MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000295488
Querying Taster for transcript #2: ENST00000510985
MT speed 1.86 s - this script 3.900178 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
HELQ	polymorphism_automatic	4.61944659968516e-07	simple_aae		affected		V306I	single base exchange	rs1494961		show file
HELQ	polymorphism_automatic	4.61944659968516e-07	simple_aae		affected		V306I	single base exchange	rs1494961		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999953805534 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM112383)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:84374480C>TN/A show variant in all transcripts IGV

HGNC symbol

HELQ

Ensembl transcript ID

ENST00000295488

Genbank transcript ID

NM_133636

UniProt peptide

Q8TDG4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.916G>A
cDNA.1079G>A
g.2530G>A

AA changes

V306I Score: 29 explain score(s)

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

306

frameshift

known variant

Reference ID: rs1494961

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1154	1020	2174
ExAC	19756	-6745	13011

known disease mutation at this position, please check HGMD for details (HGMD ID CM112383)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.06	0.988
	0.62	0.973
(flanking)	-0.018	0.962

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	2522	wt: 0.9632 / mu: 0.9899 (marginal change - not scored)	wt: TGCTAAGAAAACAGT mu: TGCTAAGAAAACAAT	CTAA\|gaaa
Donor increased	2534	wt: 0.63 / mu: 0.74	wt: AGTTGAGTCATCATC mu: AATTGAGTCATCATC	TTGA\|gtca
Donor gained	2525	0.31	mu: TAAGAAAACAATTGA	AGAA\|aaca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

306

mutated

all conserved

306

Ptroglodytes

all conserved

ENSPTRG00000016232

304

Mmulatta

all conserved

ENSMMUG00000015350

306

Fcatus

all conserved

ENSFCAG00000009921

302

Mmusculus

all conserved

ENSMUSG00000035266

265

Ggallus

all conserved

ENSGALG00000011208

213

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000079818

226

SIT

Dmelanogaster

not conserved

FBgn0002899

225

NWET

IDKFPSK

Celegans

not conserved

Y55B1AL.3

138

Xtropicalis

all identical

ENSXETG00000001831

protein features

start (aa)	end (aa)	feature	details
306	306	CONFLICT	V -> I (in Ref. 1; AAL85274, 2; BAC87559 and 4; AAH95473).	lost
346	518	DOMAIN	Helicase ATP-binding.	might get lost (downstream of altered splice site)
359	366	NP_BIND	ATP (By similarity).	might get lost (downstream of altered splice site)
365	365	MUTAGEN	K->M: Abolishes ATPase and DNA helicase activity.	might get lost (downstream of altered splice site)
463	466	MOTIF	DEAH box.	might get lost (downstream of altered splice site)
566	758	DOMAIN	Helicase C-terminal.	might get lost (downstream of altered splice site)
1062	1086	COILED	Potential.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3306 / 3306

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

1102 / 1102

position of stopcodon in wt / mu cDNA

3469 / 3469

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

164 / 164

chromosome

strand

-1

last intron/exon boundary

3362

theoretical NMD boundary in CDS

3148

length of CDS

3306

coding sequence (CDS) position

916

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

1079

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

2530

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

84374480

original gDNA sequence snippet

TTAATGTTGCTAAGAAAACAGTTGAGTCATCATCAAATGAC

altered gDNA sequence snippet

TTAATGTTGCTAAGAAAACAATTGAGTCATCATCAAATGAC

original cDNA sequence snippet

TTAATGTTGCTAAGAAAACAGTTGAGTCATCATCAAATGAC

altered cDNA sequence snippet

TTAATGTTGCTAAGAAAACAATTGAGTCATCATCAAATGAC

wildtype AA sequence

MDECGSRIRR RVSLPKRNRP SLGCIFGAPT AAELVPGDEG KEEEEMVAEN RRRKTAGVLP
VEVQPLLLSD SPECLVLGGG DTNPDLLRHM PTDRGVGDQP NDSEVDMFGD YDSFTENSFI
AQVDDLEQKY MQLPEHKKHA TDFATENLCS ESIKNKLSIT TIGNLTELQT DKHTENQSGY
EGVTIEPGAD LLYDVPSSQA IYFENLQNSS NDLGDHSMKE RDWKSSSHNT VNEELPHNCI
EQPQQNDESS SKVRTSSDMN RRKSIKDHLK NAMTGNAKAQ TPIFSRSKQL KDTLLSEEIN
VAKKTVESSS NDLGPFYSLP SKVRDLYAQF KGIEKLYEWQ HTCLTLNSVQ ERKNLIYSLP
TSGGKTLVAE ILMLQELLCC RKDVLMILPY VAIVQEKISG LSSFGIELGF FVEEYAGSKG
RFPPTKRREK KSLYIATIEK GHSLVNSLIE TGRIDSLGLV VVDELHMIGE GSRGATLEMT
LAKILYTSKT TQIIGMSATL NNVEDLQKFL QAEYYTSQFR PVELKEYLKI NDTIYEVDSK
AENGMTFSRL LNYKYSDTLK KMDPDHLVAL VTEVIPNYSC LVFCPSKKNC ENVAEMICKF
LSKEYLKHKE KEKCEVIKNL KNIGNGNLCP VLKRTIPFGV AYHHSGLTSD ERKLLEEAYS
TGVLCLFTCT STLAAGVNLP ARRVILRAPY VAKEFLKRNQ YKQMIGRAGR AGIDTIGESI
LILQEKDKQQ VLELITKPLE NCYSHLVQEF TKGIQTLFLS LIGLKIATNL DDIYHFMNGT
FFGVQQKVLL KEKSLWEITV ESLRYLTEKG LLQKDTIYKS EEEVQYNFHI TKLGRASFKG
TIDLAYCDIL YRDLKKGLEG LVLESLLHLI YLTTPYDLVS QCNPDWMIYF RQFSQLSPAE
QNVAAILGVS ESFIGKKASG QAIGKKVDKN VVNRLYLSFV LYTLLKETNI WTVSEKFNMP
RGYIQNLLTG TASFSSCVLH FCEELEEFWV YRALLVELTK KLTYCVKAEL IPLMEVTGVL
EGRAKQLYSA GYKSLMHLAN ANPEVLVRTI DHLSRRQAKQ IVSSAKMLLH EKAEALQEEV
EELLRLPSDF PGAVASSTDK A*

mutated AA sequence

MDECGSRIRR RVSLPKRNRP SLGCIFGAPT AAELVPGDEG KEEEEMVAEN RRRKTAGVLP
VEVQPLLLSD SPECLVLGGG DTNPDLLRHM PTDRGVGDQP NDSEVDMFGD YDSFTENSFI
AQVDDLEQKY MQLPEHKKHA TDFATENLCS ESIKNKLSIT TIGNLTELQT DKHTENQSGY
EGVTIEPGAD LLYDVPSSQA IYFENLQNSS NDLGDHSMKE RDWKSSSHNT VNEELPHNCI
EQPQQNDESS SKVRTSSDMN RRKSIKDHLK NAMTGNAKAQ TPIFSRSKQL KDTLLSEEIN
VAKKTIESSS NDLGPFYSLP SKVRDLYAQF KGIEKLYEWQ HTCLTLNSVQ ERKNLIYSLP
TSGGKTLVAE ILMLQELLCC RKDVLMILPY VAIVQEKISG LSSFGIELGF FVEEYAGSKG
RFPPTKRREK KSLYIATIEK GHSLVNSLIE TGRIDSLGLV VVDELHMIGE GSRGATLEMT
LAKILYTSKT TQIIGMSATL NNVEDLQKFL QAEYYTSQFR PVELKEYLKI NDTIYEVDSK
AENGMTFSRL LNYKYSDTLK KMDPDHLVAL VTEVIPNYSC LVFCPSKKNC ENVAEMICKF
LSKEYLKHKE KEKCEVIKNL KNIGNGNLCP VLKRTIPFGV AYHHSGLTSD ERKLLEEAYS
TGVLCLFTCT STLAAGVNLP ARRVILRAPY VAKEFLKRNQ YKQMIGRAGR AGIDTIGESI
LILQEKDKQQ VLELITKPLE NCYSHLVQEF TKGIQTLFLS LIGLKIATNL DDIYHFMNGT
FFGVQQKVLL KEKSLWEITV ESLRYLTEKG LLQKDTIYKS EEEVQYNFHI TKLGRASFKG
TIDLAYCDIL YRDLKKGLEG LVLESLLHLI YLTTPYDLVS QCNPDWMIYF RQFSQLSPAE
QNVAAILGVS ESFIGKKASG QAIGKKVDKN VVNRLYLSFV LYTLLKETNI WTVSEKFNMP
RGYIQNLLTG TASFSSCVLH FCEELEEFWV YRALLVELTK KLTYCVKAEL IPLMEVTGVL
EGRAKQLYSA GYKSLMHLAN ANPEVLVRTI DHLSRRQAKQ IVSSAKMLLH EKAEALQEEV
EELLRLPSDF PGAVASSTDK A*

speed

0.48 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: 0.99999953805534 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM112383)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr4:84374480C>TN/A show variant in all transcripts IGV

HGNC symbol

HELQ

Ensembl transcript ID

ENST00000510985

Genbank transcript ID

N/A

UniProt peptide

Q8TDG4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.916G>A
cDNA.1046G>A
g.2530G>A

AA changes

V306I Score: 29 explain score(s)

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

306

frameshift

known variant

Reference ID: rs1494961

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1154	1020	2174
ExAC	19756	-6745	13011

known disease mutation at this position, please check HGMD for details (HGMD ID CM112383)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.06	0.988
	0.62	0.973
(flanking)	-0.018	0.962

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	2522	wt: 0.9632 / mu: 0.9899 (marginal change - not scored)	wt: TGCTAAGAAAACAGT mu: TGCTAAGAAAACAAT	CTAA\|gaaa
Donor increased	2534	wt: 0.63 / mu: 0.74	wt: AGTTGAGTCATCATC mu: AATTGAGTCATCATC	TTGA\|gtca
Donor gained	2525	0.31	mu: TAAGAAAACAATTGA	AGAA\|aaca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

306

mutated

all conserved

306

Ptroglodytes

all conserved

ENSPTRG00000016232

335

LYEWQHSCL

Mmulatta

all conserved

ENSMMUG00000015350

337

LYEWQHTCL

Fcatus

all conserved

ENSFCAG00000009921

302

Mmusculus

all conserved

ENSMUSG00000035266

286

KLYDWQHTCL

Ggallus

all conserved

ENSGALG00000011208

213

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000079818

299

LIL

Dmelanogaster

not conserved

FBgn0002899

225

NWET

IDKFPSK

Celegans

not conserved

Y55B1AL.3

138

Xtropicalis

all identical

ENSXETG00000001831

protein features

start (aa)	end (aa)	feature	details
306	306	CONFLICT	V -> I (in Ref. 1; AAL85274, 2; BAC87559 and 4; AAH95473).	lost
346	518	DOMAIN	Helicase ATP-binding.	might get lost (downstream of altered splice site)
359	366	NP_BIND	ATP (By similarity).	might get lost (downstream of altered splice site)
365	365	MUTAGEN	K->M: Abolishes ATPase and DNA helicase activity.	might get lost (downstream of altered splice site)
463	466	MOTIF	DEAH box.	might get lost (downstream of altered splice site)
566	758	DOMAIN	Helicase C-terminal.	might get lost (downstream of altered splice site)
1062	1086	COILED	Potential.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3105 / 3105

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

1035 / 1035

position of stopcodon in wt / mu cDNA

3235 / 3235

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

131 / 131

chromosome

strand

-1

last intron/exon boundary

3128

theoretical NMD boundary in CDS

2947

length of CDS

3105

coding sequence (CDS) position

916

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

1046

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

2530

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

84374480

original gDNA sequence snippet

TTAATGTTGCTAAGAAAACAGTTGAGTCATCATCAAATGAC

altered gDNA sequence snippet

TTAATGTTGCTAAGAAAACAATTGAGTCATCATCAAATGAC

original cDNA sequence snippet

TTAATGTTGCTAAGAAAACAGTTGAGTCATCATCAAATGAC

altered cDNA sequence snippet

TTAATGTTGCTAAGAAAACAATTGAGTCATCATCAAATGAC

wildtype AA sequence

MDECGSRIRR RVSLPKRNRP SLGCIFGAPT AAELVPGDEG KEEEEMVAEN RRRKTAGVLP
VEVQPLLLSD SPECLVLGGG DTNPDLLRHM PTDRGVGDQP NDSEVDMFGD YDSFTENSFI
AQVDDLEQKY MQLPEHKKHA TDFATENLCS ESIKNKLSIT TIGNLTELQT DKHTENQSGY
EGVTIEPGAD LLYDVPSSQA IYFENLQNSS NDLGDHSMKE RDWKSSSHNT VNEELPHNCI
EQPQQNDESS SKVRTSSDMN RRKSIKDHLK NAMTGNAKAQ TPIFSRSKQL KDTLLSEEIN
VAKKTVESSS NDLGPFYSLP SKVRDLYAQF KGIEKLYEWQ HTCLTLNSVQ ERKNLIYSLP
TSGGKTLVAE ILMLQELLCC RKDVLMILPY VAIVQEKLHM IGEGSRGATL EMTLAKILYT
SKTTQIIGMS ATLNNVEDLQ KFLQAEYYTS QFRPVELKEY LKINDTIYEV DSKAENGMTF
SRLLNYKYSD TLKKMDPDHL VALVTEVIPN YSCLVFCPSK KNCENVAEMI CKFLSKEYLK
HKEKEKCEVI KNLKNIGNGN LCPVLKRTIP FGVAYHHSGL TSDERKLLEE AYSTGVLCLF
TCTSTLAAGV NLPARRVILR APYVAKEFLK RNQYKQMIGR AGRAGIDTIG ESILILQEKD
KQQVLELITK PLENCYSHLV QEFTKGIQTL FLSLIGLKIA TNLDDIYHFM NGTFFGVQQK
VLLKEKSLWE ITVESLRYLT EKGLLQKDTI YKSEEEVQYN FHITKLGRAS FKGTIDLAYC
DILYRDLKKG LEGLVLESLL HLIYLTTPYD LVSQCNPDWM IYFRQFSQLS PAEQNVAAIL
GVSESFIGKK ASGQAIGKKV DKNVVNRLYL SFVLYTLLKE TNIWTVSEKF NMPRGYIQNL
LTGTASFSSC VLHFCEELEE FWVYRALLVE LTKKLTYCVK AELIPLMEVT GVLEGRAKQL
YSAGYKSLMH LANANPEVLV RTIDHLSRRQ AKQIVSSAKM LLHEKAEALQ EEVEELLRLP
SDFPGAVASS TDKA*

mutated AA sequence

MDECGSRIRR RVSLPKRNRP SLGCIFGAPT AAELVPGDEG KEEEEMVAEN RRRKTAGVLP
VEVQPLLLSD SPECLVLGGG DTNPDLLRHM PTDRGVGDQP NDSEVDMFGD YDSFTENSFI
AQVDDLEQKY MQLPEHKKHA TDFATENLCS ESIKNKLSIT TIGNLTELQT DKHTENQSGY
EGVTIEPGAD LLYDVPSSQA IYFENLQNSS NDLGDHSMKE RDWKSSSHNT VNEELPHNCI
EQPQQNDESS SKVRTSSDMN RRKSIKDHLK NAMTGNAKAQ TPIFSRSKQL KDTLLSEEIN
VAKKTIESSS NDLGPFYSLP SKVRDLYAQF KGIEKLYEWQ HTCLTLNSVQ ERKNLIYSLP
TSGGKTLVAE ILMLQELLCC RKDVLMILPY VAIVQEKLHM IGEGSRGATL EMTLAKILYT
SKTTQIIGMS ATLNNVEDLQ KFLQAEYYTS QFRPVELKEY LKINDTIYEV DSKAENGMTF
SRLLNYKYSD TLKKMDPDHL VALVTEVIPN YSCLVFCPSK KNCENVAEMI CKFLSKEYLK
HKEKEKCEVI KNLKNIGNGN LCPVLKRTIP FGVAYHHSGL TSDERKLLEE AYSTGVLCLF
TCTSTLAAGV NLPARRVILR APYVAKEFLK RNQYKQMIGR AGRAGIDTIG ESILILQEKD
KQQVLELITK PLENCYSHLV QEFTKGIQTL FLSLIGLKIA TNLDDIYHFM NGTFFGVQQK
VLLKEKSLWE ITVESLRYLT EKGLLQKDTI YKSEEEVQYN FHITKLGRAS FKGTIDLAYC
DILYRDLKKG LEGLVLESLL HLIYLTTPYD LVSQCNPDWM IYFRQFSQLS PAEQNVAAIL
GVSESFIGKK ASGQAIGKKV DKNVVNRLYL SFVLYTLLKE TNIWTVSEKF NMPRGYIQNL
LTGTASFSSC VLHFCEELEE FWVYRALLVE LTKKLTYCVK AELIPLMEVT GVLEGRAKQL
YSAGYKSLMH LANANPEVLV RTIDHLSRRQ AKQIVSSAKM LLHEKAEALQ EEVEELLRLP
SDFPGAVASS TDKA*

speed

1.38 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems