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: ENST00000242351
Querying Taster for transcript #2: ENST00000464606
MT speed 0 s - this script 3.540325 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ZC3HAV1	polymorphism_automatic	5.5187898695408e-10	simple_aae		affected		Q701E	single base exchange	rs2297236		show file
ZC3HAV1	polymorphism_automatic	4.15067202830244e-09	simple_aae		affected		Q823E	single base exchange	rs2297236		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999448121 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:138740037G>CN/A show variant in all transcripts IGV

HGNC symbol

ZC3HAV1

Ensembl transcript ID

ENST00000242351

Genbank transcript ID

NM_020119

UniProt peptide

Q7Z2W4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2101C>G
cDNA.2418C>G
g.54429C>G

AA changes

Q701E Score: 29 explain score(s)

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

701

frameshift

known variant

Reference ID: rs2297236

database	homozygous (C/C)	heterozygous	allele carriers
1000G	799	1232	2031
ExAC	19176	-5585	13591

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.801	0.045
	0.496	0.032
(flanking)	0.309	0.015

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 marginally increased	54422	wt: 0.9653 / mu: 0.9672 (marginal change - not scored)	wt: GAATTCTTTCTCTTTATTTGTAGCCATCAGCCAGCAAAGAC mu: GAATTCTTTCTCTTTATTTGTAGCCATGAGCCAGCAAAGAC	ttgt\|AGCC
Acc marginally increased	54423	wt: 0.2208 / mu: 0.2300 (marginal change - not scored)	wt: AATTCTTTCTCTTTATTTGTAGCCATCAGCCAGCAAAGACC mu: AATTCTTTCTCTTTATTTGTAGCCATGAGCCAGCAAAGACC	tgta\|GCCA
Acc marginally increased	54421	wt: 0.9166 / mu: 0.9296 (marginal change - not scored)	wt: TGAATTCTTTCTCTTTATTTGTAGCCATCAGCCAGCAAAGA mu: TGAATTCTTTCTCTTTATTTGTAGCCATGAGCCAGCAAAGA	tttg\|TAGC
Donor marginally increased	54434	wt: 0.9989 / mu: 0.9989 (marginal change - not scored)	wt: CAGCCAGCAAAGACC mu: GAGCCAGCAAAGACC	GCCA\|gcaa
Donor increased	54423	wt: 0.24 / mu: 0.91	wt: TTTGTAGCCATCAGC mu: TTTGTAGCCATGAGC	TGTA\|gcca
Acc gained	54428	0.81	mu: TTTCTCTTTATTTGTAGCCATGAGCCAGCAAAGACCTCGTC	ccat\|GAGC
Donor gained	54425	0.48	mu: TGTAGCCATGAGCCA	TAGC\|catg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

701

mutated

all conserved

701

Ptroglodytes

all identical

ENSPTRG00000019750

701

Mmulatta

all identical

ENSMMUG00000006550

703

Fcatus

all identical

ENSFCAG00000012408

701

Mmusculus

all identical

ENSMUSG00000029826

791

Ggallus

all conserved

ENSGALG00000013911

503

Trubripes

not conserved

ENSTRUG00000007328

475

Drerio

not conserved

ENSDARG00000042496

459

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000008921

701

protein features

start (aa)	end (aa)	feature	details
716	902	DOMAIN	PARP catalytic.	might get lost (downstream of altered splice site)
729	732	STRAND		might get lost (downstream of altered splice site)
738	748	HELIX		might get lost (downstream of altered splice site)
754	763	STRAND		might get lost (downstream of altered splice site)
765	778	HELIX		might get lost (downstream of altered splice site)
783	790	STRAND		might get lost (downstream of altered splice site)
791	793	HELIX		might get lost (downstream of altered splice site)
794	800	HELIX		might get lost (downstream of altered splice site)
804	807	HELIX		might get lost (downstream of altered splice site)
812	814	STRAND		might get lost (downstream of altered splice site)
816	823	STRAND		might get lost (downstream of altered splice site)
824	830	HELIX		might get lost (downstream of altered splice site)
835	837	HELIX		might get lost (downstream of altered splice site)
838	845	STRAND		might get lost (downstream of altered splice site)
849	852	STRAND		might get lost (downstream of altered splice site)
866	869	STRAND		might get lost (downstream of altered splice site)
871	873	STRAND		might get lost (downstream of altered splice site)
876	879	STRAND		might get lost (downstream of altered splice site)
882	884	HELIX		might get lost (downstream of altered splice site)
885	895	STRAND		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2709 / 2709

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

903 / 903

position of stopcodon in wt / mu cDNA

3026 / 3026

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

318 / 318

chromosome

strand

-1

last intron/exon boundary

2767

theoretical NMD boundary in CDS

2399

length of CDS

2709

coding sequence (CDS) position

2101

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

2418

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

54429

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

138740037

original gDNA sequence snippet

TTCTCTTTATTTGTAGCCATCAGCCAGCAAAGACCTCGTCA

altered gDNA sequence snippet

TTCTCTTTATTTGTAGCCATGAGCCAGCAAAGACCTCGTCA

original cDNA sequence snippet

TGAAGAGAGGGCCAGACCATCAGCCAGCAAAGACCTCGTCA

altered cDNA sequence snippet

TGAAGAGAGGGCCAGACCATGAGCCAGCAAAGACCTCGTCA

wildtype AA sequence

MADPEVCCFI TKILCAHGGR MALDALLQEI ALSEPQLCEV LQVAGPDRFV VLETGGEAGI
TRSVVATTRA RVCRRKYCQR PCDNLHLCKL NLLGRCNYSQ SERNLCKYSH EVLSEENFKV
LKNHELSGLN KEELAVLLLQ SDPFFMPEIC KSYKGEGRQQ ICNQQPPCSR LHICDHFTRG
NCRFPNCLRS HNLMDRKVLA IMREHGLNPD VVQNIQDICN SKHMQKNPPG PRAPSSHRRN
MAYRARSKSR DRFFQGSQEF LASASASAER SCTPSPDQIS HRASLEDAPV DDLTRKFTYL
GSQDRARPPS GSSKATDLGG TSQAGTSQRF LENGSQEDLL HGNPGSTYLA SNSTSAPNWK
SLTSWTNDQG ARRKTVFSPT LPAARSSLGS LQTPEAVTTR KGTGLLSSDY RIINGKSGTQ
DIQPGPLFNN NADGVATDIT STRSLNYKST SSGHREISSP RIQDAGPASR DVQATGRIAD
DADPRVALVN DSLSDVTSTT SSRVDDHDSE EICLDHLCKG CPLNGSCSKV HFHLPYRWQM
LIGKTWTDFE HMETIEKGYC NPGIHLCSVG SYTINFRVMS CDSFPIRRLS TPSSVTKPAN
SVFTTKWIWY WKNESGTWIQ YGEEKDKRKN SNVDSSYLES LYQSCPRGVV PFQAGSRNYE
LSFQGMIQTN IASKTQKDVI RRPTFVPQWY VQQMKRGPDH QPAKTSSVSL TATFRPQEDF
CFLSSKKYKL SEIHHLHPEY VRVSEHFKAS MKNFKIEKIK KIENSELLDK FTWKKSQMKE
EGKLLFYATS RAYVESICSN NFDSFLHETH ENKYGKGIYF AKDAIYSHKN CPYDAKNVVM
FVAQVLVGKF TEGNITYTSP PPQFDSCVDT RSNPSVFVIF QKDQVYPQYV IEYTEDKACV
IS*

mutated AA sequence

MADPEVCCFI TKILCAHGGR MALDALLQEI ALSEPQLCEV LQVAGPDRFV VLETGGEAGI
TRSVVATTRA RVCRRKYCQR PCDNLHLCKL NLLGRCNYSQ SERNLCKYSH EVLSEENFKV
LKNHELSGLN KEELAVLLLQ SDPFFMPEIC KSYKGEGRQQ ICNQQPPCSR LHICDHFTRG
NCRFPNCLRS HNLMDRKVLA IMREHGLNPD VVQNIQDICN SKHMQKNPPG PRAPSSHRRN
MAYRARSKSR DRFFQGSQEF LASASASAER SCTPSPDQIS HRASLEDAPV DDLTRKFTYL
GSQDRARPPS GSSKATDLGG TSQAGTSQRF LENGSQEDLL HGNPGSTYLA SNSTSAPNWK
SLTSWTNDQG ARRKTVFSPT LPAARSSLGS LQTPEAVTTR KGTGLLSSDY RIINGKSGTQ
DIQPGPLFNN NADGVATDIT STRSLNYKST SSGHREISSP RIQDAGPASR DVQATGRIAD
DADPRVALVN DSLSDVTSTT SSRVDDHDSE EICLDHLCKG CPLNGSCSKV HFHLPYRWQM
LIGKTWTDFE HMETIEKGYC NPGIHLCSVG SYTINFRVMS CDSFPIRRLS TPSSVTKPAN
SVFTTKWIWY WKNESGTWIQ YGEEKDKRKN SNVDSSYLES LYQSCPRGVV PFQAGSRNYE
LSFQGMIQTN IASKTQKDVI RRPTFVPQWY VQQMKRGPDH EPAKTSSVSL TATFRPQEDF
CFLSSKKYKL SEIHHLHPEY VRVSEHFKAS MKNFKIEKIK KIENSELLDK FTWKKSQMKE
EGKLLFYATS RAYVESICSN NFDSFLHETH ENKYGKGIYF AKDAIYSHKN CPYDAKNVVM
FVAQVLVGKF TEGNITYTSP PPQFDSCVDT RSNPSVFVIF QKDQVYPQYV IEYTEDKACV
IS*

speed

0.41 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: 0.999999995849328 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:138740037G>CN/A show variant in all transcripts IGV

HGNC symbol

ZC3HAV1

Ensembl transcript ID

ENST00000464606

Genbank transcript ID

N/A

UniProt peptide

Q7Z2W4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2467C>G
cDNA.2490C>G
g.54429C>G

AA changes

Q823E Score: 29 explain score(s)

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

823

frameshift

known variant

Reference ID: rs2297236

database	homozygous (C/C)	heterozygous	allele carriers
1000G	799	1232	2031
ExAC	19176	-5585	13591

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.801	0.045
	0.496	0.032
(flanking)	0.309	0.015

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 marginally increased	54422	wt: 0.9653 / mu: 0.9672 (marginal change - not scored)	wt: GAATTCTTTCTCTTTATTTGTAGCCATCAGCCAGCAAAGAC mu: GAATTCTTTCTCTTTATTTGTAGCCATGAGCCAGCAAAGAC	ttgt\|AGCC
Acc marginally increased	54423	wt: 0.2208 / mu: 0.2300 (marginal change - not scored)	wt: AATTCTTTCTCTTTATTTGTAGCCATCAGCCAGCAAAGACC mu: AATTCTTTCTCTTTATTTGTAGCCATGAGCCAGCAAAGACC	tgta\|GCCA
Acc marginally increased	54421	wt: 0.9166 / mu: 0.9296 (marginal change - not scored)	wt: TGAATTCTTTCTCTTTATTTGTAGCCATCAGCCAGCAAAGA mu: TGAATTCTTTCTCTTTATTTGTAGCCATGAGCCAGCAAAGA	tttg\|TAGC
Donor marginally increased	54434	wt: 0.9989 / mu: 0.9989 (marginal change - not scored)	wt: CAGCCAGCAAAGACC mu: GAGCCAGCAAAGACC	GCCA\|gcaa
Donor increased	54423	wt: 0.24 / mu: 0.91	wt: TTTGTAGCCATCAGC mu: TTTGTAGCCATGAGC	TGTA\|gcca
Acc gained	54428	0.81	mu: TTTCTCTTTATTTGTAGCCATGAGCCAGCAAAGACCTCGTC	ccat\|GAGC
Donor gained	54425	0.48	mu: TGTAGCCATGAGCCA	TAGC\|catg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

823

mutated

all conserved

823

Ptroglodytes

all identical

ENSPTRG00000019750

701

Mmulatta

all identical

ENSMMUG00000006550

706

Fcatus

all identical

ENSFCAG00000012408

701

Mmusculus

all identical

ENSMUSG00000029826

791

Ggallus

all conserved

ENSGALG00000013911

503

Trubripes

not conserved

ENSTRUG00000007328

476

Drerio

not conserved

ENSDARG00000042496

459

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000008921

701

protein features

start (aa)	end (aa)	feature	details
716	902	DOMAIN	PARP catalytic.	lost
816	823	STRAND		lost
824	830	HELIX		might get lost (downstream of altered splice site)
835	837	HELIX		might get lost (downstream of altered splice site)
838	845	STRAND		might get lost (downstream of altered splice site)
849	852	STRAND		might get lost (downstream of altered splice site)
866	869	STRAND		might get lost (downstream of altered splice site)
871	873	STRAND		might get lost (downstream of altered splice site)
876	879	STRAND		might get lost (downstream of altered splice site)
882	884	HELIX		might get lost (downstream of altered splice site)
885	895	STRAND		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3075 / 3075

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

1025 / 1025

position of stopcodon in wt / mu cDNA

3098 / 3098

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

24 / 24

chromosome

strand

-1

last intron/exon boundary

2839

theoretical NMD boundary in CDS

2765

length of CDS

3075

coding sequence (CDS) position

2467

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

2490

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

54429

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

138740037

original gDNA sequence snippet

TTCTCTTTATTTGTAGCCATCAGCCAGCAAAGACCTCGTCA

altered gDNA sequence snippet

TTCTCTTTATTTGTAGCCATGAGCCAGCAAAGACCTCGTCA

original cDNA sequence snippet

TGAAGAGAGGGCCAGACCATCAGCCAGCAAAGACCTCGTCA

altered cDNA sequence snippet

TGAAGAGAGGGCCAGACCATGAGCCAGCAAAGACCTCGTCA

wildtype AA sequence

MADPEVCCFI TKILCAHGGR MALDALLQEI ALSEPQLCEV LQVAGPDRFV VLETGGEAGI
TRSVVATTRA RVCRRKYCQR PCDNLHLCKL NLLGRCNYSQ SERNLCKYSH EVLSEENFKV
LKNHELSGLN KEELAVLLLQ SDPFFMPEIC KSYKGEGRQQ ICNQQPPCSR LHICDHFTRG
NCRFPNCLRS HNLMDRKVLA IMREHGLNPD VVQNIQDICN SKHMQKNPPG PRAPSSHRRN
MAYRARSKSR DRFFQGSQEF LASASASAER SCTPSPDQIS HRASLEDAPV DDLTRKFTYL
GSQDRARPPS GSSKATDLGG TSQAGTSQRF LENGSQEDLL HGNPGSTYLA SNSTSAPNWK
SLTSWTNDQG ARRKTVFSPT LPAARSSLGS LQTPEAVTTR KGTGLLSSDY RIINGKSGTQ
DIQPGPLFNN NADGVATDIT STRSLNYKST SSGHREISSP RIQDAGPASR DVQATGRIAD
DADPRVALVN GKYKGKTLWA STFVHDIPNG SSQVVDKTTD VEKTGATGFG LTMAVKAEKD
MLRTGSQSLR NLVPTTPGES TAPAQVSTLP QSPAALSSSN RAAVWGAQGQ NCTQVPVSSA
SELTRKTTGS AQYSLSDVTS TTSSRVDDHD SEEICLDHLC KGCPLNGSCS KVHFHLPYRW
QMLIGKTWTD FEHMETIEKG YCNPGIHLCS VGSYTINFRV MSCDSFPIRR LSTPSSVTKP
ANSVFTTKWI WYWKNESGTW IQYGEEKDKR KNSNVDSSYL ESLYQSCPRG VVPFQAGSRN
YELSFQGMIQ TNIASKTQKD VIRRPTFVPQ WYVQQMKRGP DHQPAKTSSV SLTATFRPQE
DFCFLSSKKY KLSEIHHLHP EYVRVSEHFK ASMKNFKIEK IKKIENSELL DKFTWKKSQM
KEEGKLLFYA TSRAYVESIC SNNFDSFLHE THENKYGKGI YFAKDAIYSH KNCPYDAKNV
VMFVAQVLVG KFTEGNITYT SPPPQFDSCV DTRSNPSVFV IFQKDQVYPQ YVIEYTEDKA
CVIS*

mutated AA sequence

MADPEVCCFI TKILCAHGGR MALDALLQEI ALSEPQLCEV LQVAGPDRFV VLETGGEAGI
TRSVVATTRA RVCRRKYCQR PCDNLHLCKL NLLGRCNYSQ SERNLCKYSH EVLSEENFKV
LKNHELSGLN KEELAVLLLQ SDPFFMPEIC KSYKGEGRQQ ICNQQPPCSR LHICDHFTRG
NCRFPNCLRS HNLMDRKVLA IMREHGLNPD VVQNIQDICN SKHMQKNPPG PRAPSSHRRN
MAYRARSKSR DRFFQGSQEF LASASASAER SCTPSPDQIS HRASLEDAPV DDLTRKFTYL
GSQDRARPPS GSSKATDLGG TSQAGTSQRF LENGSQEDLL HGNPGSTYLA SNSTSAPNWK
SLTSWTNDQG ARRKTVFSPT LPAARSSLGS LQTPEAVTTR KGTGLLSSDY RIINGKSGTQ
DIQPGPLFNN NADGVATDIT STRSLNYKST SSGHREISSP RIQDAGPASR DVQATGRIAD
DADPRVALVN GKYKGKTLWA STFVHDIPNG SSQVVDKTTD VEKTGATGFG LTMAVKAEKD
MLRTGSQSLR NLVPTTPGES TAPAQVSTLP QSPAALSSSN RAAVWGAQGQ NCTQVPVSSA
SELTRKTTGS AQYSLSDVTS TTSSRVDDHD SEEICLDHLC KGCPLNGSCS KVHFHLPYRW
QMLIGKTWTD FEHMETIEKG YCNPGIHLCS VGSYTINFRV MSCDSFPIRR LSTPSSVTKP
ANSVFTTKWI WYWKNESGTW IQYGEEKDKR KNSNVDSSYL ESLYQSCPRG VVPFQAGSRN
YELSFQGMIQ TNIASKTQKD VIRRPTFVPQ WYVQQMKRGP DHEPAKTSSV SLTATFRPQE
DFCFLSSKKY KLSEIHHLHP EYVRVSEHFK ASMKNFKIEK IKKIENSELL DKFTWKKSQM
KEEGKLLFYA TSRAYVESIC SNNFDSFLHE THENKYGKGI YFAKDAIYSH KNCPYDAKNV
VMFVAQVLVG KFTEGNITYT SPPPQFDSCV DTRSNPSVFV IFQKDQVYPQ YVIEYTEDKA
CVIS*

speed

1.02 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems