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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000441560
Querying Taster for transcript #2: ENST00000358385
Querying Taster for transcript #3: ENST00000357032
Querying Taster for transcript #4: ENST00000354525
MT speed 0 s - this script 5.278219 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ATL1	disease_causing_automatic	0.999999994124099	simple_aae		affected	0	R217Q	single base exchange	rs119476049		show file
ATL1	disease_causing_automatic	0.999999994124099	simple_aae		affected	0	R217Q	single base exchange	rs119476049		show file
ATL1	disease_causing_automatic	0.999999994124099	simple_aae		affected	0	R217Q	single base exchange	rs119476049		show file
ATL1	disease_causing_automatic	0.999999994124099	simple_aae		affected	0	R217Q	single base exchange	rs119476049		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999994124099 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM024427)
known disease mutation: rs4349 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:51079996G>AN/A show variant in all transcripts IGV

HGNC symbol

ATL1

Ensembl transcript ID

ENST00000441560

Genbank transcript ID

NM_001127713

UniProt peptide

Q8WXF7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.650G>A
cDNA.1131G>A
g.80770G>A

AA changes

R217Q Score: 43 explain score(s)

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

217

frameshift

known variant

Reference ID: rs119476049
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs4349 (pathogenic for Hereditary spastic paraplegia 3A) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM024427)

known disease mutation at this position, please check HGMD for details (HGMD ID CM024427)
known disease mutation at this position, please check HGMD for details (HGMD ID CM024427)

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.144	1
	4.353	1
(flanking)	0.661	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 increased	80773	wt: 0.51 / mu: 0.67	wt: TCTGATATTTCTTGTTCGAGACTGGAGTTTCCCATACGAAT mu: TCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACGAAT	gaga\|CTGG
Acc marginally increased	80770	wt: 0.2625 / mu: 0.3056 (marginal change - not scored)	wt: GAGTCTGATATTTCTTGTTCGAGACTGGAGTTTCCCATACG mu: GAGTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACG	ttcg\|AGAC
Acc marginally increased	80771	wt: 0.8160 / mu: 0.8190 (marginal change - not scored)	wt: AGTCTGATATTTCTTGTTCGAGACTGGAGTTTCCCATACGA mu: AGTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACGA	tcga\|GACT
Acc marginally increased	80767	wt: 0.2206 / mu: 0.2473 (marginal change - not scored)	wt: TTAGAGTCTGATATTTCTTGTTCGAGACTGGAGTTTCCCAT mu: TTAGAGTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCAT	ttgt\|TCGA
Donor marginally increased	80773	wt: 0.9866 / mu: 0.9886 (marginal change - not scored)	wt: TCGAGACTGGAGTTT mu: TCAAGACTGGAGTTT	GAGA\|ctgg
Donor increased	80771	wt: 0.37 / mu: 0.71	wt: GTTCGAGACTGGAGT mu: GTTCAAGACTGGAGT	TCGA\|gact
Acc gained	80772	0.33	mu: GTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACGAA	caag\|ACTG
Donor gained	80766	0.70	mu: TTCTTGTTCAAGACT	CTTG\|ttca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

217

mutated

all conserved

217

Ptroglodytes

all identical

ENSPTRG00000023829

217

Mmulatta

all identical

ENSMMUG00000009577

206

Fcatus

all identical

ENSFCAG00000006674

Mmusculus

all identical

ENSMUSG00000021066

217

Ggallus

all identical

ENSGALG00000012339

205

Trubripes

no homologue

Drerio

all identical

ENSDARG00000060481

218

Dmelanogaster

all identical

FBgn0039213

192

Celegans

all identical

Y54G2A.2

228

Xtropicalis

all identical

ENSXETG00000009126

217

protein features

start (aa)	end (aa)	feature	details
1	449	TOPO_DOM	Cytoplasmic.	lost
208	219	STRAND		lost
222	224	TURN		might get lost (downstream of altered splice site)
229	241	HELIX		might get lost (downstream of altered splice site)
247	250	STRAND		might get lost (downstream of altered splice site)
253	260	HELIX		might get lost (downstream of altered splice site)
261	270	STRAND		might get lost (downstream of altered splice site)
274	278	HELIX		might get lost (downstream of altered splice site)
286	288	HELIX		might get lost (downstream of altered splice site)
291	305	HELIX		might get lost (downstream of altered splice site)
307	309	TURN		might get lost (downstream of altered splice site)
322	338	HELIX		might get lost (downstream of altered splice site)
347	375	HELIX		might get lost (downstream of altered splice site)
377	380	STRAND		might get lost (downstream of altered splice site)
384	402	HELIX		might get lost (downstream of altered splice site)
398	398	MUTAGEN	S->Y: Affects endoplasmic reticulum and Golgi morphology.	might get lost (downstream of altered splice site)
411	437	HELIX		might get lost (downstream of altered splice site)
412	439	COILED	Potential.	might get lost (downstream of altered splice site)
448	558	REGION	Sufficient for membrane association.	might get lost (downstream of altered splice site)
450	470	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
471	471	TOPO_DOM	Lumenal (Potential).	might get lost (downstream of altered splice site)
472	492	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
493	558	TOPO_DOM	Cytoplasmic.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1662 / 1662

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

554 / 554

position of stopcodon in wt / mu cDNA

2143 / 2143

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

482 / 482

chromosome

strand

last intron/exon boundary

2033

theoretical NMD boundary in CDS

1501

length of CDS

1662

coding sequence (CDS) position

650

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

1131

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

80770

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

51079996

original gDNA sequence snippet

GAGTCTGATATTTCTTGTTCGAGACTGGAGTTTCCCATACG

altered gDNA sequence snippet

GAGTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACG

original cDNA sequence snippet

GAGTCTGATATTTCTTGTTCGAGACTGGAGTTTCCCATACG

altered cDNA sequence snippet

GAGTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACG

wildtype AA sequence

MAKNRRDRNS WGGFSEKTYE WSSEEEEPVK KAGPVQVLIV KDDHSFELDE TALNRILLSE
AVRDKEVVAV SVAGAFRKGK SFLMDFMLRY MYNQESVDWV GDYNEPLTGF SWRGGSERET
TGIQIWSEIF LINKPDGKKV AVLLMDTQGT FDSQSTLRDS ATVFALSTMI SSIQVYNLSQ
NVQEDDLQHL QLFTEYGRLA MEETFLKPFQ SLIFLVRDWS FPYEFSYGAD GGAKFLEKRL
KVSGNQHEEL QNVRKHIHSC FTNISCFLLP HPGLKVATNP NFDGKLKEID DEFIKNLKIL
IPWLLSPESL DIKEINGNKI TCRGLVEYFK AYIKIYQGEE LPHPKSMLQA TAEANNLAAV
ATAKDTYNKK MEEICGGDKP FLAPNDLQTK HLQLKEESVK LFRGVKKMGG EEFSRRYLQQ
LESEIDELYI QYIKHNDSKN IFHAARTPAT LFVVIFITYV IAGVTGFIGL DIIASLCNMI
MGLTLITLCT WAYIRYSGEY RELGAVIDQV AAALWDQALY KLYSAAATHR HLYHQAFPTP
KSESTEQSEK KKM*

mutated AA sequence

MAKNRRDRNS WGGFSEKTYE WSSEEEEPVK KAGPVQVLIV KDDHSFELDE TALNRILLSE
AVRDKEVVAV SVAGAFRKGK SFLMDFMLRY MYNQESVDWV GDYNEPLTGF SWRGGSERET
TGIQIWSEIF LINKPDGKKV AVLLMDTQGT FDSQSTLRDS ATVFALSTMI SSIQVYNLSQ
NVQEDDLQHL QLFTEYGRLA MEETFLKPFQ SLIFLVQDWS FPYEFSYGAD GGAKFLEKRL
KVSGNQHEEL QNVRKHIHSC FTNISCFLLP HPGLKVATNP NFDGKLKEID DEFIKNLKIL
IPWLLSPESL DIKEINGNKI TCRGLVEYFK AYIKIYQGEE LPHPKSMLQA TAEANNLAAV
ATAKDTYNKK MEEICGGDKP FLAPNDLQTK HLQLKEESVK LFRGVKKMGG EEFSRRYLQQ
LESEIDELYI QYIKHNDSKN IFHAARTPAT LFVVIFITYV IAGVTGFIGL DIIASLCNMI
MGLTLITLCT WAYIRYSGEY RELGAVIDQV AAALWDQALY KLYSAAATHR HLYHQAFPTP
KSESTEQSEK KKM*

speed

1.22 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: 0.999999994124099 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM024427)
known disease mutation: rs4349 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:51079996G>AN/A show variant in all transcripts IGV

HGNC symbol

ATL1

Ensembl transcript ID

ENST00000358385

Genbank transcript ID

NM_015915

UniProt peptide

Q8WXF7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.650G>A
cDNA.891G>A
g.80770G>A

AA changes

R217Q Score: 43 explain score(s)

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

217

frameshift

known variant

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.144	1
	4.353	1
(flanking)	0.661	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 increased	80773	wt: 0.51 / mu: 0.67	wt: TCTGATATTTCTTGTTCGAGACTGGAGTTTCCCATACGAAT mu: TCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACGAAT	gaga\|CTGG
Acc marginally increased	80770	wt: 0.2625 / mu: 0.3056 (marginal change - not scored)	wt: GAGTCTGATATTTCTTGTTCGAGACTGGAGTTTCCCATACG mu: GAGTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACG	ttcg\|AGAC
Acc marginally increased	80771	wt: 0.8160 / mu: 0.8190 (marginal change - not scored)	wt: AGTCTGATATTTCTTGTTCGAGACTGGAGTTTCCCATACGA mu: AGTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACGA	tcga\|GACT
Acc marginally increased	80767	wt: 0.2206 / mu: 0.2473 (marginal change - not scored)	wt: TTAGAGTCTGATATTTCTTGTTCGAGACTGGAGTTTCCCAT mu: TTAGAGTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCAT	ttgt\|TCGA
Donor marginally increased	80773	wt: 0.9866 / mu: 0.9886 (marginal change - not scored)	wt: TCGAGACTGGAGTTT mu: TCAAGACTGGAGTTT	GAGA\|ctgg
Donor increased	80771	wt: 0.37 / mu: 0.71	wt: GTTCGAGACTGGAGT mu: GTTCAAGACTGGAGT	TCGA\|gact
Acc gained	80772	0.33	mu: GTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACGAA	caag\|ACTG
Donor gained	80766	0.70	mu: TTCTTGTTCAAGACT	CTTG\|ttca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

217

mutated

all conserved

217

Ptroglodytes

all identical

ENSPTRG00000023829

217

Mmulatta

all identical

ENSMMUG00000009577

206

Fcatus

all identical

ENSFCAG00000006674

Mmusculus

all identical

ENSMUSG00000021066

217

Ggallus

all identical

ENSGALG00000012339

205

Trubripes

no homologue

Drerio

all identical

ENSDARG00000060481

218

Dmelanogaster

all identical

FBgn0039213

192

Celegans

all identical

Y54G2A.2

228

Xtropicalis

all identical

ENSXETG00000009126

217

protein features

start (aa)	end (aa)	feature	details
1	449	TOPO_DOM	Cytoplasmic.	lost
208	219	STRAND		lost
222	224	TURN		might get lost (downstream of altered splice site)
229	241	HELIX		might get lost (downstream of altered splice site)
247	250	STRAND		might get lost (downstream of altered splice site)
253	260	HELIX		might get lost (downstream of altered splice site)
261	270	STRAND		might get lost (downstream of altered splice site)
274	278	HELIX		might get lost (downstream of altered splice site)
286	288	HELIX		might get lost (downstream of altered splice site)
291	305	HELIX		might get lost (downstream of altered splice site)
307	309	TURN		might get lost (downstream of altered splice site)
322	338	HELIX		might get lost (downstream of altered splice site)
347	375	HELIX		might get lost (downstream of altered splice site)
377	380	STRAND		might get lost (downstream of altered splice site)
384	402	HELIX		might get lost (downstream of altered splice site)
398	398	MUTAGEN	S->Y: Affects endoplasmic reticulum and Golgi morphology.	might get lost (downstream of altered splice site)
411	437	HELIX		might get lost (downstream of altered splice site)
412	439	COILED	Potential.	might get lost (downstream of altered splice site)
448	558	REGION	Sufficient for membrane association.	might get lost (downstream of altered splice site)
450	470	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
471	471	TOPO_DOM	Lumenal (Potential).	might get lost (downstream of altered splice site)
472	492	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
493	558	TOPO_DOM	Cytoplasmic.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1677 / 1677

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

559 / 559

position of stopcodon in wt / mu cDNA

1918 / 1918

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

242 / 242

chromosome

strand

last intron/exon boundary

1808

theoretical NMD boundary in CDS

1516

length of CDS

1677

coding sequence (CDS) position

650

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

891

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

80770

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

51079996

original gDNA sequence snippet

GAGTCTGATATTTCTTGTTCGAGACTGGAGTTTCCCATACG

altered gDNA sequence snippet

GAGTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACG

original cDNA sequence snippet

GAGTCTGATATTTCTTGTTCGAGACTGGAGTTTCCCATACG

altered cDNA sequence snippet

GAGTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACG

wildtype AA sequence

mutated AA sequence

MAKNRRDRNS WGGFSEKTYE WSSEEEEPVK KAGPVQVLIV KDDHSFELDE TALNRILLSE
AVRDKEVVAV SVAGAFRKGK SFLMDFMLRY MYNQESVDWV GDYNEPLTGF SWRGGSERET
TGIQIWSEIF LINKPDGKKV AVLLMDTQGT FDSQSTLRDS ATVFALSTMI SSIQVYNLSQ
NVQEDDLQHL QLFTEYGRLA MEETFLKPFQ SLIFLVQDWS FPYEFSYGAD GGAKFLEKRL
KVSGNQHEEL QNVRKHIHSC FTNISCFLLP HPGLKVATNP NFDGKLKEID DEFIKNLKIL
IPWLLSPESL DIKEINGNKI TCRGLVEYFK AYIKIYQGEE LPHPKSMLQA TAEANNLAAV
ATAKDTYNKK MEEICGGDKP FLAPNDLQTK HLQLKEESVK LFRGVKKMGG EEFSRRYLQQ
LESEIDELYI QYIKHNDSKN IFHAARTPAT LFVVIFITYV IAGVTGFIGL DIIASLCNMI
MGLTLITLCT WAYIRYSGEY RELGAVIDQV AAALWDQGST NEALYKLYSA AATHRHLYHQ
AFPTPKSEST EQSEKKKM*

speed

1.22 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999994124099 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM024427)
known disease mutation: rs4349 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:51079996G>AN/A show variant in all transcripts IGV

HGNC symbol

ATL1

Ensembl transcript ID

ENST00000357032

Genbank transcript ID

N/A

UniProt peptide

Q8WXF7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.650G>A
cDNA.891G>A
g.80770G>A

AA changes

R217Q Score: 43 explain score(s)

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

217

frameshift

known variant

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.144	1
	4.353	1
(flanking)	0.661	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 increased	80773	wt: 0.51 / mu: 0.67	wt: TCTGATATTTCTTGTTCGAGACTGGAGTTTCCCATACGAAT mu: TCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACGAAT	gaga\|CTGG
Acc marginally increased	80770	wt: 0.2625 / mu: 0.3056 (marginal change - not scored)	wt: GAGTCTGATATTTCTTGTTCGAGACTGGAGTTTCCCATACG mu: GAGTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACG	ttcg\|AGAC
Acc marginally increased	80771	wt: 0.8160 / mu: 0.8190 (marginal change - not scored)	wt: AGTCTGATATTTCTTGTTCGAGACTGGAGTTTCCCATACGA mu: AGTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACGA	tcga\|GACT
Acc marginally increased	80767	wt: 0.2206 / mu: 0.2473 (marginal change - not scored)	wt: TTAGAGTCTGATATTTCTTGTTCGAGACTGGAGTTTCCCAT mu: TTAGAGTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCAT	ttgt\|TCGA
Donor marginally increased	80773	wt: 0.9866 / mu: 0.9886 (marginal change - not scored)	wt: TCGAGACTGGAGTTT mu: TCAAGACTGGAGTTT	GAGA\|ctgg
Donor increased	80771	wt: 0.37 / mu: 0.71	wt: GTTCGAGACTGGAGT mu: GTTCAAGACTGGAGT	TCGA\|gact
Acc gained	80772	0.33	mu: GTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACGAA	caag\|ACTG
Donor gained	80766	0.70	mu: TTCTTGTTCAAGACT	CTTG\|ttca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

217

mutated

all conserved

217

Ptroglodytes

all identical

ENSPTRG00000023829

217

Mmulatta

all identical

ENSMMUG00000009577

206

Fcatus

all identical

ENSFCAG00000006674

Mmusculus

all identical

ENSMUSG00000021066

217

Ggallus

all identical

ENSGALG00000012339

205

Trubripes

no homologue

Drerio

all identical

ENSDARG00000060481

218

Dmelanogaster

all identical

FBgn0039213

192

Celegans

all identical

Y54G2A.2

228

Xtropicalis

all identical

ENSXETG00000009126

217

protein features

start (aa)	end (aa)	feature	details
1	449	TOPO_DOM	Cytoplasmic.	lost
208	219	STRAND		lost
222	224	TURN		might get lost (downstream of altered splice site)
229	241	HELIX		might get lost (downstream of altered splice site)
247	250	STRAND		might get lost (downstream of altered splice site)
253	260	HELIX		might get lost (downstream of altered splice site)
261	270	STRAND		might get lost (downstream of altered splice site)
274	278	HELIX		might get lost (downstream of altered splice site)
286	288	HELIX		might get lost (downstream of altered splice site)
291	305	HELIX		might get lost (downstream of altered splice site)
307	309	TURN		might get lost (downstream of altered splice site)
322	338	HELIX		might get lost (downstream of altered splice site)
347	375	HELIX		might get lost (downstream of altered splice site)
377	380	STRAND		might get lost (downstream of altered splice site)
384	402	HELIX		might get lost (downstream of altered splice site)
398	398	MUTAGEN	S->Y: Affects endoplasmic reticulum and Golgi morphology.	might get lost (downstream of altered splice site)
411	437	HELIX		might get lost (downstream of altered splice site)
412	439	COILED	Potential.	might get lost (downstream of altered splice site)
448	558	REGION	Sufficient for membrane association.	might get lost (downstream of altered splice site)
450	470	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
471	471	TOPO_DOM	Lumenal (Potential).	might get lost (downstream of altered splice site)
472	492	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
493	558	TOPO_DOM	Cytoplasmic.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1677 / 1677

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

559 / 559

position of stopcodon in wt / mu cDNA

1918 / 1918

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

242 / 242

chromosome

strand

last intron/exon boundary

1808

theoretical NMD boundary in CDS

1516

length of CDS

1677

coding sequence (CDS) position

650

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

891

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

80770

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

51079996

original gDNA sequence snippet

GAGTCTGATATTTCTTGTTCGAGACTGGAGTTTCCCATACG

altered gDNA sequence snippet

GAGTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACG

original cDNA sequence snippet

GAGTCTGATATTTCTTGTTCGAGACTGGAGTTTCCCATACG

altered cDNA sequence snippet

GAGTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACG

wildtype AA sequence

mutated AA sequence

MAKNRRDRNS WGGFSEKTYE WSSEEEEPVK KAGPVQVLIV KDDHSFELDE TALNRILLSE
AVRDKEVVAV SVAGAFRKGK SFLMDFMLRY MYNQESVDWV GDYNEPLTGF SWRGGSERET
TGIQIWSEIF LINKPDGKKV AVLLMDTQGT FDSQSTLRDS ATVFALSTMI SSIQVYNLSQ
NVQEDDLQHL QLFTEYGRLA MEETFLKPFQ SLIFLVQDWS FPYEFSYGAD GGAKFLEKRL
KVSGNQHEEL QNVRKHIHSC FTNISCFLLP HPGLKVATNP NFDGKLKEID DEFIKNLKIL
IPWLLSPESL DIKEINGNKI TCRGLVEYFK AYIKIYQGEE LPHPKSMLQA TAEANNLAAV
ATAKDTYNKK MEEICGGDKP FLAPNDLQTK HLQLKEESVK LFRGVKKMGG EEFSRRYLQQ
LESEIDELYI QYIKHNDSKN IFHAARTPAT LFVVIFITYV IAGVTGFIGL DIIASLCNMI
MGLTLITLCT WAYIRYSGEY RELGAVIDQV AAALWDQGPS HQALYKLYSA AATHRHLYHQ
AFPTPKSEST EQSEKKKM*

speed

0.60 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999994124099 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM024427)
known disease mutation: rs4349 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:51079996G>AN/A show variant in all transcripts IGV

HGNC symbol

ATL1

Ensembl transcript ID

ENST00000354525

Genbank transcript ID

NM_181598

UniProt peptide

Q8WXF7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.650G>A
cDNA.891G>A
g.80770G>A

AA changes

R217Q Score: 43 explain score(s)

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

217

frameshift

known variant

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.144	1
	4.353	1
(flanking)	0.661	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 increased	80773	wt: 0.51 / mu: 0.67	wt: TCTGATATTTCTTGTTCGAGACTGGAGTTTCCCATACGAAT mu: TCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACGAAT	gaga\|CTGG
Acc marginally increased	80770	wt: 0.2625 / mu: 0.3056 (marginal change - not scored)	wt: GAGTCTGATATTTCTTGTTCGAGACTGGAGTTTCCCATACG mu: GAGTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACG	ttcg\|AGAC
Acc marginally increased	80771	wt: 0.8160 / mu: 0.8190 (marginal change - not scored)	wt: AGTCTGATATTTCTTGTTCGAGACTGGAGTTTCCCATACGA mu: AGTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACGA	tcga\|GACT
Acc marginally increased	80767	wt: 0.2206 / mu: 0.2473 (marginal change - not scored)	wt: TTAGAGTCTGATATTTCTTGTTCGAGACTGGAGTTTCCCAT mu: TTAGAGTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCAT	ttgt\|TCGA
Donor marginally increased	80773	wt: 0.9866 / mu: 0.9886 (marginal change - not scored)	wt: TCGAGACTGGAGTTT mu: TCAAGACTGGAGTTT	GAGA\|ctgg
Donor increased	80771	wt: 0.37 / mu: 0.71	wt: GTTCGAGACTGGAGT mu: GTTCAAGACTGGAGT	TCGA\|gact
Acc gained	80772	0.33	mu: GTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACGAA	caag\|ACTG
Donor gained	80766	0.70	mu: TTCTTGTTCAAGACT	CTTG\|ttca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

217

mutated

all conserved

217

Ptroglodytes

all identical

ENSPTRG00000023829

217

Mmulatta

all identical

ENSMMUG00000009577

206

Fcatus

all identical

ENSFCAG00000006674

Mmusculus

all identical

ENSMUSG00000021066

217

Ggallus

all identical

ENSGALG00000012339

205

Trubripes

no homologue

Drerio

all identical

ENSDARG00000060481

218

Dmelanogaster

all identical

FBgn0039213

192

Celegans

all identical

Y54G2A.2

228

Xtropicalis

all identical

ENSXETG00000009126

217

protein features

start (aa)	end (aa)	feature	details
1	449	TOPO_DOM	Cytoplasmic.	lost
208	219	STRAND		lost
222	224	TURN		might get lost (downstream of altered splice site)
229	241	HELIX		might get lost (downstream of altered splice site)
247	250	STRAND		might get lost (downstream of altered splice site)
253	260	HELIX		might get lost (downstream of altered splice site)
261	270	STRAND		might get lost (downstream of altered splice site)
274	278	HELIX		might get lost (downstream of altered splice site)
286	288	HELIX		might get lost (downstream of altered splice site)
291	305	HELIX		might get lost (downstream of altered splice site)
307	309	TURN		might get lost (downstream of altered splice site)
322	338	HELIX		might get lost (downstream of altered splice site)
347	375	HELIX		might get lost (downstream of altered splice site)
377	380	STRAND		might get lost (downstream of altered splice site)
384	402	HELIX		might get lost (downstream of altered splice site)
398	398	MUTAGEN	S->Y: Affects endoplasmic reticulum and Golgi morphology.	might get lost (downstream of altered splice site)
411	437	HELIX		might get lost (downstream of altered splice site)
412	439	COILED	Potential.	might get lost (downstream of altered splice site)
448	558	REGION	Sufficient for membrane association.	might get lost (downstream of altered splice site)
450	470	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
471	471	TOPO_DOM	Lumenal (Potential).	might get lost (downstream of altered splice site)
472	492	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
493	558	TOPO_DOM	Cytoplasmic.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1662 / 1662

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

554 / 554

position of stopcodon in wt / mu cDNA

1903 / 1903

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

242 / 242

chromosome

strand

last intron/exon boundary

1793

theoretical NMD boundary in CDS

1501

length of CDS

1662

coding sequence (CDS) position

650

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

891

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

80770

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

51079996

original gDNA sequence snippet

GAGTCTGATATTTCTTGTTCGAGACTGGAGTTTCCCATACG

altered gDNA sequence snippet

GAGTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACG

original cDNA sequence snippet

GAGTCTGATATTTCTTGTTCGAGACTGGAGTTTCCCATACG

altered cDNA sequence snippet

GAGTCTGATATTTCTTGTTCAAGACTGGAGTTTCCCATACG

wildtype AA sequence

mutated AA sequence

MAKNRRDRNS WGGFSEKTYE WSSEEEEPVK KAGPVQVLIV KDDHSFELDE TALNRILLSE
AVRDKEVVAV SVAGAFRKGK SFLMDFMLRY MYNQESVDWV GDYNEPLTGF SWRGGSERET
TGIQIWSEIF LINKPDGKKV AVLLMDTQGT FDSQSTLRDS ATVFALSTMI SSIQVYNLSQ
NVQEDDLQHL QLFTEYGRLA MEETFLKPFQ SLIFLVQDWS FPYEFSYGAD GGAKFLEKRL
KVSGNQHEEL QNVRKHIHSC FTNISCFLLP HPGLKVATNP NFDGKLKEID DEFIKNLKIL
IPWLLSPESL DIKEINGNKI TCRGLVEYFK AYIKIYQGEE LPHPKSMLQA TAEANNLAAV
ATAKDTYNKK MEEICGGDKP FLAPNDLQTK HLQLKEESVK LFRGVKKMGG EEFSRRYLQQ
LESEIDELYI QYIKHNDSKN IFHAARTPAT LFVVIFITYV IAGVTGFIGL DIIASLCNMI
MGLTLITLCT WAYIRYSGEY RELGAVIDQV AAALWDQALY KLYSAAATHR HLYHQAFPTP
KSESTEQSEK KKM*

speed

1.25 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems