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: ENST00000300027
Querying Taster for transcript #2: ENST00000310775
MT speed 0 s - this script 4.951533 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FANCI	polymorphism_automatic	0.969570523742319	simple_aae		affected		C742S	single base exchange	rs2283432		show file
FANCI	polymorphism_automatic	0.996761964571327	simple_aae		affected		C742S	single base exchange	rs2283432		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.0304294762576812 (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)

chr15:89836228G>CN/A show variant in all transcripts IGV

HGNC symbol

FANCI

Ensembl transcript ID

ENST00000300027

Genbank transcript ID

NM_018193

UniProt peptide

Q9NVI1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2225G>C
cDNA.2329G>C
g.49049G>C

AA changes

C742S Score: 112 explain score(s)

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

742

frameshift

known variant

Reference ID: rs2283432

database	homozygous (C/C)	heterozygous	allele carriers
1000G	230	867	1097
ExAC	8539	15689	24228

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.287	1
	3.711	1
(flanking)	0.505	1

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	49060	wt: 0.8827 / mu: 0.9222 (marginal change - not scored)	wt: ATAATATCTGTGCTTTTCTTGTGATGGGAGTTTGTGAGGTT mu: ATAATATCTCTGCTTTTCTTGTGATGGGAGTTTGTGAGGTT	cttg\|TGAT
Acc increased	49058	wt: 0.57 / mu: 0.80	wt: AAATAATATCTGTGCTTTTCTTGTGATGGGAGTTTGTGAGG mu: AAATAATATCTCTGCTTTTCTTGTGATGGGAGTTTGTGAGG	ttct\|TGTG
Acc increased	49057	wt: 0.24 / mu: 0.49	wt: AAAATAATATCTGTGCTTTTCTTGTGATGGGAGTTTGTGAG mu: AAAATAATATCTCTGCTTTTCTTGTGATGGGAGTTTGTGAG	tttc\|TTGT
Acc marginally increased	49059	wt: 0.9833 / mu: 0.9904 (marginal change - not scored)	wt: AATAATATCTGTGCTTTTCTTGTGATGGGAGTTTGTGAGGT mu: AATAATATCTCTGCTTTTCTTGTGATGGGAGTTTGTGAGGT	tctt\|GTGA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

742

mutated

not conserved

742

Ptroglodytes

all identical

ENSPTRG00000007430

742

Mmulatta

all identical

ENSMMUG00000011155

742

Fcatus

no alignment

ENSFCAG00000012886

n/a

Mmusculus

all identical

ENSMUSG00000039187

741

Ggallus

not conserved

ENSGALG00000006658

567

Trubripes

not conserved

ENSTRUG00000000347

741

Drerio

not conserved

ENSDARG00000026224

747

Dmelanogaster

not conserved

FBgn0033354

734

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000017742

739

protein features

start (aa)	end (aa)	feature	details
877	877	CONFLICT	I -> L (in Ref. 6; BAB47423).	might get lost (downstream of altered splice site)
952	952	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
1121	1121	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

3807 / 3807

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

1269 / 1269

position of stopcodon in wt / mu cDNA

3911 / 3911

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

105 / 105

chromosome

strand

last intron/exon boundary

3849

theoretical NMD boundary in CDS

3694

length of CDS

3807

coding sequence (CDS) position

2225

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

2329

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

49049

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

89836228

original gDNA sequence snippet

TGGCATAAAAAATAATATCTGTGCTTTTCTTGTGATGGGAG

altered gDNA sequence snippet

TGGCATAAAAAATAATATCTCTGCTTTTCTTGTGATGGGAG

original cDNA sequence snippet

TGGCATAAAAAATAATATCTGTGCTTTTCTTGTGATGGGAG

altered cDNA sequence snippet

TGGCATAAAAAATAATATCTCTGCTTTTCTTGTGATGGGAG

wildtype AA sequence

MDQKILSLAA EKTADKLQEF LQTLREGDLT NLLQNQAVKG KVAGALLRAI FKGSPCSEEA
GTLRRRKIYT CCIQLVESGD LQKEIASEII GLLMLEAHHF PGPLLVELAN EFISAVREGS
LVNGKSLELL PIILTALATK KENLAYGKGV LSGEECKKQL INTLCSGRWD QQYVIQLTSM
FKDVPLTAEE VEFVVEKALS MFSKMNLQEI PPLVYQLLVL SSKGSRKSVL EGIIAFFSAL
DKQHNEEQSG DELLDVVTVP SGELRHVEGT IILHIVFAIK LDYELGRELV KHLKVGQQGD
SNNNLSPFSI ALLLSVTRIQ RFQDQVLDLL KTSVVKSFKD LQLLQGSKFL QNLVPHRSYV
STMILEVVKN SVHSWDHVTQ GLVELGFILM DSYGPKKVLD GKTIETSPSL SRMPNQHACK
LGANILLETF KIHEMIRQEI LEQVLNRVVT RASSPISHFL DLLSNIVMYA PLVLQSCSSK
VTEAFDYLSF LPLQTVQRLL KAVQPLLKVS MSMRDCLILV LRKAMFANQL DARKSAVAGF
LLLLKNFKVL GSLSSSQCSQ SLSVSQVHVD VHSHYNSVAN ETFCLEIMDS LRRCLSQQAD
VRLMLYEGFY DVLRRNSQLA NSVMQTLLSQ LKQFYEPKPD LLPPLKLEAC ILTQGDKISL
QEPLDYLLCC IQHCLAWYKN TVIPLQQGEE EEEEEEAFYE DLDDILESIT NRMIKSELED
FELDKSADFS QSTSIGIKNN ICAFLVMGVC EVLIEYNFSI SSFSKNRFED ILSLFMCYKK
LSDILNEKAG KAKTKMANKT SDSLLSMKFV SSLLTALFRV LLWRYTSIPT SVEESGKKEK
GKSISLLCLE GLQKIFSAVQ QFYQPKIQQF LRALDVTDKE GEEREDADVS VTQRTAFQIR
QFQRSLLNLL SSQEEDFNSK EALLLVTVLT SLSKLLEPSS PQFVQMLSWT SKICKENSRE
DALFCKSLMN LLFSLHVSYK SPVILLRDLS QDIHGHLGDI DQDVEVEKTN HFAIVNLRTA
APTVCLLVLS QAEKVLEEVD WLITKLKGQV SQETLSEEAS SQATLPNQPV EKAIIMQLGT
LLTFFHELVQ TALPSGSCVD TLLKDLCKMY TTLTALVRYY LQVCQSSGGI PKNMEKLVKL
SGSHLTPLCY SFISYVQNKS KSLNYTGEKK EKPAAVATAM ARVLRETKPI PNLIFAIEQY
EKFLIHLSKK SKVNLMQHMK LSTSRDFKIK GNILDMVLRE DGEDENEEGT ASEHGGQNKE
PAKKKRKK*

mutated AA sequence

MDQKILSLAA EKTADKLQEF LQTLREGDLT NLLQNQAVKG KVAGALLRAI FKGSPCSEEA
GTLRRRKIYT CCIQLVESGD LQKEIASEII GLLMLEAHHF PGPLLVELAN EFISAVREGS
LVNGKSLELL PIILTALATK KENLAYGKGV LSGEECKKQL INTLCSGRWD QQYVIQLTSM
FKDVPLTAEE VEFVVEKALS MFSKMNLQEI PPLVYQLLVL SSKGSRKSVL EGIIAFFSAL
DKQHNEEQSG DELLDVVTVP SGELRHVEGT IILHIVFAIK LDYELGRELV KHLKVGQQGD
SNNNLSPFSI ALLLSVTRIQ RFQDQVLDLL KTSVVKSFKD LQLLQGSKFL QNLVPHRSYV
STMILEVVKN SVHSWDHVTQ GLVELGFILM DSYGPKKVLD GKTIETSPSL SRMPNQHACK
LGANILLETF KIHEMIRQEI LEQVLNRVVT RASSPISHFL DLLSNIVMYA PLVLQSCSSK
VTEAFDYLSF LPLQTVQRLL KAVQPLLKVS MSMRDCLILV LRKAMFANQL DARKSAVAGF
LLLLKNFKVL GSLSSSQCSQ SLSVSQVHVD VHSHYNSVAN ETFCLEIMDS LRRCLSQQAD
VRLMLYEGFY DVLRRNSQLA NSVMQTLLSQ LKQFYEPKPD LLPPLKLEAC ILTQGDKISL
QEPLDYLLCC IQHCLAWYKN TVIPLQQGEE EEEEEEAFYE DLDDILESIT NRMIKSELED
FELDKSADFS QSTSIGIKNN ISAFLVMGVC EVLIEYNFSI SSFSKNRFED ILSLFMCYKK
LSDILNEKAG KAKTKMANKT SDSLLSMKFV SSLLTALFRV LLWRYTSIPT SVEESGKKEK
GKSISLLCLE GLQKIFSAVQ QFYQPKIQQF LRALDVTDKE GEEREDADVS VTQRTAFQIR
QFQRSLLNLL SSQEEDFNSK EALLLVTVLT SLSKLLEPSS PQFVQMLSWT SKICKENSRE
DALFCKSLMN LLFSLHVSYK SPVILLRDLS QDIHGHLGDI DQDVEVEKTN HFAIVNLRTA
APTVCLLVLS QAEKVLEEVD WLITKLKGQV SQETLSEEAS SQATLPNQPV EKAIIMQLGT
LLTFFHELVQ TALPSGSCVD TLLKDLCKMY TTLTALVRYY LQVCQSSGGI PKNMEKLVKL
SGSHLTPLCY SFISYVQNKS KSLNYTGEKK EKPAAVATAM ARVLRETKPI PNLIFAIEQY
EKFLIHLSKK SKVNLMQHMK LSTSRDFKIK GNILDMVLRE DGEDENEEGT ASEHGGQNKE
PAKKKRKK*

speed

1.37 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: 0.00323803542867315 (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)

chr15:89836228G>CN/A show variant in all transcripts IGV

HGNC symbol

FANCI

Ensembl transcript ID

ENST00000310775

Genbank transcript ID

NM_001113378

UniProt peptide

Q9NVI1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2225G>C
cDNA.2311G>C
g.49049G>C

AA changes

C742S Score: 112 explain score(s)

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

742

frameshift

known variant

Reference ID: rs2283432

database	homozygous (C/C)	heterozygous	allele carriers
1000G	230	867	1097
ExAC	8539	15689	24228

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.287	1
	3.711	1
(flanking)	0.505	1

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	49060	wt: 0.8827 / mu: 0.9222 (marginal change - not scored)	wt: ATAATATCTGTGCTTTTCTTGTGATGGGAGTTTGTGAGGTT mu: ATAATATCTCTGCTTTTCTTGTGATGGGAGTTTGTGAGGTT	cttg\|TGAT
Acc increased	49058	wt: 0.57 / mu: 0.80	wt: AAATAATATCTGTGCTTTTCTTGTGATGGGAGTTTGTGAGG mu: AAATAATATCTCTGCTTTTCTTGTGATGGGAGTTTGTGAGG	ttct\|TGTG
Acc increased	49057	wt: 0.24 / mu: 0.49	wt: AAAATAATATCTGTGCTTTTCTTGTGATGGGAGTTTGTGAG mu: AAAATAATATCTCTGCTTTTCTTGTGATGGGAGTTTGTGAG	tttc\|TTGT
Acc marginally increased	49059	wt: 0.9833 / mu: 0.9904 (marginal change - not scored)	wt: AATAATATCTGTGCTTTTCTTGTGATGGGAGTTTGTGAGGT mu: AATAATATCTCTGCTTTTCTTGTGATGGGAGTTTGTGAGGT	tctt\|GTGA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

742

mutated

not conserved

742

Ptroglodytes

all identical

ENSPTRG00000007430

742

Mmulatta

all identical

ENSMMUG00000011155

742

Fcatus

no alignment

ENSFCAG00000012886

n/a

Mmusculus

all identical

ENSMUSG00000039187

741

Ggallus

not conserved

ENSGALG00000006658

567

Trubripes

not conserved

ENSTRUG00000000347

741

Drerio

not conserved

ENSDARG00000026224

747

Dmelanogaster

all identical

FBgn0033354

734

KSKPQN

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000017742

739

protein features

start (aa)	end (aa)	feature	details
877	877	CONFLICT	I -> L (in Ref. 6; BAB47423).	might get lost (downstream of altered splice site)
952	952	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
1121	1121	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

3987 / 3987

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

1329 / 1329

position of stopcodon in wt / mu cDNA

4073 / 4073

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

87 / 87

chromosome

strand

last intron/exon boundary

4011

theoretical NMD boundary in CDS

3874

length of CDS

3987

coding sequence (CDS) position

2225

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

2311

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

49049

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

89836228

original gDNA sequence snippet

TGGCATAAAAAATAATATCTGTGCTTTTCTTGTGATGGGAG

altered gDNA sequence snippet

TGGCATAAAAAATAATATCTCTGCTTTTCTTGTGATGGGAG

original cDNA sequence snippet

TGGCATAAAAAATAATATCTGTGCTTTTCTTGTGATGGGAG

altered cDNA sequence snippet

TGGCATAAAAAATAATATCTCTGCTTTTCTTGTGATGGGAG

wildtype AA sequence

MDQKILSLAA EKTADKLQEF LQTLREGDLT NLLQNQAVKG KVAGALLRAI FKGSPCSEEA
GTLRRRKIYT CCIQLVESGD LQKEIASEII GLLMLEAHHF PGPLLVELAN EFISAVREGS
LVNGKSLELL PIILTALATK KENLAYGKGV LSGEECKKQL INTLCSGRWD QQYVIQLTSM
FKDVPLTAEE VEFVVEKALS MFSKMNLQEI PPLVYQLLVL SSKGSRKSVL EGIIAFFSAL
DKQHNEEQSG DELLDVVTVP SGELRHVEGT IILHIVFAIK LDYELGRELV KHLKVGQQGD
SNNNLSPFSI ALLLSVTRIQ RFQDQVLDLL KTSVVKSFKD LQLLQGSKFL QNLVPHRSYV
STMILEVVKN SVHSWDHVTQ GLVELGFILM DSYGPKKVLD GKTIETSPSL SRMPNQHACK
LGANILLETF KIHEMIRQEI LEQVLNRVVT RASSPISHFL DLLSNIVMYA PLVLQSCSSK
VTEAFDYLSF LPLQTVQRLL KAVQPLLKVS MSMRDCLILV LRKAMFANQL DARKSAVAGF
LLLLKNFKVL GSLSSSQCSQ SLSVSQVHVD VHSHYNSVAN ETFCLEIMDS LRRCLSQQAD
VRLMLYEGFY DVLRRNSQLA NSVMQTLLSQ LKQFYEPKPD LLPPLKLEAC ILTQGDKISL
QEPLDYLLCC IQHCLAWYKN TVIPLQQGEE EEEEEEAFYE DLDDILESIT NRMIKSELED
FELDKSADFS QSTSIGIKNN ICAFLVMGVC EVLIEYNFSI SSFSKNRFED ILSLFMCYKK
LSDILNEKAG KAKTKMANKT SDSLLSMKFV SSLLTALFRD SIQSHQESLS VLRSSNEFMR
YAVNVALQKV QQLKETGHVS GPDGQNPEKI FQNLCDITRV LLWRYTSIPT SVEESGKKEK
GKSISLLCLE GLQKIFSAVQ QFYQPKIQQF LRALDVTDKE GEEREDADVS VTQRTAFQIR
QFQRSLLNLL SSQEEDFNSK EALLLVTVLT SLSKLLEPSS PQFVQMLSWT SKICKENSRE
DALFCKSLMN LLFSLHVSYK SPVILLRDLS QDIHGHLGDI DQDVEVEKTN HFAIVNLRTA
APTVCLLVLS QAEKVLEEVD WLITKLKGQV SQETLSEEAS SQATLPNQPV EKAIIMQLGT
LLTFFHELVQ TALPSGSCVD TLLKDLCKMY TTLTALVRYY LQVCQSSGGI PKNMEKLVKL
SGSHLTPLCY SFISYVQNKS KSLNYTGEKK EKPAAVATAM ARVLRETKPI PNLIFAIEQY
EKFLIHLSKK SKVNLMQHMK LSTSRDFKIK GNILDMVLRE DGEDENEEGT ASEHGGQNKE
PAKKKRKK*

mutated AA sequence

MDQKILSLAA EKTADKLQEF LQTLREGDLT NLLQNQAVKG KVAGALLRAI FKGSPCSEEA
GTLRRRKIYT CCIQLVESGD LQKEIASEII GLLMLEAHHF PGPLLVELAN EFISAVREGS
LVNGKSLELL PIILTALATK KENLAYGKGV LSGEECKKQL INTLCSGRWD QQYVIQLTSM
FKDVPLTAEE VEFVVEKALS MFSKMNLQEI PPLVYQLLVL SSKGSRKSVL EGIIAFFSAL
DKQHNEEQSG DELLDVVTVP SGELRHVEGT IILHIVFAIK LDYELGRELV KHLKVGQQGD
SNNNLSPFSI ALLLSVTRIQ RFQDQVLDLL KTSVVKSFKD LQLLQGSKFL QNLVPHRSYV
STMILEVVKN SVHSWDHVTQ GLVELGFILM DSYGPKKVLD GKTIETSPSL SRMPNQHACK
LGANILLETF KIHEMIRQEI LEQVLNRVVT RASSPISHFL DLLSNIVMYA PLVLQSCSSK
VTEAFDYLSF LPLQTVQRLL KAVQPLLKVS MSMRDCLILV LRKAMFANQL DARKSAVAGF
LLLLKNFKVL GSLSSSQCSQ SLSVSQVHVD VHSHYNSVAN ETFCLEIMDS LRRCLSQQAD
VRLMLYEGFY DVLRRNSQLA NSVMQTLLSQ LKQFYEPKPD LLPPLKLEAC ILTQGDKISL
QEPLDYLLCC IQHCLAWYKN TVIPLQQGEE EEEEEEAFYE DLDDILESIT NRMIKSELED
FELDKSADFS QSTSIGIKNN ISAFLVMGVC EVLIEYNFSI SSFSKNRFED ILSLFMCYKK
LSDILNEKAG KAKTKMANKT SDSLLSMKFV SSLLTALFRD SIQSHQESLS VLRSSNEFMR
YAVNVALQKV QQLKETGHVS GPDGQNPEKI FQNLCDITRV LLWRYTSIPT SVEESGKKEK
GKSISLLCLE GLQKIFSAVQ QFYQPKIQQF LRALDVTDKE GEEREDADVS VTQRTAFQIR
QFQRSLLNLL SSQEEDFNSK EALLLVTVLT SLSKLLEPSS PQFVQMLSWT SKICKENSRE
DALFCKSLMN LLFSLHVSYK SPVILLRDLS QDIHGHLGDI DQDVEVEKTN HFAIVNLRTA
APTVCLLVLS QAEKVLEEVD WLITKLKGQV SQETLSEEAS SQATLPNQPV EKAIIMQLGT
LLTFFHELVQ TALPSGSCVD TLLKDLCKMY TTLTALVRYY LQVCQSSGGI PKNMEKLVKL
SGSHLTPLCY SFISYVQNKS KSLNYTGEKK EKPAAVATAM ARVLRETKPI PNLIFAIEQY
EKFLIHLSKK SKVNLMQHMK LSTSRDFKIK GNILDMVLRE DGEDENEEGT ASEHGGQNKE
PAKKKRKK*

speed

1.37 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems