE VDVGPPAPDA GLPVPALFDS LLTCRTRDSL FFCLKFCTAA
ISYSLCKFSS QSRDTLCSCL SPGLIKKFQF LMFRLFSEAR QPLSEEDVAS LSWRPLHLPS
ADWQRAALSL WTHRTFREVL KEEDVHLTYQ DWLHLELEIQ PEADALSDTE RQDFHQWAIH
EHFLPESSAS GGCDGDLQAA CTILVNALMD FHQSSRSYDH SENSDLVFGG RTGNEDIISR
LQEMVADLEL QQDLIVPLGH TPSQEHFLFE IFRRRLQALT SGWSVAASLQ RQRELLMYKR
ILLRLPSSVL CGSSFQAEQP ITARCEQFFH LVNSEMRNFC SHGGALTQDI TAHFFRGLLN
ACLRSRDPSL MVDFILAKCQ TKCPLILTSA LVWWPSLEPV LLCRWRRHCQ SPLPRELQKL
QEGRQFASDF LSPEAASPAP NPDWLSAAAL HFAIQQVREE NIRKQLKKLD CEREELLVFL
FFFSLMGLLS SHLTSNSTTD LPKAFHVCAA ILECLEKRKI SWLALFQLTE SDLRLGRLLL
RVAPDQHTRL LPFAFYSLLS YFHEDAAIRE EAFLHVAVDM YLKLVQLFVA GDTSTVSPPA
GRSLELKGQG NPVELITKAR LFLLQLIPRC PKKSFSHVAE LLADRGDCDP EVSAALQSRQ
QAAPDADLSQ EPHLF*

speed

0.61 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: 0.999999999999978 (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)

chr16:89836323C>TN/A show variant in all transcripts IGV

HGNC symbol

FANCA

Ensembl transcript ID

ENST00000568369

Genbank transcript ID

N/A

UniProt peptide

O15360

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2426G>A
cDNA.2457G>A
g.46743G>A

AA changes

G809D Score: 94 explain score(s)

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

809

frameshift

known variant

Reference ID: rs7195066

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1235	869	2104
ExAC	16070	627	16697

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.22	0.001
	-0.205	0
(flanking)	-0.122	0

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	46737	wt: 0.6653 / mu: 0.6832 (marginal change - not scored)	wt: GGTGGATGTGGGTCCTCCTGCACCTGGTGCTGGCCTTCCTG mu: GGTGGATGTGGGTCCTCCTGCACCTGATGCTGGCCTTCCTG	ctgc\|ACCT
Donor gained	46739	0.38	mu: CTGCACCTGATGCTG	GCAC\|ctga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

809

mutated

not conserved

809

Ptroglodytes

not conserved

ENSPTRG00000008492

746

Mmulatta

no alignment

ENSMMUG00000029067

n/a

Fcatus

not conserved

ENSFCAG00000003795

807

Mmusculus

not conserved

ENSMUSG00000032815

807

Ggallus

not conserved

ENSGALG00000000516

777

EADFG

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000033926

721

protein features

start (aa)	end (aa)	feature	details
849	849	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
850	850	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
858	858	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1449	1449	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

4275 / 4275

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

1425 / 1425

position of stopcodon in wt / mu cDNA

4306 / 4306

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

32 / 32

chromosome

strand

-1

last intron/exon boundary

4296

theoretical NMD boundary in CDS

4214

length of CDS

4275

coding sequence (CDS) position

2426

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

2457

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

46743

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

89836323

original gDNA sequence snippet

TGTGGGTCCTCCTGCACCTGGTGCTGGCCTTCCTGTCCCTG

altered gDNA sequence snippet

TGTGGGTCCTCCTGCACCTGATGCTGGCCTTCCTGTCCCTG

original cDNA sequence snippet

TGTGGGTCCTCCTGCACCTGGTGCTGGCCTTCCTGTCCCTG

altered cDNA sequence snippet

TGTGGGTCCTCCTGCACCTGATGCTGGCCTTCCTGTCCCTG

wildtype AA sequence

mutated AA sequence

MSDSWVPNSA SGQDPGGRRR AWAELLAGRV KREKYNPERA QKLKESAVRL LRSHQDLNAL
LLEVEGPLCK KLSLSKVIDC DSSEAYANHS SSFIGSALQD QASRLGVPVG ILSAGMVASS
VGQICTAPAE TSHPVLLTVE QRKKLSSLLE FAQYLLAHSM FSRLSFCQEL WKIQSSLLLE
AVWHLHVQGI VSLQELLESH PDMHAVGSWL FRNLCCLCEQ MEASCQHADV ARAMLSDFVQ
MFVLRGFQKN SDLRRTVEPE KMPQVTVDVL QRMLIFALDA LAAGVQEESS THKIVRCWFG
VFSGHTLGSV ISTDPLKRFF SHTLTQILTH SPVLKASDAV QMQREWSFAR THPLLTSLYR
RLFVMLSAEE LVGHLQEVLE TQEVHWQRVL SFVSALVVCF PEAQQLLEDW VARLMAQAFE
SCQLDSMVTA FLVVRQAALE GPSAFLSYAD WFKASFGSTR GYHGCSKKAL VFLFTFLSEL
VPFESPRYLQ VHILHPPLVP GKYRSLLTDY ISLAKTRLAD LKVSIENMGL YEDLSSAGDI
TEPHSQALQD VEKAIMVFEH TGNIPVTVME ASIFRRPYYV SHFLPALLTP RVLPKVPDSR
VAFIESLKRA DKIPPSLYST YCQACSAAEE KPEDAALGVR AEPNSAEEPL GQLTAALGEL
RASMTDPSQR DVISAQVAVI SERLRAVLGH NEDDSSVEIS KIQLSINTPR LEPREHMAVD
LLLTSFCQNL MAASSVAPPE RQGPWAALFV RTMCGRVLPA VLTRLCQLLR HQGPSLSAPH
VLGLAALAVH LGESRSALPE VDVGPPAPDA GLPVPALFDS LLTCRTRDSL FFCLKFCTAA
ISYSLCKFSS QSRDTLCSCL SPGLIKKFQF LMFRLFSEAR QPLSEEDVAS LSWRPLHLPS
ADWQRAALSL WTHRTFREVL KEEDVHLTYQ DWLHLELEIQ PEADALSDTE RQDFHQWAIH
EHFLPESSAS GGCDGDLQAA CTILVNALMD FHQSSRSYDH SENSDLVFGG RTGNEDIISR
LQEMVADLEL QQDLIVPLGH TPSQEHFLFE IFRRRLQALT SGWSVAASLQ RQRELLMYKR
ILLRLPSSVL CGSSFQAEQP ITARCEQFFH LVNSEMRNFC SHGGALTQDI TAHFFRGLLN
ACLRSRDPSL MVDFILAKCQ TKCPLILTSA LVWWPSLEPV LLCRWRRHCQ SPLPRELQKL
QEGRQFASDF LSPEAASPAP NPDWLSAAAL HFAIQQVREE NIRKQLKKLD CEREELLVFL
FFFSLMGLLS SHLTSNSTTD LPKAFHVCAA ILECLEKRKI SWLALFQLTE SDLRLGRLLL
RVAPDQHTRL LPFAFYSLLS YFHEDAAIRE EAFLHVAVDM YLKLVQLFVA GDTSTVSPPA
GRSLELKGQA GQPRGTDNKS SSFSAAVNTS VPEKELLTRG RAAG*

speed

0.61 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems