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: ENST00000556553
Querying Taster for transcript #2: ENST00000393545
Querying Taster for transcript #3: ENST00000045347
Querying Taster for transcript #4: ENST00000356583
MT speed 0 s - this script 3.851416 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SPATA7	polymorphism_automatic	7.59040044040482e-07	simple_aae				V42M	single base exchange	rs3179969		show file
SPATA7	polymorphism_automatic	7.59040044040482e-07	simple_aae				V42M	single base exchange	rs3179969		show file
SPATA7	polymorphism_automatic	1.93578604001932e-06	simple_aae				V74M	single base exchange	rs3179969		show file
SPATA7	polymorphism_automatic	1.93578604001932e-06	simple_aae				V74M	single base exchange	rs3179969		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999240959956 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:88862529G>AN/A show variant in all transcripts IGV

HGNC symbol

SPATA7

Ensembl transcript ID

ENST00000556553

Genbank transcript ID

NM_001040428

UniProt peptide

Q9P0W8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.124G>A
cDNA.683G>A
g.11262G>A

AA changes

V42M Score: 21 explain score(s)

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

frameshift

known variant

Reference ID: rs3179969

database	homozygous (A/A)	heterozygous	allele carriers
1000G	455	1131	1586
ExAC	7591	17585	25176

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.559	0.908
	0.341	0.812
(flanking)	1.536	0.75

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	11255	wt: 0.6830 / mu: 0.6947 (marginal change - not scored)	wt: GTTCCAGTAAGCGTG mu: GTTCCAGTAAGCATG	TCCA\|gtaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all conserved

ENSPTRG00000006606

Mmulatta

all conserved

ENSMMUG00000021011

SAKA

Fcatus

all conserved

ENSFCAG00000002954

TLHLVKNHM

YNKILSAKXXXX

Mmusculus

all identical

ENSMUSG00000021007

SAKA

Ggallus

no homologue

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000075898

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1704 / 1704

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

568 / 568

position of stopcodon in wt / mu cDNA

2263 / 2263

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

560 / 560

chromosome

strand

last intron/exon boundary

1679

theoretical NMD boundary in CDS

1069

length of CDS

1704

coding sequence (CDS) position

124

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

683

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

11262

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

88862529

original gDNA sequence snippet

ACTGCTCGGTTCCAGTAAGCGTGAGTACCAGCATAAAGTGT

altered gDNA sequence snippet

ACTGCTCGGTTCCAGTAAGCATGAGTACCAGCATAAAGTGT

original cDNA sequence snippet

ACTGCTCGGTTCCAGTAAGCGTGAGTACCAGCATAAAGTAT

altered cDNA sequence snippet

ACTGCTCGGTTCCAGTAAGCATGAGTACCAGCATAAAGTAT

wildtype AA sequence

MDGSRRVRAT SVLPRYGPPC LFKGHLSTKS NAAVDCSVPV SVSTSIKYAD QQRREKLKKE
LAQCEKEFKL TKTAMRANYK NNSKSLFNTL QKPSGEPQIE DDMLKEEMNG FSSFARSLVP
SSERLHLSLH KSSKVITNGP EKNSSSSPSS VDYAASGPRK LSSGALYGRR PRSTFPNSHR
FQLVISKAPS GDLLDKHSEL FSNKQLPFTP RTLKTEAKSF LSQYRYYTPA KRKKDFTDQR
IEAETQTELS FKSELGTAET KNMTDSEMNI KQASNCVTYD AKEKIAPLPL EGHDSTWDEI
KDDALQHSSP RAMCQYSLKP PSTRKIYSDE EELLYLSFIE DVTDEILKLG LFSNRFLERL
FERHIKQNKH LEEEKMRHLL HVLKVDLGCT SEENSVKQND VDMLNVFDFE KAGNSEPNEL
KNESEVTIQQ ERQQYQKALD MLLSAPKDEN EIFPSPTEFF MPIYKSKHSE GVIIQQVNDE
TNLETSTLDE NHPSISDSLT DRETSVNVIE GDSDPEKVEI SNGLCGLNTS PSQSVQFSSV
KGDNNHDMEL STLKIMEMSI EDCPLDV*

mutated AA sequence

MDGSRRVRAT SVLPRYGPPC LFKGHLSTKS NAAVDCSVPV SMSTSIKYAD QQRREKLKKE
LAQCEKEFKL TKTAMRANYK NNSKSLFNTL QKPSGEPQIE DDMLKEEMNG FSSFARSLVP
SSERLHLSLH KSSKVITNGP EKNSSSSPSS VDYAASGPRK LSSGALYGRR PRSTFPNSHR
FQLVISKAPS GDLLDKHSEL FSNKQLPFTP RTLKTEAKSF LSQYRYYTPA KRKKDFTDQR
IEAETQTELS FKSELGTAET KNMTDSEMNI KQASNCVTYD AKEKIAPLPL EGHDSTWDEI
KDDALQHSSP RAMCQYSLKP PSTRKIYSDE EELLYLSFIE DVTDEILKLG LFSNRFLERL
FERHIKQNKH LEEEKMRHLL HVLKVDLGCT SEENSVKQND VDMLNVFDFE KAGNSEPNEL
KNESEVTIQQ ERQQYQKALD MLLSAPKDEN EIFPSPTEFF MPIYKSKHSE GVIIQQVNDE
TNLETSTLDE NHPSISDSLT DRETSVNVIE GDSDPEKVEI SNGLCGLNTS PSQSVQFSSV
KGDNNHDMEL STLKIMEMSI EDCPLDV*

speed

0.66 s

All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999240959956 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:88862529G>AN/A show variant in all transcripts IGV

HGNC symbol

SPATA7

Ensembl transcript ID

ENST00000356583

Genbank transcript ID

N/A

UniProt peptide

Q9P0W8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.124G>A
cDNA.299G>A
g.11262G>A

AA changes

V42M Score: 21 explain score(s)

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

frameshift

known variant

Reference ID: rs3179969

database	homozygous (A/A)	heterozygous	allele carriers
1000G	455	1131	1586
ExAC	7591	17585	25176

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.559	0.908
	0.341	0.812
(flanking)	1.536	0.75

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	11255	wt: 0.6830 / mu: 0.6947 (marginal change - not scored)	wt: GTTCCAGTAAGCGTG mu: GTTCCAGTAAGCATG	TCCA\|gtaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all conserved

ENSPTRG00000006606

Mmulatta

all conserved

ENSMMUG00000021011

SAKA

Fcatus

all conserved

ENSFCAG00000002954

TLHLVKNHM

YNKILSAKXXXX

Mmusculus

all identical

ENSMUSG00000021007

SAKA

Ggallus

no homologue

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000075898

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1704 / 1704

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

568 / 568

position of stopcodon in wt / mu cDNA

1879 / 1879

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

176 / 176

chromosome

strand

last intron/exon boundary

1295

theoretical NMD boundary in CDS

1069

length of CDS

1704

coding sequence (CDS) position

124

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

299

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

11262

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

88862529

original gDNA sequence snippet

ACTGCTCGGTTCCAGTAAGCGTGAGTACCAGCATAAAGTGT

altered gDNA sequence snippet

ACTGCTCGGTTCCAGTAAGCATGAGTACCAGCATAAAGTGT

original cDNA sequence snippet

ACTGCTCGGTTCCAGTAAGCGTGAGTACCAGCATAAAGTAT

altered cDNA sequence snippet

ACTGCTCGGTTCCAGTAAGCATGAGTACCAGCATAAAGTAT

wildtype AA sequence

mutated AA sequence

speed

0.80 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999806421396 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:88862529G>AN/A show variant in all transcripts IGV

HGNC symbol

SPATA7

Ensembl transcript ID

ENST00000045347

Genbank transcript ID

N/A

UniProt peptide

Q9P0W8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.220G>A
cDNA.220G>A
g.11262G>A

AA changes

V74M Score: 21 explain score(s)

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

frameshift

known variant

Reference ID: rs3179969

database	homozygous (A/A)	heterozygous	allele carriers
1000G	455	1131	1586
ExAC	7591	17585	25176

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.559	0.908
	0.341	0.812
(flanking)	1.536	0.75

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	11255	wt: 0.6830 / mu: 0.6947 (marginal change - not scored)	wt: GTTCCAGTAAGCGTG mu: GTTCCAGTAAGCATG	TCCA\|gtaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all conserved

ENSPTRG00000006606

Mmulatta

all conserved

ENSMMUG00000021011

Fcatus

not conserved

ENSFCAG00000002954

Mmusculus

all identical

ENSMUSG00000021007

Ggallus

no homologue

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000075898

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1377 / 1377

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

459 / 459

position of stopcodon in wt / mu cDNA

1377 / 1377

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

1 / 1

chromosome

strand

last intron/exon boundary

1282

theoretical NMD boundary in CDS

1231

length of CDS

1377

coding sequence (CDS) position

220

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

220

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

11262

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

88862529

original gDNA sequence snippet

ACTGCTCGGTTCCAGTAAGCGTGAGTACCAGCATAAAGTGT

altered gDNA sequence snippet

ACTGCTCGGTTCCAGTAAGCATGAGTACCAGCATAAAGTGT

original cDNA sequence snippet

ACTGCTCGGTTCCAGTAAGCGTGAGTACCAGCATAAAGTAT

altered cDNA sequence snippet

ACTGCTCGGTTCCAGTAAGCATGAGTACCAGCATAAAGTAT

wildtype AA sequence

MDGSRRVRAT SVLPRYGPPC LFKGHLSTKS NAFCTDSSSL RLSTLQLVKN HMAVHYNKIL
SAKAAVDCSV PVSVSTSIKY ADQQRREKLK KELAQCEKEF KLTKTAMRAN YKNNSKSLFN
TLQKPSGEPQ IEDDMLKEEM NGFSSFARSL VPSSERLHLS LHKSSKVITN GPEKNSSSSP
SSVDYAASGP RKLSSGALYG RRPRSTFPNS HRFQLVISKA PSGDLLDKHS ELFSNKQLPF
TPRTLKTEAK SFLSQYRYYT PAKRKKDFTD QRIEAETQTE LSFKSELGTA ETKNMTDSEM
NIKQASNCVT YDAKEKIAPL PLEGHDSTWD EIKDDALQHS SPRAMCQYSL KPPSTRKIYS
DEEELLYLSF IEDVTDEILK LGLFSNRFLE RLFERHIKQN KHLEEEKMRH LLHVLKVDLG
CTSEENSFSS VKGDNNHDME LSTLKIMEMS IEDCPLDV*

mutated AA sequence

MDGSRRVRAT SVLPRYGPPC LFKGHLSTKS NAFCTDSSSL RLSTLQLVKN HMAVHYNKIL
SAKAAVDCSV PVSMSTSIKY ADQQRREKLK KELAQCEKEF KLTKTAMRAN YKNNSKSLFN
TLQKPSGEPQ IEDDMLKEEM NGFSSFARSL VPSSERLHLS LHKSSKVITN GPEKNSSSSP
SSVDYAASGP RKLSSGALYG RRPRSTFPNS HRFQLVISKA PSGDLLDKHS ELFSNKQLPF
TPRTLKTEAK SFLSQYRYYT PAKRKKDFTD QRIEAETQTE LSFKSELGTA ETKNMTDSEM
NIKQASNCVT YDAKEKIAPL PLEGHDSTWD EIKDDALQHS SPRAMCQYSL KPPSTRKIYS
DEEELLYLSF IEDVTDEILK LGLFSNRFLE RLFERHIKQN KHLEEEKMRH LLHVLKVDLG
CTSEENSFSS VKGDNNHDME LSTLKIMEMS IEDCPLDV*

speed

0.40 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999806421396 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:88862529G>AN/A show variant in all transcripts IGV

HGNC symbol

SPATA7

Ensembl transcript ID

ENST00000393545

Genbank transcript ID

NM_018418

UniProt peptide

Q9P0W8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.220G>A
cDNA.509G>A
g.11262G>A

AA changes

V74M Score: 21 explain score(s)

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

frameshift

known variant

Reference ID: rs3179969

database	homozygous (A/A)	heterozygous	allele carriers
1000G	455	1131	1586
ExAC	7591	17585	25176

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.559	0.908
	0.341	0.812
(flanking)	1.536	0.75

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	11255	wt: 0.6830 / mu: 0.6947 (marginal change - not scored)	wt: GTTCCAGTAAGCGTG mu: GTTCCAGTAAGCATG	TCCA\|gtaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all conserved

ENSPTRG00000006606

Mmulatta

all conserved

ENSMMUG00000021011

Fcatus

not conserved

ENSFCAG00000002954

Mmusculus

all identical

ENSMUSG00000021007

Ggallus

no homologue

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000075898

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1800 / 1800

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

600 / 600

position of stopcodon in wt / mu cDNA

2089 / 2089

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

290 / 290

chromosome

strand

last intron/exon boundary

1505

theoretical NMD boundary in CDS

1165

length of CDS

1800

coding sequence (CDS) position

220

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

509

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

11262

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

88862529

original gDNA sequence snippet

ACTGCTCGGTTCCAGTAAGCGTGAGTACCAGCATAAAGTGT

altered gDNA sequence snippet

ACTGCTCGGTTCCAGTAAGCATGAGTACCAGCATAAAGTGT

original cDNA sequence snippet

ACTGCTCGGTTCCAGTAAGCGTGAGTACCAGCATAAAGTAT

altered cDNA sequence snippet

ACTGCTCGGTTCCAGTAAGCATGAGTACCAGCATAAAGTAT

wildtype AA sequence

mutated AA sequence

speed

0.83 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems