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: ENST00000332530
Querying Taster for transcript #2: ENST00000359318
MT speed 0 s - this script 3.706013 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AADACL3	polymorphism_automatic	7.67334288998001e-07	simple_aae		affected		C125F	single base exchange	rs7513079		show file
AADACL3	polymorphism_automatic	7.67334288998001e-07	simple_aae		affected		C195F	single base exchange	rs7513079		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999232665711 (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)

chr1:12785494G>TN/A show variant in all transcripts IGV

HGNC symbol

AADACL3

Ensembl transcript ID

ENST00000332530

Genbank transcript ID

NM_001103169

UniProt peptide

Q5VUY0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.374G>T
cDNA.600G>T
g.9377G>T

AA changes

C125F Score: 205 explain score(s)

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

125

frameshift

known variant

Reference ID: rs7513079

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1212	993	2205
ExAC	31393	-30019	1374

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.839	0.062
	0.683	0.04
(flanking)	0.41	0.012

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 increased	9380	wt: 0.29 / mu: 0.42	wt: GAGTTTCATCTGCTACTGTTTTTTTCAAAACCTGGATTTCA mu: GAGTTTCATCTGCTACTTTTTTTTTCAAAACCTGGATTTCA	gttt\|TTTT
Acc increased	9383	wt: 0.71 / mu: 0.94	wt: TTTCATCTGCTACTGTTTTTTTCAAAACCTGGATTTCAGCT mu: TTTCATCTGCTACTTTTTTTTTCAAAACCTGGATTTCAGCT	tttt\|TCAA
Acc marginally increased	9377	wt: 0.7206 / mu: 0.7451 (marginal change - not scored)	wt: CTGGAGTTTCATCTGCTACTGTTTTTTTCAAAACCTGGATT mu: CTGGAGTTTCATCTGCTACTTTTTTTTTCAAAACCTGGATT	actg\|TTTT
Acc marginally increased	9386	wt: 0.9718 / mu: 0.9939 (marginal change - not scored)	wt: CATCTGCTACTGTTTTTTTCAAAACCTGGATTTCAGCTCCT mu: CATCTGCTACTTTTTTTTTCAAAACCTGGATTTCAGCTCCT	ttca\|AAAC
Acc increased	9385	wt: 0.85 / mu: 0.97	wt: TCATCTGCTACTGTTTTTTTCAAAACCTGGATTTCAGCTCC mu: TCATCTGCTACTTTTTTTTTCAAAACCTGGATTTCAGCTCC	tttc\|AAAA
Acc increased	9382	wt: 0.67 / mu: 0.97	wt: GTTTCATCTGCTACTGTTTTTTTCAAAACCTGGATTTCAGC mu: GTTTCATCTGCTACTTTTTTTTTCAAAACCTGGATTTCAGC	tttt\|TTCA
Acc marginally increased	9387	wt: 0.9462 / mu: 0.9872 (marginal change - not scored)	wt: ATCTGCTACTGTTTTTTTCAAAACCTGGATTTCAGCTCCTC mu: ATCTGCTACTTTTTTTTTCAAAACCTGGATTTCAGCTCCTC	tcaa\|AACC
Acc increased	9384	wt: 0.71 / mu: 0.90	wt: TTCATCTGCTACTGTTTTTTTCAAAACCTGGATTTCAGCTC mu: TTCATCTGCTACTTTTTTTTTCAAAACCTGGATTTCAGCTC	tttt\|CAAA
Acc marginally increased	9374	wt: 0.2630 / mu: 0.2702 (marginal change - not scored)	wt: CACCTGGAGTTTCATCTGCTACTGTTTTTTTCAAAACCTGG mu: CACCTGGAGTTTCATCTGCTACTTTTTTTTTCAAAACCTGG	gcta\|CTGT
Acc increased	9388	wt: 0.80 / mu: 0.91	wt: TCTGCTACTGTTTTTTTCAAAACCTGGATTTCAGCTCCTCC mu: TCTGCTACTTTTTTTTTCAAAACCTGGATTTCAGCTCCTCC	caaa\|ACCT
Acc gained	9381	0.64	mu: AGTTTCATCTGCTACTTTTTTTTTCAAAACCTGGATTTCAG	tttt\|TTTC

distance from splice site

306

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

125

mutated

not conserved

125

Ptroglodytes

all identical

ENSPTRG00000000168

195

Mmulatta

all identical

ENSMMUG00000012080

197

Fcatus

all identical

ENSFCAG00000000578

195

Mmusculus

all identical

ENSMUSG00000078507

253

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000044802

265

Dmelanogaster

no homologue

Celegans

not conserved

Y43F8A.3

266

LYAGI

Xtropicalis

not conserved

ENSXETG00000001384

269

protein features

start (aa)	end (aa)	feature	details
136	136	ACT_SITE	Potential.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

843 / 843

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

281 / 281

position of stopcodon in wt / mu cDNA

1069 / 1069

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

227 / 227

chromosome

strand

last intron/exon boundary

295

theoretical NMD boundary in CDS

length of CDS

843

coding sequence (CDS) position

374

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

600

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

9377

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

12785494

original gDNA sequence snippet

CTGGAGTTTCATCTGCTACTGTTTTTTTCAAAACCTGGATT

altered gDNA sequence snippet

CTGGAGTTTCATCTGCTACTTTTTTTTTCAAAACCTGGATT

original cDNA sequence snippet

CTGGAGTTTCATCTGCTACTGTTTTTTTCAAAACCTGGATT

altered cDNA sequence snippet

CTGGAGTTTCATCTGCTACTTTTTTTTTCAAAACCTGGATT

wildtype AA sequence

METHHGICSR LCKESDSVVL AVGYRKLPKH KFPVPVRDCL VATIHFLKSL DAYGVDPARV
VVCGDSFGGA IAAVVCQQLV DRPDLPRIRA QILIYAILQA LDLQTPSFQQ RKNIPLLTWS
FICYCFFQNL DFSSSWQEVI MKGAHLPAEV WEKYRKWLGP ENIPERFKER GYQLKPHEPM
NEAAYLEVSV VLDVMCSPLI AEDDIVSQLP ETCIVSCEYD ALRDNSLLYK KRLEDLGVPV
TWHHMEDGFH GVLRTIDMSF LHFPCSMRIL SALVQFVKGL *

mutated AA sequence

METHHGICSR LCKESDSVVL AVGYRKLPKH KFPVPVRDCL VATIHFLKSL DAYGVDPARV
VVCGDSFGGA IAAVVCQQLV DRPDLPRIRA QILIYAILQA LDLQTPSFQQ RKNIPLLTWS
FICYFFFQNL DFSSSWQEVI MKGAHLPAEV WEKYRKWLGP ENIPERFKER GYQLKPHEPM
NEAAYLEVSV VLDVMCSPLI AEDDIVSQLP ETCIVSCEYD ALRDNSLLYK KRLEDLGVPV
TWHHMEDGFH GVLRTIDMSF LHFPCSMRIL SALVQFVKGL *

speed

0.77 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: 0.999999232665711 (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)

chr1:12785494G>TN/A show variant in all transcripts IGV

HGNC symbol

AADACL3

Ensembl transcript ID

ENST00000359318

Genbank transcript ID

NM_001103170

UniProt peptide

Q5VUY0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.584G>T
cDNA.789G>T
g.9377G>T

AA changes

C195F Score: 205 explain score(s)

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

195

frameshift

known variant

Reference ID: rs7513079

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1212	993	2205
ExAC	31393	-30019	1374

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.839	0.062
	0.683	0.04
(flanking)	0.41	0.012

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 increased	9380	wt: 0.29 / mu: 0.42	wt: GAGTTTCATCTGCTACTGTTTTTTTCAAAACCTGGATTTCA mu: GAGTTTCATCTGCTACTTTTTTTTTCAAAACCTGGATTTCA	gttt\|TTTT
Acc increased	9383	wt: 0.71 / mu: 0.94	wt: TTTCATCTGCTACTGTTTTTTTCAAAACCTGGATTTCAGCT mu: TTTCATCTGCTACTTTTTTTTTCAAAACCTGGATTTCAGCT	tttt\|TCAA
Acc marginally increased	9377	wt: 0.7206 / mu: 0.7451 (marginal change - not scored)	wt: CTGGAGTTTCATCTGCTACTGTTTTTTTCAAAACCTGGATT mu: CTGGAGTTTCATCTGCTACTTTTTTTTTCAAAACCTGGATT	actg\|TTTT
Acc marginally increased	9386	wt: 0.9718 / mu: 0.9939 (marginal change - not scored)	wt: CATCTGCTACTGTTTTTTTCAAAACCTGGATTTCAGCTCCT mu: CATCTGCTACTTTTTTTTTCAAAACCTGGATTTCAGCTCCT	ttca\|AAAC
Acc increased	9385	wt: 0.85 / mu: 0.97	wt: TCATCTGCTACTGTTTTTTTCAAAACCTGGATTTCAGCTCC mu: TCATCTGCTACTTTTTTTTTCAAAACCTGGATTTCAGCTCC	tttc\|AAAA
Acc increased	9382	wt: 0.67 / mu: 0.97	wt: GTTTCATCTGCTACTGTTTTTTTCAAAACCTGGATTTCAGC mu: GTTTCATCTGCTACTTTTTTTTTCAAAACCTGGATTTCAGC	tttt\|TTCA
Acc marginally increased	9387	wt: 0.9462 / mu: 0.9872 (marginal change - not scored)	wt: ATCTGCTACTGTTTTTTTCAAAACCTGGATTTCAGCTCCTC mu: ATCTGCTACTTTTTTTTTCAAAACCTGGATTTCAGCTCCTC	tcaa\|AACC
Acc increased	9384	wt: 0.71 / mu: 0.90	wt: TTCATCTGCTACTGTTTTTTTCAAAACCTGGATTTCAGCTC mu: TTCATCTGCTACTTTTTTTTTCAAAACCTGGATTTCAGCTC	tttt\|CAAA
Acc marginally increased	9374	wt: 0.2630 / mu: 0.2702 (marginal change - not scored)	wt: CACCTGGAGTTTCATCTGCTACTGTTTTTTTCAAAACCTGG mu: CACCTGGAGTTTCATCTGCTACTTTTTTTTTCAAAACCTGG	gcta\|CTGT
Acc increased	9388	wt: 0.80 / mu: 0.91	wt: TCTGCTACTGTTTTTTTCAAAACCTGGATTTCAGCTCCTCC mu: TCTGCTACTTTTTTTTTCAAAACCTGGATTTCAGCTCCTCC	caaa\|ACCT
Acc gained	9381	0.64	mu: AGTTTCATCTGCTACTTTTTTTTTCAAAACCTGGATTTCAG	tttt\|TTTC

distance from splice site

306

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

195

mutated

not conserved

195

Ptroglodytes

all identical

ENSPTRG00000000168

195

Mmulatta

all identical

ENSMMUG00000012080

197

Fcatus

all identical

ENSFCAG00000000578

195

Mmusculus

all identical

ENSMUSG00000078507

253

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000044802

265

Dmelanogaster

no homologue

Celegans

not conserved

Y43F8A.3

262

LYAGI

Xtropicalis

not conserved

ENSXETG00000001384

269

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1053 / 1053

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

351 / 351

position of stopcodon in wt / mu cDNA

1258 / 1258

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

206 / 206

chromosome

strand

last intron/exon boundary

484

theoretical NMD boundary in CDS

228

length of CDS

1053

coding sequence (CDS) position

584

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

789

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

9377

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

12785494

original gDNA sequence snippet

CTGGAGTTTCATCTGCTACTGTTTTTTTCAAAACCTGGATT

altered gDNA sequence snippet

CTGGAGTTTCATCTGCTACTTTTTTTTTCAAAACCTGGATT

original cDNA sequence snippet

CTGGAGTTTCATCTGCTACTGTTTTTTTCAAAACCTGGATT

altered cDNA sequence snippet

CTGGAGTTTCATCTGCTACTTTTTTTTTCAAAACCTGGATT

wildtype AA sequence

MIFEKLRICS MPQFFCFMQD LPPLKYDPDV VVTDFRFGTI PVKLYQSKAS TCTLKPGIVY
YHGGGGVMGS LKTHHGICSR LCKESDSVVL AVGYRKLPKH KFPVPVRDCL VATIHFLKSL
DAYGVDPARV VVCGDSFGGA IAAVVCQQLV DRPDLPRIRA QILIYAILQA LDLQTPSFQQ
RKNIPLLTWS FICYCFFQNL DFSSSWQEVI MKGAHLPAEV WEKYRKWLGP ENIPERFKER
GYQLKPHEPM NEAAYLEVSV VLDVMCSPLI AEDDIVSQLP ETCIVSCEYD ALRDNSLLYK
KRLEDLGVPV TWHHMEDGFH GVLRTIDMSF LHFPCSMRIL SALVQFVKGL *

mutated AA sequence

MIFEKLRICS MPQFFCFMQD LPPLKYDPDV VVTDFRFGTI PVKLYQSKAS TCTLKPGIVY
YHGGGGVMGS LKTHHGICSR LCKESDSVVL AVGYRKLPKH KFPVPVRDCL VATIHFLKSL
DAYGVDPARV VVCGDSFGGA IAAVVCQQLV DRPDLPRIRA QILIYAILQA LDLQTPSFQQ
RKNIPLLTWS FICYFFFQNL DFSSSWQEVI MKGAHLPAEV WEKYRKWLGP ENIPERFKER
GYQLKPHEPM NEAAYLEVSV VLDVMCSPLI AEDDIVSQLP ETCIVSCEYD ALRDNSLLYK
KRLEDLGVPV TWHHMEDGFH GVLRTIDMSF LHFPCSMRIL SALVQFVKGL *

speed

1.00 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems