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: ENST00000409900
Querying Taster for transcript #2: ENST00000409156
MT speed 0 s - this script 3.492334 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CHN1	disease_causing_automatic	0.999997563491666	simple_aae		affected	0	L20F	single base exchange	rs121912792		show file
CHN1	disease_causing_automatic	0.999997563491666	simple_aae		affected	0	L20F	single base exchange	rs121912792		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999997563491666 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM082550)
known disease mutation: rs17550 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:175809670T>AN/A show variant in all transcripts IGV

HGNC symbol

CHN1

Ensembl transcript ID

ENST00000409900

Genbank transcript ID

NM_001822

UniProt peptide

P15882

alteration type

single base exchange

alteration region

CDS

DNA changes

c.60A>T
cDNA.374A>T
g.60428A>T

AA changes

L20F Score: 22 explain score(s)

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

frameshift

known variant

Reference ID: rs121912792
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs17550 (pathogenic for Duane retraction syndrome 2) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM082550)

known disease mutation at this position, please check HGMD for details (HGMD ID CM082550)
known disease mutation at this position, please check HGMD for details (HGMD ID CM082550)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.488	0.984
	-1.001	0.863
(flanking)	2.804	0.987

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	60426.5	sequence motif lost	-	wt: caca\|GTAT mu: caca.GTTT
Acc marginally increased	60421	wt: 0.8914 / mu: 0.9022 (marginal change - not scored)	wt: CACTTTTTGTTTCTACCTTCTCACAGTATATCAGCTACAAC mu: CACTTTTTGTTTCTACCTTCTCACAGTTTATCAGCTACAAC	ttct\|CACA
Acc marginally increased	60424	wt: 0.9611 / mu: 0.9614 (marginal change - not scored)	wt: TTTTTGTTTCTACCTTCTCACAGTATATCAGCTACAACAGG mu: TTTTTGTTTCTACCTTCTCACAGTTTATCAGCTACAACAGG	tcac\|AGTA
Acc marginally increased	60426	wt: 0.9409 / mu: 0.9742 (marginal change - not scored)	wt: TTTGTTTCTACCTTCTCACAGTATATCAGCTACAACAGGAA mu: TTTGTTTCTACCTTCTCACAGTTTATCAGCTACAACAGGAA	acag\|TATA
Acc marginally increased	60420	wt: 0.7628 / mu: 0.7710 (marginal change - not scored)	wt: ACACTTTTTGTTTCTACCTTCTCACAGTATATCAGCTACAA mu: ACACTTTTTGTTTCTACCTTCTCACAGTTTATCAGCTACAA	cttc\|TCAC
Acc increased	60433	wt: 0.60 / mu: 0.97	wt: CTACCTTCTCACAGTATATCAGCTACAACAGGAAGCCCCTC mu: CTACCTTCTCACAGTTTATCAGCTACAACAGGAAGCCCCTC	atca\|GCTA

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

all identical

ENSPTRG00000012659

Mmulatta

all identical

ENSMMUG00000021797

Fcatus

no alignment

ENSFCAG00000014105

n/a

Mmusculus

all identical

ENSMUSG00000056486

Ggallus

all identical

ENSGALG00000009293

Trubripes

all identical

ENSTRUG00000012830

Drerio

no alignment

ENSDARG00000032493

n/a

Dmelanogaster

all identical

FBgn0029778

Celegans

all identical

BE0003N10.2

Xtropicalis

all identical

ENSXETG00000015003

protein features

start (aa)	end (aa)	feature	details
19	26	HELIX		lost
49	135	DOMAIN	SH2.	might get lost (downstream of altered splice site)
56	63	HELIX		might get lost (downstream of altered splice site)
69	74	STRAND		might get lost (downstream of altered splice site)
76	78	STRAND		might get lost (downstream of altered splice site)
82	87	STRAND		might get lost (downstream of altered splice site)
89	96	STRAND		might get lost (downstream of altered splice site)
98	107	STRAND		might get lost (downstream of altered splice site)
113	129	HELIX		might get lost (downstream of altered splice site)
131	136	HELIX		might get lost (downstream of altered splice site)
143	145	TURN		might get lost (downstream of altered splice site)
146	148	STRAND		might get lost (downstream of altered splice site)
164	166	HELIX		might get lost (downstream of altered splice site)
205	255	ZN_FING	Phorbol-ester/DAG-type.	might get lost (downstream of altered splice site)
208	211	STRAND		might get lost (downstream of altered splice site)
220	222	TURN		might get lost (downstream of altered splice site)
228	230	STRAND		might get lost (downstream of altered splice site)
233	236	STRAND		might get lost (downstream of altered splice site)
237	239	TURN		might get lost (downstream of altered splice site)
245	248	HELIX		might get lost (downstream of altered splice site)
257	261	HELIX		might get lost (downstream of altered splice site)
268	459	DOMAIN	Rho-GAP.	might get lost (downstream of altered splice site)
270	277	HELIX		might get lost (downstream of altered splice site)
283	295	HELIX		might get lost (downstream of altered splice site)
300	304	TURN		might get lost (downstream of altered splice site)
309	322	HELIX		might get lost (downstream of altered splice site)
323	325	HELIX		might get lost (downstream of altered splice site)
330	332	TURN		might get lost (downstream of altered splice site)
336	348	HELIX		might get lost (downstream of altered splice site)
357	359	TURN		might get lost (downstream of altered splice site)
360	368	HELIX		might get lost (downstream of altered splice site)
372	384	HELIX		might get lost (downstream of altered splice site)
388	406	HELIX		might get lost (downstream of altered splice site)
408	411	HELIX		might get lost (downstream of altered splice site)
415	426	HELIX		might get lost (downstream of altered splice site)
434	453	HELIX		might get lost (downstream of altered splice site)
455	458	HELIX		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1380 / 1380

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

460 / 460

position of stopcodon in wt / mu cDNA

1694 / 1694

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

315 / 315

chromosome

strand

-1

last intron/exon boundary

1523

theoretical NMD boundary in CDS

1158

length of CDS

1380

coding sequence (CDS) position

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

374

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

60428

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

175809670

original gDNA sequence snippet

TGTTTCTACCTTCTCACAGTATATCAGCTACAACAGGAAGC

altered gDNA sequence snippet

TGTTTCTACCTTCTCACAGTTTATCAGCTACAACAGGAAGC

original cDNA sequence snippet

CCTGTTTGGAAATCTTACTTATATCAGCTACAACAGGAAGC

altered cDNA sequence snippet

CCTGTTTGGAAATCTTACTTTTATCAGCTACAACAGGAAGC

wildtype AA sequence

MALTLFDTDE YRPPVWKSYL YQLQQEAPHP RRITCTCEVE NRPKYYGREF HGMISREAAD
QLLIVAEGSY LIRESQRQPG TYTLALRFGS QTRNFRLYYD GKHFVGEKRF ESIHDLVTDG
LITLYIETKA AEYIAKMTIN PIYEHVGYTT LNREPAYKKH MPVLKETHDE RDSTGQDGVS
EKRLTSLVRR ATLKENEQIP KYEKIHNFKV HTFRGPHWCE YCANFMWGLI AQGVKCADCG
LNVHKQCSKM VPNDCKPDLK HVKKVYSCDL TTLVKAHTTK RPMVVDMCIR EIESRGLNSE
GLYRVSGFSD LIEDVKMAFD RDGEKADISV NMYEDINIIT GALKLYFRDL PIPLITYDAY
PKFIESAKIM DPDEQLETLH EALKLLPPAH CETLRYLMAH LKRVTLHEKE NLMNAENLGI
VFGPTLMRSP ELDAMAALND IRYQRLVVEL LIKNEDILF*

mutated AA sequence

MALTLFDTDE YRPPVWKSYF YQLQQEAPHP RRITCTCEVE NRPKYYGREF HGMISREAAD
QLLIVAEGSY LIRESQRQPG TYTLALRFGS QTRNFRLYYD GKHFVGEKRF ESIHDLVTDG
LITLYIETKA AEYIAKMTIN PIYEHVGYTT LNREPAYKKH MPVLKETHDE RDSTGQDGVS
EKRLTSLVRR ATLKENEQIP KYEKIHNFKV HTFRGPHWCE YCANFMWGLI AQGVKCADCG
LNVHKQCSKM VPNDCKPDLK HVKKVYSCDL TTLVKAHTTK RPMVVDMCIR EIESRGLNSE
GLYRVSGFSD LIEDVKMAFD RDGEKADISV NMYEDINIIT GALKLYFRDL PIPLITYDAY
PKFIESAKIM DPDEQLETLH EALKLLPPAH CETLRYLMAH LKRVTLHEKE NLMNAENLGI
VFGPTLMRSP ELDAMAALND IRYQRLVVEL LIKNEDILF*

speed

0.31 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: 0.999997563491666 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM082550)
known disease mutation: rs17550 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:175809670T>AN/A show variant in all transcripts IGV

HGNC symbol

CHN1

Ensembl transcript ID

ENST00000409156

Genbank transcript ID

NM_001025201

UniProt peptide

P15882

alteration type

single base exchange

alteration region

CDS

DNA changes

c.60A>T
cDNA.392A>T
g.60428A>T

AA changes

L20F Score: 22 explain score(s)

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

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.488	0.984
	-1.001	0.863
(flanking)	2.804	0.987

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	60426.5	sequence motif lost	-	wt: caca\|GTAT mu: caca.GTTT
Acc marginally increased	60421	wt: 0.8914 / mu: 0.9022 (marginal change - not scored)	wt: CACTTTTTGTTTCTACCTTCTCACAGTATATCAGCTACAAC mu: CACTTTTTGTTTCTACCTTCTCACAGTTTATCAGCTACAAC	ttct\|CACA
Acc marginally increased	60424	wt: 0.9611 / mu: 0.9614 (marginal change - not scored)	wt: TTTTTGTTTCTACCTTCTCACAGTATATCAGCTACAACAGG mu: TTTTTGTTTCTACCTTCTCACAGTTTATCAGCTACAACAGG	tcac\|AGTA
Acc marginally increased	60426	wt: 0.9409 / mu: 0.9742 (marginal change - not scored)	wt: TTTGTTTCTACCTTCTCACAGTATATCAGCTACAACAGGAA mu: TTTGTTTCTACCTTCTCACAGTTTATCAGCTACAACAGGAA	acag\|TATA
Acc marginally increased	60420	wt: 0.7628 / mu: 0.7710 (marginal change - not scored)	wt: ACACTTTTTGTTTCTACCTTCTCACAGTATATCAGCTACAA mu: ACACTTTTTGTTTCTACCTTCTCACAGTTTATCAGCTACAA	cttc\|TCAC
Acc increased	60433	wt: 0.60 / mu: 0.97	wt: CTACCTTCTCACAGTATATCAGCTACAACAGGAAGCCCCTC mu: CTACCTTCTCACAGTTTATCAGCTACAACAGGAAGCCCCTC	atca\|GCTA

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

all identical

ENSPTRG00000012659

Mmulatta

all identical

ENSMMUG00000021797

Fcatus

no alignment

ENSFCAG00000014105

n/a

Mmusculus

all identical

ENSMUSG00000056486

Ggallus

all identical

ENSGALG00000009293

Trubripes

all identical

ENSTRUG00000012830

Drerio

no alignment

ENSDARG00000032493

n/a

Dmelanogaster

all identical

FBgn0029778

Celegans

all identical

BE0003N10.2

Xtropicalis

all identical

ENSXETG00000015003

protein features

start (aa)	end (aa)	feature	details
19	26	HELIX		lost
49	135	DOMAIN	SH2.	might get lost (downstream of altered splice site)
56	63	HELIX		might get lost (downstream of altered splice site)
69	74	STRAND		might get lost (downstream of altered splice site)
76	78	STRAND		might get lost (downstream of altered splice site)
82	87	STRAND		might get lost (downstream of altered splice site)
89	96	STRAND		might get lost (downstream of altered splice site)
98	107	STRAND		might get lost (downstream of altered splice site)
113	129	HELIX		might get lost (downstream of altered splice site)
131	136	HELIX		might get lost (downstream of altered splice site)
143	145	TURN		might get lost (downstream of altered splice site)
146	148	STRAND		might get lost (downstream of altered splice site)
164	166	HELIX		might get lost (downstream of altered splice site)
205	255	ZN_FING	Phorbol-ester/DAG-type.	might get lost (downstream of altered splice site)
208	211	STRAND		might get lost (downstream of altered splice site)
220	222	TURN		might get lost (downstream of altered splice site)
228	230	STRAND		might get lost (downstream of altered splice site)
233	236	STRAND		might get lost (downstream of altered splice site)
237	239	TURN		might get lost (downstream of altered splice site)
245	248	HELIX		might get lost (downstream of altered splice site)
257	261	HELIX		might get lost (downstream of altered splice site)
268	459	DOMAIN	Rho-GAP.	might get lost (downstream of altered splice site)
270	277	HELIX		might get lost (downstream of altered splice site)
283	295	HELIX		might get lost (downstream of altered splice site)
300	304	TURN		might get lost (downstream of altered splice site)
309	322	HELIX		might get lost (downstream of altered splice site)
323	325	HELIX		might get lost (downstream of altered splice site)
330	332	TURN		might get lost (downstream of altered splice site)
336	348	HELIX		might get lost (downstream of altered splice site)
357	359	TURN		might get lost (downstream of altered splice site)
360	368	HELIX		might get lost (downstream of altered splice site)
372	384	HELIX		might get lost (downstream of altered splice site)
388	406	HELIX		might get lost (downstream of altered splice site)
408	411	HELIX		might get lost (downstream of altered splice site)
415	426	HELIX		might get lost (downstream of altered splice site)
434	453	HELIX		might get lost (downstream of altered splice site)
455	458	HELIX		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1302 / 1302

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

434 / 434

position of stopcodon in wt / mu cDNA

1634 / 1634

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

333 / 333

chromosome

strand

-1

last intron/exon boundary

1463

theoretical NMD boundary in CDS

1080

length of CDS

1302

coding sequence (CDS) position

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

392

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

60428

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

175809670

original gDNA sequence snippet

TGTTTCTACCTTCTCACAGTATATCAGCTACAACAGGAAGC

altered gDNA sequence snippet

TGTTTCTACCTTCTCACAGTTTATCAGCTACAACAGGAAGC

original cDNA sequence snippet

CCTGTTTGGAAATCTTACTTATATCAGCTACAACAGGAAGC

altered cDNA sequence snippet

CCTGTTTGGAAATCTTACTTTTATCAGCTACAACAGGAAGC

wildtype AA sequence

MALTLFDTDE YRPPVWKSYL YQLQQEAPHP RRITCTCEVE NRPKYYGREF HGMISREAAD
QLLIVAEGSY LIRESQRQPG TYTLALRFGS QTRNFRLYYD GKHFVGEKRF ESIHDLVTDG
LITLYIETKA AEYIAKMTIN PIYEHVGYTT LNREPAYKKH MPVLKETHDE RDSTGQDGVS
EKRVHTFRGP HWCEYCANFM WGLIAQGVKC ADCGLNVHKQ CSKMVPNDCK PDLKHVKKVY
SCDLTTLVKA HTTKRPMVVD MCIREIESRG LNSEGLYRVS GFSDLIEDVK MAFDRDGEKA
DISVNMYEDI NIITGALKLY FRDLPIPLIT YDAYPKFIES AKIMDPDEQL ETLHEALKLL
PPAHCETLRY LMAHLKRVTL HEKENLMNAE NLGIVFGPTL MRSPELDAMA ALNDIRYQRL
VVELLIKNED ILF*

mutated AA sequence

MALTLFDTDE YRPPVWKSYF YQLQQEAPHP RRITCTCEVE NRPKYYGREF HGMISREAAD
QLLIVAEGSY LIRESQRQPG TYTLALRFGS QTRNFRLYYD GKHFVGEKRF ESIHDLVTDG
LITLYIETKA AEYIAKMTIN PIYEHVGYTT LNREPAYKKH MPVLKETHDE RDSTGQDGVS
EKRVHTFRGP HWCEYCANFM WGLIAQGVKC ADCGLNVHKQ CSKMVPNDCK PDLKHVKKVY
SCDLTTLVKA HTTKRPMVVD MCIREIESRG LNSEGLYRVS GFSDLIEDVK MAFDRDGEKA
DISVNMYEDI NIITGALKLY FRDLPIPLIT YDAYPKFIES AKIMDPDEQL ETLHEALKLL
PPAHCETLRY LMAHLKRVTL HEKENLMNAE NLGIVFGPTL MRSPELDAMA ALNDIRYQRL
VVELLIKNED ILF*

speed

1.18 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems