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: ENST00000560206
Querying Taster for transcript #2: ENST00000419474
MT speed 0 s - this script 3.034898 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ZFHX2	polymorphism_automatic	1.14615983370925e-10	simple_aae				S2137R	single base exchange	rs223124		show file
ZFHX2	polymorphism_automatic	5.84675527104395e-06	without_aae					single base exchange	rs223124		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999885384 (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)

chr14:23992742T>GN/A show variant in all transcripts IGV

HGNC symbol

ZFHX2

Ensembl transcript ID

ENST00000419474

Genbank transcript ID

NM_033400

UniProt peptide

Q9C0A1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.6409A>C
cDNA.6499A>C
g.32660A>C

AA changes

S2137R Score: 110 explain score(s)

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

2137

frameshift

known variant

Reference ID: rs223124

database	homozygous (G/G)	heterozygous	allele carriers
1000G	161	953	1114
ExAC	230	2279	2509

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.651	0.078
	0.557	0.073
(flanking)	1.539	0.07

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

331

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

2137

mutated

not conserved

2137

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

not conserved

ENSFCAG00000012057

1078

Mmusculus

all identical

ENSMUSG00000040721

2130

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000088880

n/a

Dmelanogaster

no alignment

FBgn0004607

n/a

Celegans

no alignment

ZC123.3

n/a

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

7719 / 7719

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

2573 / 2573

position of stopcodon in wt / mu cDNA

7809 / 7809

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

91 / 91

chromosome

strand

-1

last intron/exon boundary

6830

theoretical NMD boundary in CDS

6689

length of CDS

7719

coding sequence (CDS) position

6409

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

6499

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

32660

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

23992742

original gDNA sequence snippet

CTGGGAGCACTGGGGGCAGCAGTGAGGGCCTCTTAGCAGCC

altered gDNA sequence snippet

CTGGGAGCACTGGGGGCAGCCGTGAGGGCCTCTTAGCAGCC

original cDNA sequence snippet

CTGGGAGCACTGGGGGCAGCAGTGAGGGCCTCTTAGCAGCC

altered cDNA sequence snippet

CTGGGAGCACTGGGGGCAGCCGTGAGGGCCTCTTAGCAGCC

wildtype AA sequence

MATLNSASTT GTTPSPGHNA PSLPSDTFSS STPSDPVTKD PPAASSTSEN MRSSEPGGQL
LESGCGLVPP KEIGEPQEGP DCGHFPPNDP GVEKDKEQEE EEEGLPPMDL SNHLFFTAGG
EAYLVAKLSL PGGSELLLPK GFPWGEAGIK EEPSLPFLAY PPPSHLTALH IQHGFDPIQG
FSSSDQILSH DTSAPSPAAC EERHGAFWSY QLAPNPPGDP KDGPMGNSGG NHVAVFWLCL
LCRLGFSKPQ AFMDHTQSHG VKLTPAQYQG LSGSPAVLQE GDEGCKALIS FLEPKLPARP
SSDIPLDNSS TVNMEANVAQ TEDGPPEAEV QALILLDEEV MALSPPSPPT ATWDPSPTQA
KESPVAAGEA GPDWFPEGQE EDGGLCPPLN QSSPTSKEGG TLPAPVGSPE DPSDPPQPYR
LADDYTPAPA AFQGLSLSSH MSLLHSRNSC KTLKCPKCNW HYKYQQTLDV HMREKHPESN
SHCSYCSAGG AHPRLARGES YNCGYKPYRC DVCNYSTTTK GNLSIHMQSD KHLANLQGFQ
AGPGGQGSPP EASLPPSAGD KEPKTKSSWQ CKVCSYETNI SRNLRIHMTS EKHMQNVLML
HQGLPLGLPP GLMGPGPPPP PGATPTSPPE LFQYFGPQAL GQPQTPLAGP GLRPDKPLEA
QLLLNGFHHV GAPARKFPTS APGSLSPDAH LPPSQLLGSS SDSLPTSPPP DDSLSLKVFR
CLVCQAFSTD SLELLLYHCS IGRSLPEAEW KEVAGDTHRC KLCCYGTQLK ANFQLHLKTD
KHAQKYQLAA HLREGGGAMG TPSPASLGDG APYGSVSPLH LRCNICDFES NSKEKMQLHA
RGAAHEENSQ IYKFLLDMEG AEAGAELGLY HCLLCAWETP SRLAVLQHLR TPAHRDAQAQ
RRLQLLQNGP TTEEGLAALQ SILSFSHGQL RTPGKAPVTP LAEPPTPEKD AQNKTEQLAS
EETENKTGPS RDSANQTTVY CCPYCSFLSP ESSQVRAHTL SQHAVQPKYR CPLCQEQLVG
RPALHFHLSH LHNVVPECVE KLLLVATTVE MTFTTKVLSA PTLSPLDNGQ EPPTHGPEPT
PSRDQAAEGP NLTPEASPDP LPEPPLASVE VPDKPSGSPG QPPSPAPSPV PEPDAQAEDV
APPPTMAEEE EGTTGELRSA EPAPADSRHP LTYRKTTNFA LDKFLDPARP YKCTVCKESF
TQKNILLVHY NSVSHLHKMK KAAIDPSAPA RGEAGAPPTT TAATDKPFKC TVCRVSYNQS
STLEIHMRSV LHQTRSRGTK TDSKIEGPER SQEEPKEGET EGEVGTEKKG PDTSGFISGL
PFLSPPPPPL DLHRFPAPLF TPPVLPPFPL VPESLLKLQQ QQLLLPFYLH DLKVGPKLTL
AGPAPVLSLP AATPPPPPQP PKAELAEREW ERPPMAKEGN EAGPSSPPDP LPNEAARTAA
KALLENFGFE LVIQYNEGKQ AVPPPPTPPP PEALGGGDKL ACGACGKLFS NMLILKTHEE
HVHRRFLPFE ALSRYAAQFR KSYDSLYPPL AEPPKPPDGS LDSPVPHLGP PFLVPEPEAG
GTRAPEERSR AGGHWPIEEE ESSRGNLPPL VPAGRRFSRT KFTEFQTQAL QSFFETSAYP
KDGEVERLAS LLGLASRVVV VWFQNARQKA RKNACEGGSM PTGGGTGGAS GCRRCHATFS
CVFELVRHLK KCYDDQTLEE EEEEAERGEE EEEVEEEEVE EEQGLEPPAG PEGPLPEPPD
GEELSQAEAT KAGGKEPEEK ATPSPSPAHT CDQCAISFSS QDLLTSHRRL HFLPSLQPSA
PPQLLDLPLL VFGERNPLVA ATSPMPGPPL KRKHEDGSLS PTGSEAGGGG EGEPPRDKRL
RTTILPEQLE ILYRWYMQDS NPTRKMLDCI SEEVGLKKRV VQVWFQNTRA RERKGQFRST
PGGVPSPAVK PPATATPASL PKFNLLLGKV DDGTGREAPK REAPAFPYPT ATLASGPQPF
LPPGKEATTP TPEPPLPLLP PPPPSEEEGP EEPPKASPES EACSLSAGDL SDSSASSLAE
PESPGAGGTS GGPGGGTGVP DGMGQRRYRT QMSSLQLKIM KACYEAYRTP TMQECEVLGE
EIGLPKRVIQ VWFQNARAKE KKAKLQGTAA GSTGGSSEGL LAAQRTDCPY CDVKYDFYVS
CRGHLFSRQH LAKLKEAVRA QLKSESKCYD LAPAPEAPPA LKAPPATTPA SMPLGAAPTL
PRLAPVLLSG PALAQPPLGN LAPFNSGPAA SSGLLGLATS VLPTTTVVQT AGPGRPLPQR
PMPDQTNTST AGTTDPVPGP PTEPLGDKVS SERKPVAGPT SSSNDALKNL KALKTTVPAL
LGGQFLPFPL PPAGGTAPPA VFGPQLQGAY FQQLYGMKKG LFPMNPMIPQ TLIGLLPNAL
LQPPPQPPEP TATAPPKPPE LPAPGEGEAG EVDELLTGST GISTVDVTHR YLCRQCKMAF
DGEAPATAHQ RSFCFFGRGS GGSMPPPLRV PICTYHCLAC EVLLSGREAL ASHLRSSAHR
RKAAPPQGGP PISITNAATA ASAAVAFAKE EARLPHTDSN PKTTTTSTLL AL*

mutated AA sequence

MATLNSASTT GTTPSPGHNA PSLPSDTFSS STPSDPVTKD PPAASSTSEN MRSSEPGGQL
LESGCGLVPP KEIGEPQEGP DCGHFPPNDP GVEKDKEQEE EEEGLPPMDL SNHLFFTAGG
EAYLVAKLSL PGGSELLLPK GFPWGEAGIK EEPSLPFLAY PPPSHLTALH IQHGFDPIQG
FSSSDQILSH DTSAPSPAAC EERHGAFWSY QLAPNPPGDP KDGPMGNSGG NHVAVFWLCL
LCRLGFSKPQ AFMDHTQSHG VKLTPAQYQG LSGSPAVLQE GDEGCKALIS FLEPKLPARP
SSDIPLDNSS TVNMEANVAQ TEDGPPEAEV QALILLDEEV MALSPPSPPT ATWDPSPTQA
KESPVAAGEA GPDWFPEGQE EDGGLCPPLN QSSPTSKEGG TLPAPVGSPE DPSDPPQPYR
LADDYTPAPA AFQGLSLSSH MSLLHSRNSC KTLKCPKCNW HYKYQQTLDV HMREKHPESN
SHCSYCSAGG AHPRLARGES YNCGYKPYRC DVCNYSTTTK GNLSIHMQSD KHLANLQGFQ
AGPGGQGSPP EASLPPSAGD KEPKTKSSWQ CKVCSYETNI SRNLRIHMTS EKHMQNVLML
HQGLPLGLPP GLMGPGPPPP PGATPTSPPE LFQYFGPQAL GQPQTPLAGP GLRPDKPLEA
QLLLNGFHHV GAPARKFPTS APGSLSPDAH LPPSQLLGSS SDSLPTSPPP DDSLSLKVFR
CLVCQAFSTD SLELLLYHCS IGRSLPEAEW KEVAGDTHRC KLCCYGTQLK ANFQLHLKTD
KHAQKYQLAA HLREGGGAMG TPSPASLGDG APYGSVSPLH LRCNICDFES NSKEKMQLHA
RGAAHEENSQ IYKFLLDMEG AEAGAELGLY HCLLCAWETP SRLAVLQHLR TPAHRDAQAQ
RRLQLLQNGP TTEEGLAALQ SILSFSHGQL RTPGKAPVTP LAEPPTPEKD AQNKTEQLAS
EETENKTGPS RDSANQTTVY CCPYCSFLSP ESSQVRAHTL SQHAVQPKYR CPLCQEQLVG
RPALHFHLSH LHNVVPECVE KLLLVATTVE MTFTTKVLSA PTLSPLDNGQ EPPTHGPEPT
PSRDQAAEGP NLTPEASPDP LPEPPLASVE VPDKPSGSPG QPPSPAPSPV PEPDAQAEDV
APPPTMAEEE EGTTGELRSA EPAPADSRHP LTYRKTTNFA LDKFLDPARP YKCTVCKESF
TQKNILLVHY NSVSHLHKMK KAAIDPSAPA RGEAGAPPTT TAATDKPFKC TVCRVSYNQS
STLEIHMRSV LHQTRSRGTK TDSKIEGPER SQEEPKEGET EGEVGTEKKG PDTSGFISGL
PFLSPPPPPL DLHRFPAPLF TPPVLPPFPL VPESLLKLQQ QQLLLPFYLH DLKVGPKLTL
AGPAPVLSLP AATPPPPPQP PKAELAEREW ERPPMAKEGN EAGPSSPPDP LPNEAARTAA
KALLENFGFE LVIQYNEGKQ AVPPPPTPPP PEALGGGDKL ACGACGKLFS NMLILKTHEE
HVHRRFLPFE ALSRYAAQFR KSYDSLYPPL AEPPKPPDGS LDSPVPHLGP PFLVPEPEAG
GTRAPEERSR AGGHWPIEEE ESSRGNLPPL VPAGRRFSRT KFTEFQTQAL QSFFETSAYP
KDGEVERLAS LLGLASRVVV VWFQNARQKA RKNACEGGSM PTGGGTGGAS GCRRCHATFS
CVFELVRHLK KCYDDQTLEE EEEEAERGEE EEEVEEEEVE EEQGLEPPAG PEGPLPEPPD
GEELSQAEAT KAGGKEPEEK ATPSPSPAHT CDQCAISFSS QDLLTSHRRL HFLPSLQPSA
PPQLLDLPLL VFGERNPLVA ATSPMPGPPL KRKHEDGSLS PTGSEAGGGG EGEPPRDKRL
RTTILPEQLE ILYRWYMQDS NPTRKMLDCI SEEVGLKKRV VQVWFQNTRA RERKGQFRST
PGGVPSPAVK PPATATPASL PKFNLLLGKV DDGTGREAPK REAPAFPYPT ATLASGPQPF
LPPGKEATTP TPEPPLPLLP PPPPSEEEGP EEPPKASPES EACSLSAGDL SDSSASSLAE
PESPGAGGTS GGPGGGTGVP DGMGQRRYRT QMSSLQLKIM KACYEAYRTP TMQECEVLGE
EIGLPKRVIQ VWFQNARAKE KKAKLQGTAA GSTGGSREGL LAAQRTDCPY CDVKYDFYVS
CRGHLFSRQH LAKLKEAVRA QLKSESKCYD LAPAPEAPPA LKAPPATTPA SMPLGAAPTL
PRLAPVLLSG PALAQPPLGN LAPFNSGPAA SSGLLGLATS VLPTTTVVQT AGPGRPLPQR
PMPDQTNTST AGTTDPVPGP PTEPLGDKVS SERKPVAGPT SSSNDALKNL KALKTTVPAL
LGGQFLPFPL PPAGGTAPPA VFGPQLQGAY FQQLYGMKKG LFPMNPMIPQ TLIGLLPNAL
LQPPPQPPEP TATAPPKPPE LPAPGEGEAG EVDELLTGST GISTVDVTHR YLCRQCKMAF
DGEAPATAHQ RSFCFFGRGS GGSMPPPLRV PICTYHCLAC EVLLSGREAL ASHLRSSAHR
RKAAPPQGGP PISITNAATA ASAAVAFAKE EARLPHTDSN PKTTTTSTLL AL*

speed

0.81 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: without_aae, prob: 0.999994153244729 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:23992742T>GN/A show variant in all transcripts IGV

HGNC symbol

ZFHX2

Ensembl transcript ID

ENST00000560206

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

3'UTR

DNA changes

cDNA.9819A>C
g.32660A>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs223124

database	homozygous (G/G)	heterozygous	allele carriers
1000G	161	953	1114
ExAC	230	2279	2509

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.651	0.078
	0.557	0.073
(flanking)	1.539	0.07

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

2674

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

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

signal is predicted to be ok

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

357 / 357

chromosome

strand

-1

last intron/exon boundary

2916

theoretical NMD boundary in CDS

2509

length of CDS

2595

coding sequence (CDS) position

N/A

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

9819

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

32660

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

23992742

original gDNA sequence snippet

CTGGGAGCACTGGGGGCAGCAGTGAGGGCCTCTTAGCAGCC

altered gDNA sequence snippet

CTGGGAGCACTGGGGGCAGCCGTGAGGGCCTCTTAGCAGCC

original cDNA sequence snippet

CTGGGAGCACTGGGGGCAGCAGTGAGGGCCTCTTAGCAGCC

altered cDNA sequence snippet

CTGGGAGCACTGGGGGCAGCCGTGAGGGCCTCTTAGCAGCC

wildtype AA sequence

mutated AA sequence

N/A

speed

0.28 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems