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: ENST00000378466
Querying Taster for transcript #2: ENST00000435556
MT speed 0 s - this script 2.236035 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PANK4	polymorphism_automatic	2.12059036996948e-10	simple_aae		affected		A547V	single base exchange	rs7535528		show file
PANK4	polymorphism_automatic	2.12059036996948e-10	simple_aae		affected		A508V	single base exchange	rs7535528		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999787941 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:2444414G>AN/A show variant in all transcripts IGV

HGNC symbol

PANK4

Ensembl transcript ID

ENST00000378466

Genbank transcript ID

NM_018216

UniProt peptide

Q9NVE7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1640C>T
cDNA.1653C>T
g.13626C>T

AA changes

A547V Score: 64 explain score(s)

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

547

frameshift

known variant

Reference ID: rs7535528

database	homozygous (A/A)	heterozygous	allele carriers
1000G	184	762	946
ExAC	6419	19929	26348

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.911	0.001
	3.425	0.047
(flanking)	-1.516	0.001

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 increased	13619	wt: 0.34 / mu: 0.81	wt: GCTCCCTGGACGCGC mu: GCTCCCTGGACGTGC	TCCC\|tgga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

547

mutated

not conserved

547

Ptroglodytes

all identical

ENSPTRG00000000052

547

Mmulatta

not conserved

ENSMMUG00000014686

547

Fcatus

all identical

ENSFCAG00000009521

503

Mmusculus

all conserved

ENSMUSG00000029056

547

Ggallus

all conserved

ENSGALG00000001165

544

Trubripes

no alignment

ENSTRUG00000002683

n/a

Drerio

not conserved

ENSDARG00000040238

543

Dmelanogaster

no homologue

Celegans

no alignment

C10G11.5

n/a

Xtropicalis

all identical

ENSXETG00000012083

549

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2322 / 2322

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

774 / 774

position of stopcodon in wt / mu cDNA

2335 / 2335

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

14 / 14

chromosome

strand

-1

last intron/exon boundary

2122

theoretical NMD boundary in CDS

2058

length of CDS

2322

coding sequence (CDS) position

1640

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

1653

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

13626

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

2444414

original gDNA sequence snippet

GGTCGTGCGCTCCCTGGACGCGCTGGGCTGGGAGGAACGGC

altered gDNA sequence snippet

GGTCGTGCGCTCCCTGGACGTGCTGGGCTGGGAGGAACGGC

original cDNA sequence snippet

GGTCGTGCGCTCCCTGGACGCGCTGGGCTGGGAGGAACGGC

altered cDNA sequence snippet

GGTCGTGCGCTCCCTGGACGTGCTGGGCTGGGAGGAACGGC

wildtype AA sequence

MAECGASGSG SSGDSLDKSI TLPPDEIFRN LENAKRFAID IGGSLTKLAY YSTVQHKVAK
VRSFDHSGKD TEREHEPPYE ISVQEEITAR LHFIKFENTY IEACLDFIKD HLVNTETKVI
QATGGGAYKF KDLIEEKLRL KVDKEDVMTC LIKGCNFVLK NIPHEAFVYQ KDSDPEFRFQ
TNHPHIFPYL LVNIGSGVSI VKVETEDRFE WVGGSSIGGG TFWGLGALLT KTKKFDELLH
LASRGQHSNV DMLVRDVYGG AHQTLGLSGN LIASSFGKSA TADQEFSKED MAKSLLHMIS
NDIGQLACLH ARLHSLDRVY FGGFFIRGHP VTMRTITYSI NFFSKGEVQA LFLRHEGYLG
AIGAFLKGAE QDNPNQYSWG ENYAGSSGLM SASPELGPAQ RARSGTFDLL EMDRLERPLV
DLPLLLDPPS YVPDTVDLTD DALARKYWLT CFEEALDGVV KRAVASQPDS VDAAERAEKF
RQKYWNKLQT LRQQPFAYGT LTVRSLLDTR EHCLNEFNFP DPYSKVKQRE NGVALRCFPG
VVRSLDALGW EERQLALVKG LLAGNVFDWG AKAVSAVLES DPYFGFEEAK RKLQERPWLV
DSYSEWLQRL KGPPHKCALI FADNSGIDII LGVFPFVREL LLRGTEVILA CNSGPALNDV
THSESLIVAE RIAGMDPVVH SALQEERLLL VQTGSSSPCL DLSRLDKGLA ALVRERGADL
VVIEGMGRAV HTNYHAALRC ESLKLAVIKN AWLAERLGGR LFSVIFKYEV PAE*

mutated AA sequence

MAECGASGSG SSGDSLDKSI TLPPDEIFRN LENAKRFAID IGGSLTKLAY YSTVQHKVAK
VRSFDHSGKD TEREHEPPYE ISVQEEITAR LHFIKFENTY IEACLDFIKD HLVNTETKVI
QATGGGAYKF KDLIEEKLRL KVDKEDVMTC LIKGCNFVLK NIPHEAFVYQ KDSDPEFRFQ
TNHPHIFPYL LVNIGSGVSI VKVETEDRFE WVGGSSIGGG TFWGLGALLT KTKKFDELLH
LASRGQHSNV DMLVRDVYGG AHQTLGLSGN LIASSFGKSA TADQEFSKED MAKSLLHMIS
NDIGQLACLH ARLHSLDRVY FGGFFIRGHP VTMRTITYSI NFFSKGEVQA LFLRHEGYLG
AIGAFLKGAE QDNPNQYSWG ENYAGSSGLM SASPELGPAQ RARSGTFDLL EMDRLERPLV
DLPLLLDPPS YVPDTVDLTD DALARKYWLT CFEEALDGVV KRAVASQPDS VDAAERAEKF
RQKYWNKLQT LRQQPFAYGT LTVRSLLDTR EHCLNEFNFP DPYSKVKQRE NGVALRCFPG
VVRSLDVLGW EERQLALVKG LLAGNVFDWG AKAVSAVLES DPYFGFEEAK RKLQERPWLV
DSYSEWLQRL KGPPHKCALI FADNSGIDII LGVFPFVREL LLRGTEVILA CNSGPALNDV
THSESLIVAE RIAGMDPVVH SALQEERLLL VQTGSSSPCL DLSRLDKGLA ALVRERGADL
VVIEGMGRAV HTNYHAALRC ESLKLAVIKN AWLAERLGGR LFSVIFKYEV PAE*

speed

0.13 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: 0.999999999787941 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:2444414G>AN/A show variant in all transcripts IGV

HGNC symbol

PANK4

Ensembl transcript ID

ENST00000435556

Genbank transcript ID

N/A

UniProt peptide

Q9NVE7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1523C>T
cDNA.1532C>T
g.13626C>T

AA changes

A508V Score: 64 explain score(s)

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

508

frameshift

known variant

Reference ID: rs7535528

database	homozygous (A/A)	heterozygous	allele carriers
1000G	184	762	946
ExAC	6419	19929	26348

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.911	0.001
	3.425	0.047
(flanking)	-1.516	0.001

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 increased	13619	wt: 0.34 / mu: 0.81	wt: GCTCCCTGGACGCGC mu: GCTCCCTGGACGTGC	TCCC\|tgga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

508

mutated

not conserved

508

Ptroglodytes

all identical

ENSPTRG00000000052

547

Mmulatta

not conserved

ENSMMUG00000014686

547

Fcatus

all identical

ENSFCAG00000009521

503

Mmusculus

all conserved

ENSMUSG00000029056

547

Ggallus

all conserved

ENSGALG00000001165

544

Trubripes

no alignment

ENSTRUG00000002683

n/a

Drerio

not conserved

ENSDARG00000040238

543

Dmelanogaster

no homologue

Celegans

no alignment

C10G11.5

n/a

Xtropicalis

all identical

ENSXETG00000012083

549

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2205 / 2205

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

735 / 735

position of stopcodon in wt / mu cDNA

2214 / 2214

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

10 / 10

chromosome

strand

-1

last intron/exon boundary

2001

theoretical NMD boundary in CDS

1941

length of CDS

2205

coding sequence (CDS) position

1523

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

1532

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

13626

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

2444414

original gDNA sequence snippet

GGTCGTGCGCTCCCTGGACGCGCTGGGCTGGGAGGAACGGC

altered gDNA sequence snippet

GGTCGTGCGCTCCCTGGACGTGCTGGGCTGGGAGGAACGGC

original cDNA sequence snippet

GGTCGTGCGCTCCCTGGACGCGCTGGGCTGGGAGGAACGGC

altered cDNA sequence snippet

GGTCGTGCGCTCCCTGGACGTGCTGGGCTGGGAGGAACGGC

wildtype AA sequence

MAECGASGSG SSGDSLDKSI TLPPDEIFRN LENAKRFAID IGGSLTKLAY YSTVQHKVAK
VRSFDHSGKD TEREHEPPYE ISVQEEITAR LHFIKFENTY IEACLDFIKD HLVNTETKVI
QATGGGAFVY QKDSDPEFRF QTNHPHIFPY LLVNIGSGVS IVKVETEDRF EWVGGSSIGG
GTFWGLGALL TKTKKFDELL HLASRGQHSN VDMLVRDVYG GAHQTLGLSG NLIASSFGKS
ATADQEFSKE DMAKSLLHMI SNDIGQLACL HARLHSLDRV YFGGFFIRGH PVTMRTITYS
INFFSKGEVQ ALFLRHEGYL GAIGAFLKGA EQDNPNQYSW GENYAGSSGL MSASPELGPA
QRARSGTFDL LEMDRLERPL VDLPLLLDPP SYVPDTVDLT DDALARKYWL TCFEEALDGV
VKRAVASQPD SVDAAERAEK FRQKYWNKLQ TLRQQPFAYG TLTVRSLLDT REHCLNEFNF
PDPYSKVKQR ENGVALRCFP GVVRSLDALG WEERQLALVK GLLAGNVFDW GAKAVSAVLE
SDPYFGFEEA KRKLQERPWL VDSYSEWLQR LKGPPHKCAL IFADNSGIDI ILGVFPFVRE
LLLRGTEVIL ACNSGPALND VTHSESLIVA ERIAGMDPVV HSALQEERLL LVQTGSSSPC
LDLSRLDKGL AALVRERGAD LVVIEGMGRA VHTNYHAALR CESLKLAVIK NAWLAERLGG
RLFSVIFKYE VPAE*

mutated AA sequence

MAECGASGSG SSGDSLDKSI TLPPDEIFRN LENAKRFAID IGGSLTKLAY YSTVQHKVAK
VRSFDHSGKD TEREHEPPYE ISVQEEITAR LHFIKFENTY IEACLDFIKD HLVNTETKVI
QATGGGAFVY QKDSDPEFRF QTNHPHIFPY LLVNIGSGVS IVKVETEDRF EWVGGSSIGG
GTFWGLGALL TKTKKFDELL HLASRGQHSN VDMLVRDVYG GAHQTLGLSG NLIASSFGKS
ATADQEFSKE DMAKSLLHMI SNDIGQLACL HARLHSLDRV YFGGFFIRGH PVTMRTITYS
INFFSKGEVQ ALFLRHEGYL GAIGAFLKGA EQDNPNQYSW GENYAGSSGL MSASPELGPA
QRARSGTFDL LEMDRLERPL VDLPLLLDPP SYVPDTVDLT DDALARKYWL TCFEEALDGV
VKRAVASQPD SVDAAERAEK FRQKYWNKLQ TLRQQPFAYG TLTVRSLLDT REHCLNEFNF
PDPYSKVKQR ENGVALRCFP GVVRSLDVLG WEERQLALVK GLLAGNVFDW GAKAVSAVLE
SDPYFGFEEA KRKLQERPWL VDSYSEWLQR LKGPPHKCAL IFADNSGIDI ILGVFPFVRE
LLLRGTEVIL ACNSGPALND VTHSESLIVA ERIAGMDPVV HSALQEERLL LVQTGSSSPC
LDLSRLDKGL AALVRERGAD LVVIEGMGRA VHTNYHAALR CESLKLAVIK NAWLAERLGG
RLFSVIFKYE VPAE*

speed

0.12 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems