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 10 transcript(s)...
Querying Taster for transcript #1: ENST00000378043
Querying Taster for transcript #2: ENST00000534553
Querying Taster for transcript #3: ENST00000449131
Querying Taster for transcript #4: ENST00000526988
Querying Taster for transcript #5: ENST00000435278
Querying Taster for transcript #6: ENST00000378042
Querying Taster for transcript #7: ENST00000301774
Querying Taster for transcript #8: ENST00000529191
Querying Taster for transcript #9: ENST00000529631
Querying Taster for transcript #10: ENST00000530019
MT speed 0 s - this script 5.791844 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FTH1	disease_causing_automatic	0.996663284651111	simple_aae			0	P43S	single base exchange	rs121918287		show file
BEST1	disease_causing_automatic	0.999999999404928	simple_aae		affected	0	V230M	single base exchange	rs121918287		show file
BEST1	disease_causing_automatic	0.999999999966326	simple_aae		affected	0	V317M	single base exchange	rs121918287		show file
BEST1	disease_causing_automatic	0.999999999966326	simple_aae		affected	0	V257M	single base exchange	rs121918287		show file
BEST1	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs121918287		show file
FTH1	disease_causing_automatic	1	without_aae			0		single base exchange	rs121918287		show file
BEST1	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs121918287		show file
BEST1	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs121918287		show file
BEST1	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs121918287		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.996663284651111 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM080107)
known disease mutation: rs2742 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:61727364G>AN/A show variant in all transcripts IGV

HGNC symbol

FTH1

Ensembl transcript ID

ENST00000529631

Genbank transcript ID

N/A

UniProt peptide

P02794

alteration type

single base exchange

alteration region

CDS

DNA changes

c.127C>T
cDNA.333C>T
g.7769C>T

AA changes

P43S Score: 74 explain score(s)

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

frameshift

known variant

Reference ID: rs121918287
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2742 (pathogenic for Bestrophinopathy, autosomal recessive) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM080107)

known disease mutation at this position, please check HGMD for details (HGMD ID CM080107)
known disease mutation at this position, please check HGMD for details (HGMD ID CM080107)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.712	1
	5.712	1
(flanking)	4.717	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
Donor marginally increased	7762	wt: 0.9544 / mu: 0.9772 (marginal change - not scored)	wt: CCAACAGGGACACCT mu: CCAACAGGGACATCT	AACA\|ggga
Donor marginally increased	7772	wt: 0.3808 / mu: 0.4015 (marginal change - not scored)	wt: CACCTGGTCACCAGG mu: CATCTGGTCACCAGG	CCTG\|gtca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

no alignment

ENSFCAG00000007382

n/a

Mmusculus

no alignment

ENSMUSG00000024661

n/a

Ggallus

no alignment

ENSGALG00000007220

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000015551

n/a

Dmelanogaster

no homologue

Celegans

no alignment

D1037.3

n/a

Xtropicalis

no alignment

ENSXETG00000006737

n/a

protein features

start (aa)	end (aa)	feature	details
11	160	DOMAIN	Ferritin-like diiron.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

246 / 246

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

82 / 82

position of stopcodon in wt / mu cDNA

452 / 452

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

207 / 207

chromosome

strand

-1

last intron/exon boundary

321

theoretical NMD boundary in CDS

length of CDS

246

coding sequence (CDS) position

127

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

333

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

7769

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

61727364

original gDNA sequence snippet

ATCCACAGCCAACAGGGACACCTGGTCACCAGGGACAGAAG

altered gDNA sequence snippet

ATCCACAGCCAACAGGGACATCTGGTCACCAGGGACAGAAG

original cDNA sequence snippet

TGTCCATGCCAACAGGGACACCTGGTCACCAGGGACAGAAG

altered cDNA sequence snippet

TGTCCATGCCAACAGGGACATCTGGTCACCAGGGACAGAAG

wildtype AA sequence

MTTASTSQVR QNYHQDSEAA INRQINLELY ASYVYLSMPT GTPGHQGQKK SHRKIIPGRT
LYVPDDLEES LPLSGPQFPC L*

mutated AA sequence

MTTASTSQVR QNYHQDSEAA INRQINLELY ASYVYLSMPT GTSGHQGQKK SHRKIIPGRT
LYVPDDLEES LPLSGPQFPC L*

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

disease causing

Model: simple_aae, prob: 0.999999999404928 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM080107)
known disease mutation: rs2742 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:61727364G>AN/A show variant in all transcripts IGV

HGNC symbol

BEST1

Ensembl transcript ID

ENST00000378042

Genbank transcript ID

N/A

UniProt peptide

O76090

alteration type

single base exchange

alteration region

CDS

DNA changes

c.688G>A
cDNA.1448G>A
g.10072G>A

AA changes

V230M Score: 21 explain score(s)

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

230

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.712	1
	5.712	1
(flanking)	4.717	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	10071	sequence motif lost	-	wt: ccag\|GTGT mu: ccag.ATGT
Acc marginally increased	10083	wt: 0.5601 / mu: 0.5851 (marginal change - not scored)	wt: GGTGACCAGGTGTCCCTGTTGGCTGTGGATGAGATGCACCA mu: GGTGACCAGATGTCCCTGTTGGCTGTGGATGAGATGCACCA	gttg\|GCTG
Acc marginally increased	10062	wt: 0.9015 / mu: 0.9032 (marginal change - not scored)	wt: TGTGGGACTTCTTCTGTCCCTGGTGACCAGGTGTCCCTGTT mu: TGTGGGACTTCTTCTGTCCCTGGTGACCAGATGTCCCTGTT	ccct\|GGTG
Donor gained	10068	0.89	mu: GGTGACCAGATGTCC	TGAC\|caga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

230

mutated

all conserved

230

Ptroglodytes

not conserved

ENSPTRG00000003756

290

VAEQLINPFGE

Mmulatta

not conserved

ENSMMUG00000015147

290

VAEQLINPFGE

Fcatus

all identical

ENSFCAG00000007380

331

DDDDFETNWIVDRSLQ

Mmusculus

all identical

ENSMUSG00000037418

301

DDDDFETNWIIDRNLQ

Ggallus

all identical

ENSGALG00000007217

301

DDDDFETNWLIDRNLQ

Trubripes

no homologue

Drerio

all identical

ENSDARG00000078331

301

DDDDFETNWLVDRNLQ

Dmelanogaster

all identical

FBgn0040238

303

NPFGEDDDDFEVNWMVDRNLQ

Celegans

all identical

C01B12.3

290

AEVLLNPL

Xtropicalis

all identical

ENSXETG00000006740

302

DDDFETNWLIDRNLQ

protein features

start (aa)	end (aa)	feature	details
229	249	INTRAMEM	Potential.	lost
250	270	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
271	291	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
292	585	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1497 / 1497

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

499 / 499

position of stopcodon in wt / mu cDNA

2257 / 2257

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

761 / 761

chromosome

strand

last intron/exon boundary

2239

theoretical NMD boundary in CDS

1428

length of CDS

1497

coding sequence (CDS) position

688

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

1448

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

10072

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

61727364

original gDNA sequence snippet

CTTCTGTCCCTGGTGACCAGGTGTCCCTGTTGGCTGTGGAT

altered gDNA sequence snippet

CTTCTGTCCCTGGTGACCAGATGTCCCTGTTGGCTGTGGAT

original cDNA sequence snippet

TCTATGTTGGCTGGCTGAAGGTGTCCCTGTTGGCTGTGGAT

altered cDNA sequence snippet

TCTATGTTGGCTGGCTGAAGATGTCCCTGTTGGCTGTGGAT

wildtype AA sequence

MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYTQVV
TVAVYSFFLT CLVGRQFLNP AKAYPGHELD LVVPVFTFLQ FFFYVGWLKV SLLAVDEMHQ
DLPRMEPDMY WNKPEPQPPY TAASAQFRRA SFMGSTFNIS LNKEEMEFQP NQEDEEDAHA
GIIGRFLGLQ SHDHHPPRAN SRTKLLWPKR ESLLHEGLPK NHKAAKQNVR GQEDNKAWKL
KAVDAFKSAP LYQRPGYYSA PQTPLSPTPM FFPLEPSAPS KLHSVTGIDT KDKSLKTVSS
GAKKSFELLS ESDGALMEHP EVSQVRRKTV EFNLTDMPEI PENHLKEPLE QSPTNIHTTL
KDHMDPYWAL ENRDEAHS*

mutated AA sequence

MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYTQVV
TVAVYSFFLT CLVGRQFLNP AKAYPGHELD LVVPVFTFLQ FFFYVGWLKM SLLAVDEMHQ
DLPRMEPDMY WNKPEPQPPY TAASAQFRRA SFMGSTFNIS LNKEEMEFQP NQEDEEDAHA
GIIGRFLGLQ SHDHHPPRAN SRTKLLWPKR ESLLHEGLPK NHKAAKQNVR GQEDNKAWKL
KAVDAFKSAP LYQRPGYYSA PQTPLSPTPM FFPLEPSAPS KLHSVTGIDT KDKSLKTVSS
GAKKSFELLS ESDGALMEHP EVSQVRRKTV EFNLTDMPEI PENHLKEPLE QSPTNIHTTL
KDHMDPYWAL ENRDEAHS*

speed

0.77 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999966326 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM080107)
known disease mutation: rs2742 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:61727364G>AN/A show variant in all transcripts IGV

HGNC symbol

BEST1

Ensembl transcript ID

ENST00000378043

Genbank transcript ID

NM_004183

UniProt peptide

O76090

alteration type

single base exchange

alteration region

CDS

DNA changes

c.949G>A
cDNA.1592G>A
g.10072G>A

AA changes

V317M Score: 21 explain score(s)

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

317

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.712	1
	5.712	1
(flanking)	4.717	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	10071	sequence motif lost	-	wt: ccag\|GTGT mu: ccag.ATGT
Acc marginally increased	10083	wt: 0.5601 / mu: 0.5851 (marginal change - not scored)	wt: GGTGACCAGGTGTCCCTGTTGGCTGTGGATGAGATGCACCA mu: GGTGACCAGATGTCCCTGTTGGCTGTGGATGAGATGCACCA	gttg\|GCTG
Acc marginally increased	10062	wt: 0.9015 / mu: 0.9032 (marginal change - not scored)	wt: TGTGGGACTTCTTCTGTCCCTGGTGACCAGGTGTCCCTGTT mu: TGTGGGACTTCTTCTGTCCCTGGTGACCAGATGTCCCTGTT	ccct\|GGTG
Donor gained	10068	0.89	mu: GGTGACCAGATGTCC	TGAC\|caga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

317

mutated

all conserved

317

Ptroglodytes

all identical

ENSPTRG00000003756

317

Mmulatta

all identical

ENSMMUG00000015147

317

Fcatus

all identical

ENSFCAG00000007380

347

Mmusculus

all identical

ENSMUSG00000037418

317

Ggallus

all identical

ENSGALG00000007217

317

Trubripes

no homologue

Drerio

all identical

ENSDARG00000078331

317

Dmelanogaster

all identical

FBgn0040238

324

Celegans

all identical

C01B12.3

320

Xtropicalis

all identical

ENSXETG00000006740

317

protein features

start (aa)	end (aa)	feature	details
292	585	TOPO_DOM	Cytoplasmic (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1758 / 1758

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

586 / 586

position of stopcodon in wt / mu cDNA

2401 / 2401

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

644 / 644

chromosome

strand

last intron/exon boundary

2383

theoretical NMD boundary in CDS

1689

length of CDS

1758

coding sequence (CDS) position

949

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

1592

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

10072

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

61727364

original gDNA sequence snippet

CTTCTGTCCCTGGTGACCAGGTGTCCCTGTTGGCTGTGGAT

altered gDNA sequence snippet

CTTCTGTCCCTGGTGACCAGATGTCCCTGTTGGCTGTGGAT

original cDNA sequence snippet

TTGTCGACAGGAATTTGCAGGTGTCCCTGTTGGCTGTGGAT

altered cDNA sequence snippet

TTGTCGACAGGAATTTGCAGATGTCCCTGTTGGCTGTGGAT

wildtype AA sequence

MTITYTSQVA NARLGSFSRL LLCWRGSIYK LLYGEFLIFL LCYYIIRFIY RLALTEEQQL
MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYTQVV
TVAVYSFFLT CLVGRQFLNP AKAYPGHELD LVVPVFTFLQ FFFYVGWLKV AEQLINPFGE
DDDDFETNWI VDRNLQVSLL AVDEMHQDLP RMEPDMYWNK PEPQPPYTAA SAQFRRASFM
GSTFNISLNK EEMEFQPNQE DEEDAHAGII GRFLGLQSHD HHPPRANSRT KLLWPKRESL
LHEGLPKNHK AAKQNVRGQE DNKAWKLKAV DAFKSAPLYQ RPGYYSAPQT PLSPTPMFFP
LEPSAPSKLH SVTGIDTKDK SLKTVSSGAK KSFELLSESD GALMEHPEVS QVRRKTVEFN
LTDMPEIPEN HLKEPLEQSP TNIHTTLKDH MDPYWALENR DEAHS*

mutated AA sequence

MTITYTSQVA NARLGSFSRL LLCWRGSIYK LLYGEFLIFL LCYYIIRFIY RLALTEEQQL
MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYTQVV
TVAVYSFFLT CLVGRQFLNP AKAYPGHELD LVVPVFTFLQ FFFYVGWLKV AEQLINPFGE
DDDDFETNWI VDRNLQMSLL AVDEMHQDLP RMEPDMYWNK PEPQPPYTAA SAQFRRASFM
GSTFNISLNK EEMEFQPNQE DEEDAHAGII GRFLGLQSHD HHPPRANSRT KLLWPKRESL
LHEGLPKNHK AAKQNVRGQE DNKAWKLKAV DAFKSAPLYQ RPGYYSAPQT PLSPTPMFFP
LEPSAPSKLH SVTGIDTKDK SLKTVSSGAK KSFELLSESD GALMEHPEVS QVRRKTVEFN
LTDMPEIPEN HLKEPLEQSP TNIHTTLKDH MDPYWALENR DEAHS*

speed

0.80 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999966326 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM080107)
known disease mutation: rs2742 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:61727364G>AN/A show variant in all transcripts IGV

HGNC symbol

BEST1

Ensembl transcript ID

ENST00000449131

Genbank transcript ID

NM_001139443

UniProt peptide

O76090

alteration type

single base exchange

alteration region

CDS

DNA changes

c.769G>A
cDNA.855G>A
g.10072G>A

AA changes

V257M Score: 21 explain score(s)

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

257

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.712	1
	5.712	1
(flanking)	4.717	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	10071	sequence motif lost	-	wt: ccag\|GTGT mu: ccag.ATGT
Acc marginally increased	10083	wt: 0.5601 / mu: 0.5851 (marginal change - not scored)	wt: GGTGACCAGGTGTCCCTGTTGGCTGTGGATGAGATGCACCA mu: GGTGACCAGATGTCCCTGTTGGCTGTGGATGAGATGCACCA	gttg\|GCTG
Acc marginally increased	10062	wt: 0.9015 / mu: 0.9032 (marginal change - not scored)	wt: TGTGGGACTTCTTCTGTCCCTGGTGACCAGGTGTCCCTGTT mu: TGTGGGACTTCTTCTGTCCCTGGTGACCAGATGTCCCTGTT	ccct\|GGTG
Donor gained	10068	0.89	mu: GGTGACCAGATGTCC	TGAC\|caga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

257

mutated

all conserved

257

Ptroglodytes

all identical

ENSPTRG00000003756

317

Mmulatta

all identical

ENSMMUG00000015147

317

Fcatus

all identical

ENSFCAG00000007380

347

Mmusculus

all identical

ENSMUSG00000037418

317

Ggallus

all identical

ENSGALG00000007217

317

Trubripes

no homologue

Drerio

all identical

ENSDARG00000078331

317

Dmelanogaster

all identical

FBgn0040238

324

Celegans

all identical

C01B12.3

320

Xtropicalis

all identical

ENSXETG00000006740

317

protein features

start (aa)	end (aa)	feature	details
250	270	TOPO_DOM	Extracellular (Potential).	lost
271	291	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
292	585	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1815 / 1815

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

605 / 605

position of stopcodon in wt / mu cDNA

1901 / 1901

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

1007

theoretical NMD boundary in CDS

870

length of CDS

1815

coding sequence (CDS) position

769

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

855

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

10072

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

61727364

original gDNA sequence snippet

CTTCTGTCCCTGGTGACCAGGTGTCCCTGTTGGCTGTGGAT

altered gDNA sequence snippet

CTTCTGTCCCTGGTGACCAGATGTCCCTGTTGGCTGTGGAT

original cDNA sequence snippet

TTGTCGACAGGAATTTGCAGGTGTCCCTGTTGGCTGTGGAT

altered cDNA sequence snippet

TTGTCGACAGGAATTTGCAGATGTCCCTGTTGGCTGTGGAT

wildtype AA sequence

MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYTQVV
TVAVYSFFLT CLVGRQFLNP AKAYPGHELD LVVPVFTFLQ FFFYVGWLKV AEQLINPFGE
DDDDFETNWI VDRNLQVSLL AVDEMHQDLP RMEPDMYWNK PEPQPPYTAA SAQFRRASFM
GSTFNISLNK EEMEFQPNQE DEEDAHAGII GRFLGLQSHD HHPPRANSRT KLLWPKRESL
LHEGLPKNHK AAKQNVRGQE DNKAWKLKAV DAFKSAPLYQ RPGYYSAPQT PLSPTPMFFP
LEPSAPSKLH SVTGIDTKDK SLKTVSSGAK KSFELLSESD GALMEHPEVS QVRRKTVEFN
LTDMPEIPEN HLKEPLEQSP TNIHTTLKDH MDPYWALENR SVLHLNQGHC IALCPTPASL
ALSLPFLHNF LGFHHCQSTL DLRPALAWGI YLATFTGILG KCSGPFLTSP WYHPEDFLGP
GEGR*

mutated AA sequence

MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYTQVV
TVAVYSFFLT CLVGRQFLNP AKAYPGHELD LVVPVFTFLQ FFFYVGWLKV AEQLINPFGE
DDDDFETNWI VDRNLQMSLL AVDEMHQDLP RMEPDMYWNK PEPQPPYTAA SAQFRRASFM
GSTFNISLNK EEMEFQPNQE DEEDAHAGII GRFLGLQSHD HHPPRANSRT KLLWPKRESL
LHEGLPKNHK AAKQNVRGQE DNKAWKLKAV DAFKSAPLYQ RPGYYSAPQT PLSPTPMFFP
LEPSAPSKLH SVTGIDTKDK SLKTVSSGAK KSFELLSESD GALMEHPEVS QVRRKTVEFN
LTDMPEIPEN HLKEPLEQSP TNIHTTLKDH MDPYWALENR SVLHLNQGHC IALCPTPASL
ALSLPFLHNF LGFHHCQSTL DLRPALAWGI YLATFTGILG KCSGPFLTSP WYHPEDFLGP
GEGR*

speed

0.77 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM080107)
known disease mutation: rs2742 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:61727364G>AN/A show variant in all transcripts IGV

HGNC symbol

BEST1

Ensembl transcript ID

ENST00000534553

Genbank transcript ID

N/A

UniProt peptide

O76090

alteration type

single base exchange

alteration region

intron

DNA changes

g.10072G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.712	1
	5.712	1
(flanking)	4.717	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	10083	wt: 0.5601 / mu: 0.5851 (marginal change - not scored)	wt: GGTGACCAGGTGTCCCTGTTGGCTGTGGATGAGATGCACCA mu: GGTGACCAGATGTCCCTGTTGGCTGTGGATGAGATGCACCA	gttg\|GCTG
Acc marginally increased	10062	wt: 0.9015 / mu: 0.9032 (marginal change - not scored)	wt: TGTGGGACTTCTTCTGTCCCTGGTGACCAGGTGTCCCTGTT mu: TGTGGGACTTCTTCTGTCCCTGGTGACCAGATGTCCCTGTT	ccct\|GGTG
Donor gained	10068	0.89	mu: GGTGACCAGATGTCC	TGAC\|caga

distance from splice site

2363

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
47	70	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
71	91	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
92	178	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
179	199	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
200	228	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
229	249	INTRAMEM	Potential.	might get lost (downstream of altered splice site)
250	270	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
271	291	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
292	585	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

577 / 577

chromosome

strand

last intron/exon boundary

740

theoretical NMD boundary in CDS

113

length of CDS

168

coding sequence (CDS) position

N/A

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

N/A

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

10072

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

61727364

original gDNA sequence snippet

CTTCTGTCCCTGGTGACCAGGTGTCCCTGTTGGCTGTGGAT

altered gDNA sequence snippet

CTTCTGTCCCTGGTGACCAGATGTCCCTGTTGGCTGTGGAT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MSLVSGFVEG KDEQGRLLRR TLIRYANLGN VLILRSVSTA VYKRFPSAQH LVQAA*

mutated AA sequence

N/A

speed

0.62 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM080107)
known disease mutation: rs2742 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:61727364G>AN/A show variant in all transcripts IGV

HGNC symbol

FTH1

Ensembl transcript ID

ENST00000529191

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

CDS

DNA changes

c.150C>T
cDNA.356C>T
g.7769C>T

AA changes

no AA changes

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

N/A

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.712	1
	5.712	1
(flanking)	4.717	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
Donor marginally increased	7762	wt: 0.9544 / mu: 0.9772 (marginal change - not scored)	wt: CCAACAGGGACACCT mu: CCAACAGGGACATCT	AACA\|ggga
Donor marginally increased	7772	wt: 0.3808 / mu: 0.4015 (marginal change - not scored)	wt: CACCTGGTCACCAGG mu: CATCTGGTCACCAGG	CCTG\|gtca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

normal

AA sequence altered

position of stopcodon in wt / mu CDS

309 / 309

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

103 / 103

position of stopcodon in wt / mu cDNA

515 / 515

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

207 / 207

chromosome

strand

-1

last intron/exon boundary

321

theoretical NMD boundary in CDS

length of CDS

309

coding sequence (CDS) position

150

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

356

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

7769

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

61727364

original gDNA sequence snippet

ATCCACAGCCAACAGGGACACCTGGTCACCAGGGACAGAAG

altered gDNA sequence snippet

ATCCACAGCCAACAGGGACATCTGGTCACCAGGGACAGAAG

original cDNA sequence snippet

ATCCACAGCCAACAGGGACACCTGGTCACCAGGGACAGAAG

altered cDNA sequence snippet

ATCCACAGCCAACAGGGACATCTGGTCACCAGGGACAGAAG

wildtype AA sequence

MTTASTSQVR QNYHQDSEAA INRQINLELY ASYVYLSMVL VHLIHSQQGH LVTRDRRSPT
ERSSQAGPCM CLMTWRNLSL SLDLSFPACE MGRWVPACSL KD*

mutated AA sequence

MTTASTSQVR QNYHQDSEAA INRQINLELY ASYVYLSMVL VHLIHSQQGH LVTRDRRSPT
ERSSQAGPCM CLMTWRNLSL SLDLSFPACE MGRWVPACSL KD*

speed

0.70 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM080107)
known disease mutation: rs2742 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:61727364G>AN/A show variant in all transcripts IGV

HGNC symbol

BEST1

Ensembl transcript ID

ENST00000526988

Genbank transcript ID

N/A

UniProt peptide

O76090

alteration type

single base exchange

alteration region

CDS

DNA changes

c.834G>A
cDNA.995G>A
g.10072G>A

AA changes

no AA changes

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

N/A

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.712	1
	5.712	1
(flanking)	4.717	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	10071	sequence motif lost	-	wt: ccag\|GTGT mu: ccag.ATGT
Acc marginally increased	10083	wt: 0.5601 / mu: 0.5851 (marginal change - not scored)	wt: GGTGACCAGGTGTCCCTGTTGGCTGTGGATGAGATGCACCA mu: GGTGACCAGATGTCCCTGTTGGCTGTGGATGAGATGCACCA	gttg\|GCTG
Acc marginally increased	10062	wt: 0.9015 / mu: 0.9032 (marginal change - not scored)	wt: TGTGGGACTTCTTCTGTCCCTGGTGACCAGGTGTCCCTGTT mu: TGTGGGACTTCTTCTGTCCCTGGTGACCAGATGTCCCTGTT	ccct\|GGTG
Donor gained	10068	0.89	mu: GGTGACCAGATGTCC	TGAC\|caga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
271	291	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
292	585	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

position of stopcodon in wt / mu CDS

990 / 990

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

330 / 330

position of stopcodon in wt / mu cDNA

1151 / 1151

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

162 / 162

chromosome

strand

last intron/exon boundary

1147

theoretical NMD boundary in CDS

935

length of CDS

990

coding sequence (CDS) position

834

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

995

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

10072

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

61727364

original gDNA sequence snippet

CTTCTGTCCCTGGTGACCAGGTGTCCCTGTTGGCTGTGGAT

altered gDNA sequence snippet

CTTCTGTCCCTGGTGACCAGATGTCCCTGTTGGCTGTGGAT

original cDNA sequence snippet

TTGTCGACAGGAATTTGCAGGTGTCCCTGTTGGCTGTGGAT

altered cDNA sequence snippet

TTGTCGACAGGAATTTGCAGATGTCCCTGTTGGCTGTGGAT

wildtype AA sequence

MSLVSGFVEG KDEQGRLLRR TLIRYANLGN VLILRSVSTA VYKRFPSAQH LVQAGFMTPA
EHKQLEKLSL PHNMFWVPWV WFANLSMKAW LGGRIRDPIL LQSLLNEMNT LRTQCGHLYA
YDWISIPLVY TQVVTVAVYS FFLTCLVGRQ FLNPAKAYPG HELDLVVPVF TFLQFFFYVG
WLKVGLSRAL LGWRHGQRGH GQQLPETRMQ CQERKVSRVE SSQAWWRTPV IPATREAEAG
ESLEPGRRRL WWQSSSSTPL ERMMMILRPT GLSTGICRCP CWLWMRCTRT CLGWSRTCTG
ISPSHSPPTQ LLPPSSVEPP LWAPPSTSA*

mutated AA sequence

speed

0.73 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM080107)
known disease mutation: rs2742 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:61727364G>AN/A show variant in all transcripts IGV

HGNC symbol

BEST1

Ensembl transcript ID

ENST00000435278

Genbank transcript ID

N/A

UniProt peptide

O76090

alteration type

single base exchange

alteration region

intron

DNA changes

g.10072G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.712	1
	5.712	1
(flanking)	4.717	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	10083	wt: 0.5601 / mu: 0.5851 (marginal change - not scored)	wt: GGTGACCAGGTGTCCCTGTTGGCTGTGGATGAGATGCACCA mu: GGTGACCAGATGTCCCTGTTGGCTGTGGATGAGATGCACCA	gttg\|GCTG
Acc marginally increased	10062	wt: 0.9015 / mu: 0.9032 (marginal change - not scored)	wt: TGTGGGACTTCTTCTGTCCCTGGTGACCAGGTGTCCCTGTT mu: TGTGGGACTTCTTCTGTCCCTGGTGACCAGATGTCCCTGTT	ccct\|GGTG
Donor gained	10068	0.89	mu: GGTGACCAGATGTCC	TGAC\|caga

distance from splice site

2363

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
229	249	INTRAMEM	Potential.	might get lost (downstream of altered splice site)
250	270	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
271	291	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
292	585	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

114 / 114

chromosome

strand

last intron/exon boundary

828

theoretical NMD boundary in CDS

664

length of CDS

813

coding sequence (CDS) position

N/A

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

N/A

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

10072

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

61727364

original gDNA sequence snippet

CTTCTGTCCCTGGTGACCAGGTGTCCCTGTTGGCTGTGGAT

altered gDNA sequence snippet

CTTCTGTCCCTGGTGACCAGATGTCCCTGTTGGCTGTGGAT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

mutated AA sequence

N/A

speed

0.73 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM080107)
known disease mutation: rs2742 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:61727364G>AN/A show variant in all transcripts IGV

HGNC symbol

BEST1

Ensembl transcript ID

ENST00000301774

Genbank transcript ID

N/A

UniProt peptide

O76090

alteration type

single base exchange

alteration region

intron

DNA changes

g.10072G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.712	1
	5.712	1
(flanking)	4.717	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

splice site change before start ATG (at aa -4) |

effect	gDNA position	score	detection sequence	exon-intron border
Acc marginally increased	10083	wt: 0.5601 / mu: 0.5851 (marginal change - not scored)	wt: GGTGACCAGGTGTCCCTGTTGGCTGTGGATGAGATGCACCA mu: GGTGACCAGATGTCCCTGTTGGCTGTGGATGAGATGCACCA	gttg\|GCTG
Acc marginally increased	10062	wt: 0.9015 / mu: 0.9032 (marginal change - not scored)	wt: TGTGGGACTTCTTCTGTCCCTGGTGACCAGGTGTCCCTGTT mu: TGTGGGACTTCTTCTGTCCCTGGTGACCAGATGTCCCTGTT	ccct\|GGTG
Donor gained	10068	0.89	mu: GGTGACCAGATGTCC	TGAC\|caga

distance from splice site

2363

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	25	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
26	46	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
47	70	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
71	91	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
92	178	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
179	199	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
200	228	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
229	249	INTRAMEM	Potential.	might get lost (downstream of altered splice site)
250	270	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
271	291	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
292	585	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

756 / 756

chromosome

strand

last intron/exon boundary

740

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

879

coding sequence (CDS) position

N/A

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

N/A

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

10072

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

61727364

original gDNA sequence snippet

CTTCTGTCCCTGGTGACCAGGTGTCCCTGTTGGCTGTGGAT

altered gDNA sequence snippet

CTTCTGTCCCTGGTGACCAGATGTCCCTGTTGGCTGTGGAT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MEFQPNQEDE EDAHAGIIGR FLGLQSHDHH PPRANSRTKL LWPKRESLLH EGLPKNHKAA
KQNVRGQEDN KAWKLKAVDA FKSAPLYQRP GYYSAPQTPL SPTPMFFPLE PSAPSKLHSV
TGIDTKDKSL KTVSSGAKKS FELLSESDGA LMEHPEVSQV RRKTVEFNLT DMPEIPENHL
KEPLEQSPTN IHTTLKDHMD PYWALENRSV LHLNQGHCIA LCPTPASLAL SLPFLHNFLG
FHHCQSTLDL RPALAWGIYL ATFTGILGKC SGPFLTSPWY HPEDFLGPGE GR*

mutated AA sequence

N/A

speed

0.76 s

Problems

annotation problem

The chosen transcript ENST00000530019 on chromosome 11 has no correct in-frame stop codon (TGA, TAA or TAG) annotated
This is likely to cause a false prediction. You should choose another transcript.

back to results table