MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 4 transcript(s)...
Querying Taster for transcript #1: ENST00000573597
Querying Taster for transcript #2: ENST00000456349
Querying Taster for transcript #3: ENST00000263080
Querying Taster for transcript #4: ENST00000541913
MT speed 0 s - this script 4.568855 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ASPA	disease_causing_automatic	0.999987538582957	simple_aae			0	Y231C	single base exchange	rs104894550		show file
ASPA	disease_causing_automatic	0.999987538582957	simple_aae			0	Y231C	single base exchange	rs104894550		show file
SPATA22	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs104894550		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999987538582957 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM994594)
known disease mutation: rs2612 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:3397701A>GN/A show variant in all transcripts IGV

HGNC symbol

ASPA

Ensembl transcript ID

ENST00000456349

Genbank transcript ID

N/A

UniProt peptide

P45381

alteration type

single base exchange

alteration region

CDS

DNA changes

c.692A>G
cDNA.840A>G
g.22034A>G

AA changes

Y231C Score: 194 explain score(s)

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

231

frameshift

known variant

Reference ID: rs104894550

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation: rs2612 (pathogenic for Spongy degeneration of central nervous system) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM994594)

known disease mutation at this position, please check HGMD for details (HGMD ID CM994594)
known disease mutation at this position, please check HGMD for details (HGMD ID CM994594)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.374	1
	1.295	1
(flanking)	0.883	1

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

231

mutated

not conserved

231

Ptroglodytes

all identical

ENSPTRG00000008568

231

Mmulatta

all identical

ENSMMUG00000030388

231

Fcatus

all identical

ENSFCAG00000007919

231

Mmusculus

all identical

ENSMUSG00000020774

230

Ggallus

all identical

ENSGALG00000004669

232

Trubripes

no homologue

Drerio

all identical

ENSDARG00000005154

233

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000005789

230

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

942 / 942

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

314 / 314

position of stopcodon in wt / mu cDNA

1090 / 1090

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

149 / 149

chromosome

strand

last intron/exon boundary

893

theoretical NMD boundary in CDS

694

length of CDS

942

coding sequence (CDS) position

692

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

840

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

22034

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

3397701

original gDNA sequence snippet

AATTATAGAGAAAGTTGATTACCCCCGGGATGAAAATGGAG

altered gDNA sequence snippet

AATTATAGAGAAAGTTGATTGCCCCCGGGATGAAAATGGAG

original cDNA sequence snippet

AATTATAGAGAAAGTTGATTACCCCCGGGATGAAAATGGAG

altered cDNA sequence snippet

AATTATAGAGAAAGTTGATTGCCCCCGGGATGAAAATGGAG

wildtype AA sequence

MTSCHIAEEH IQKVAIFGGT HGNELTGVFL VKHWLENGAE IQRTGLEVKP FITNPRAVKK
CTRYIDCDLN RIFDLENLGK KMSEDLPYEV RRAQEINHLF GPKDSEDSYD IIFDLHNTTS
NMGCTLILED SRNNFLIQMF HYIKTSLAPL PCYVYLIEHP SLKYATTRSI AKYPVGIEVG
PQPQGVLRAD ILDQMRKMIK HALDFIHHFN EGKEFPPCAI EVYKIIEKVD YPRDENGEIA
AIIHPNLQDQ DWKPLHPGDP MFLTLDGKTI PLGGDCTVYP VFVNEAAYYE KKEAFAKTTK
LTLNAKSIRC CLH*

mutated AA sequence

MTSCHIAEEH IQKVAIFGGT HGNELTGVFL VKHWLENGAE IQRTGLEVKP FITNPRAVKK
CTRYIDCDLN RIFDLENLGK KMSEDLPYEV RRAQEINHLF GPKDSEDSYD IIFDLHNTTS
NMGCTLILED SRNNFLIQMF HYIKTSLAPL PCYVYLIEHP SLKYATTRSI AKYPVGIEVG
PQPQGVLRAD ILDQMRKMIK HALDFIHHFN EGKEFPPCAI EVYKIIEKVD CPRDENGEIA
AIIHPNLQDQ DWKPLHPGDP MFLTLDGKTI PLGGDCTVYP VFVNEAAYYE KKEAFAKTTK
LTLNAKSIRC CLH*

speed

0.96 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: 0.999987538582957 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM994594)
known disease mutation: rs2612 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:3397701A>GN/A show variant in all transcripts IGV

HGNC symbol

ASPA

Ensembl transcript ID

ENST00000263080

Genbank transcript ID

NM_000049

UniProt peptide

P45381

alteration type

single base exchange

alteration region

CDS

DNA changes

c.692A>G
cDNA.850A>G
g.22034A>G

AA changes

Y231C Score: 194 explain score(s)

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

231

frameshift

known variant

Reference ID: rs104894550

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.374	1
	1.295	1
(flanking)	0.883	1

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

231

mutated

not conserved

231

Ptroglodytes

all identical

ENSPTRG00000008568

231

Mmulatta

all identical

ENSMMUG00000030388

231

Fcatus

all identical

ENSFCAG00000007919

231

Mmusculus

all identical

ENSMUSG00000020774

230

Ggallus

all identical

ENSGALG00000004669

232

Trubripes

no homologue

Drerio

all identical

ENSDARG00000005154

233

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000005789

230

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

942 / 942

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

314 / 314

position of stopcodon in wt / mu cDNA

1100 / 1100

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

159 / 159

chromosome

strand

last intron/exon boundary

903

theoretical NMD boundary in CDS

694

length of CDS

942

coding sequence (CDS) position

692

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

850

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

22034

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

3397701

original gDNA sequence snippet

AATTATAGAGAAAGTTGATTACCCCCGGGATGAAAATGGAG

altered gDNA sequence snippet

AATTATAGAGAAAGTTGATTGCCCCCGGGATGAAAATGGAG

original cDNA sequence snippet

AATTATAGAGAAAGTTGATTACCCCCGGGATGAAAATGGAG

altered cDNA sequence snippet

AATTATAGAGAAAGTTGATTGCCCCCGGGATGAAAATGGAG

wildtype AA sequence

mutated AA sequence

MTSCHIAEEH IQKVAIFGGT HGNELTGVFL VKHWLENGAE IQRTGLEVKP FITNPRAVKK
CTRYIDCDLN RIFDLENLGK KMSEDLPYEV RRAQEINHLF GPKDSEDSYD IIFDLHNTTS
NMGCTLILED SRNNFLIQMF HYIKTSLAPL PCYVYLIEHP SLKYATTRSI AKYPVGIEVG
PQPQGVLRAD ILDQMRKMIK HALDFIHHFN EGKEFPPCAI EVYKIIEKVD CPRDENGEIA
AIIHPNLQDQ DWKPLHPGDP MFLTLDGKTI PLGGDCTVYP VFVNEAAYYE KKEAFAKTTK
LTLNAKSIRC CLH*

speed

0.94 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 CM994594)
known disease mutation: rs2612 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:3397701A>GN/A show variant in all transcripts IGV

HGNC symbol

SPATA22

Ensembl transcript ID

ENST00000541913

Genbank transcript ID

N/A

UniProt peptide

Q8NHS9

alteration type

single base exchange

alteration region

intron

DNA changes

g.19446T>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs104894550

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.374	1
	1.295	1
(flanking)	0.883	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 -23) |

effect	gDNA position	score	detection sequence	exon-intron border
Acc marginally increased	19440	wt: 0.9432 / mu: 0.9580 (marginal change - not scored)	wt: CAATTTCTCCATTTTCATCCCGGGGGTAATCAACTTTCTCT mu: CAATTTCTCCATTTTCATCCCGGGGGCAATCAACTTTCTCT	tccc\|GGGG
Acc increased	19439	wt: 0.57 / mu: 0.67	wt: GCAATTTCTCCATTTTCATCCCGGGGGTAATCAACTTTCTC mu: GCAATTTCTCCATTTTCATCCCGGGGGCAATCAACTTTCTC	atcc\|CGGG
Acc marginally increased	19437	wt: 0.9307 / mu: 0.9394 (marginal change - not scored)	wt: CAGCAATTTCTCCATTTTCATCCCGGGGGTAATCAACTTTC mu: CAGCAATTTCTCCATTTTCATCCCGGGGGCAATCAACTTTC	tcat\|CCCG
Acc increased	19441	wt: 0.82 / mu: 0.91	wt: AATTTCTCCATTTTCATCCCGGGGGTAATCAACTTTCTCTA mu: AATTTCTCCATTTTCATCCCGGGGGCAATCAACTTTCTCTA	cccg\|GGGG
Donor increased	19443	wt: 0.22 / mu: 0.41	wt: CCCGGGGGTAATCAA mu: CCCGGGGGCAATCAA	CGGG\|ggta
Donor gained	19447	0.54	mu: GGGGCAATCAACTTT	GGCA\|atca

distance from splice site

19005

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
6	6	CONFLICT	N -> S (in Ref. 1; AAK51120/AAK53408/ AAK61373/AAK61374).	might get lost (downstream of altered splice site)
84	84	CONFLICT	V -> A (in Ref. 1; AAK53408/AAK61373/ AAK61374).	might get lost (downstream of altered splice site)
279	279	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
280	280	MOD_RES	Phosphotyrosine.	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

515 / 515

chromosome

strand

-1

last intron/exon boundary

1367

theoretical NMD boundary in CDS

802

length of CDS

1044

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)

19446

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

3397701

original gDNA sequence snippet

CTCCATTTTCATCCCGGGGGTAATCAACTTTCTCTATAATT

altered gDNA sequence snippet

CTCCATTTTCATCCCGGGGGCAATCAACTTTCTCTATAATT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MKRSLNENSA RSTAGCLPVP LFNQKKRNRQ PLTSNPLKDD SDWAWEAVNP ELAPVMKTVD
TGQIPHSVSR PLRSQDSVFN SIQSNTGRSQ GGWSYRDGNK NTSLKTWNKN DFKPQCKRTN
LVANDGKNSC PVSSGAQQQK QLRIPEPPNL SRNKETELLR QTHSSKISGC TMRGLDKNSA
LQTLKPNFQQ NQYKKQMLDD IPEDNTLKET SLYQLQFKEK ASSLRIISAV IESMKYWREH
AQKTVLLFEV LAVLDSAVTP GPYYSKTFLM RDGKNTLPCV FYEIDRELPR LIRGRVHRCV
GNYDQKKNIF QCVSVRPASV SEQKTFQAFV KIADVEMQYY INVMNET*

mutated AA sequence

N/A

speed

0.67 s

Problems

data problem

No NCBI gene ID found for this transcript

back to results table