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: ENST00000411641
Querying Taster for transcript #2: ENST00000273784
MT speed 0 s - this script 4.649049 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
AHSG	polymorphism_automatic	9.99200722162641e-16	simple_aae		affected		S256T	single base exchange	rs4918		show file
AHSG	polymorphism_automatic	9.99200722162641e-16	simple_aae		affected		S257T	single base exchange	rs4918		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999999 (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 CM052828)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:186338382G>CN/A show variant in all transcripts IGV

HGNC symbol

AHSG

Ensembl transcript ID

ENST00000411641

Genbank transcript ID

NM_001622

UniProt peptide

P02765

alteration type

single base exchange

alteration region

CDS

DNA changes

c.767G>C
cDNA.986G>C
g.7671G>C

AA changes

S256T Score: 58 explain score(s)

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

256

frameshift

known variant

Reference ID: rs4918

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1289	996	2285
ExAC	27901	-23035	4866

known disease mutation at this position, please check HGMD for details (HGMD ID CM052828)

regulatory features

Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
FOSL2, Transcription Factor, FOSL2 Transcription Factor Binding
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Jund, Transcription Factor, Jund TF binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.55	0
	-0.699	0
(flanking)	-0.491	0

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 decreased	7663	wt: 0.68 / mu: 0.53	wt: AGGAAATGGTCCTTTTTCCAGCCCGTGAGCTCACAGCCCCA mu: AGGAAATGGTCCTTTTTCCAGCCCGTGACCTCACAGCCCCA	ccag\|CCCG
Acc marginally increased	7668	wt: 0.8268 / mu: 0.8827 (marginal change - not scored)	wt: ATGGTCCTTTTTCCAGCCCGTGAGCTCACAGCCCCAACCAG mu: ATGGTCCTTTTTCCAGCCCGTGACCTCACAGCCCCAACCAG	ccgt\|GAGC
Acc marginally increased	7666	wt: 0.9684 / mu: 0.9717 (marginal change - not scored)	wt: AAATGGTCCTTTTTCCAGCCCGTGAGCTCACAGCCCCAACC mu: AAATGGTCCTTTTTCCAGCCCGTGACCTCACAGCCCCAACC	gccc\|GTGA
Acc marginally increased	7661	wt: 0.6992 / mu: 0.7279 (marginal change - not scored)	wt: GAAGGAAATGGTCCTTTTTCCAGCCCGTGAGCTCACAGCCC mu: GAAGGAAATGGTCCTTTTTCCAGCCCGTGACCTCACAGCCC	ttcc\|AGCC
Acc marginally increased	7662	wt: 0.6581 / mu: 0.6846 (marginal change - not scored)	wt: AAGGAAATGGTCCTTTTTCCAGCCCGTGAGCTCACAGCCCC mu: AAGGAAATGGTCCTTTTTCCAGCCCGTGACCTCACAGCCCC	tcca\|GCCC
Donor increased	7666	wt: 0.22 / mu: 0.76	wt: CAGCCCGTGAGCTCA mu: CAGCCCGTGACCTCA	GCCC\|gtga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

256

mutated

all conserved

256

Ptroglodytes

all conserved

ENSPTRG00000015714

256

Mmulatta

all conserved

ENSMMUG00000017567

256

Fcatus

not conserved

ENSFCAG00000012056

256

Mmusculus

not conserved

ENSMUSG00000022868

256

Ggallus

not conserved

ENSGALG00000008601

257

Trubripes

not conserved

ENSTRUG00000009139

261

Drerio

not conserved

ENSDARG00000069293

285

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000019385

253

protein features

start (aa)	end (aa)	feature	details
144	255	DOMAIN	Cystatin fetuin-A-type 2.	might get lost (downstream of altered splice site)
256	256	CARBOHYD	O-linked (GalNAc...). /FTId=CAR_000066.	lost
270	270	CARBOHYD	O-linked (GalNAc...). /FTId=CAR_000067.	might get lost (downstream of altered splice site)
301	340	PROPEP	Connecting peptide. /FTId=PRO_0000008888.	might get lost (downstream of altered splice site)
325	325	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
328	328	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
330	330	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
334	334	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
346	346	CARBOHYD	O-linked (GalNAc...). /FTId=CAR_000068.	might get lost (downstream of altered splice site)
358	358	DISULFID	Interchain (between A and B chains).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1104 / 1104

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

368 / 368

position of stopcodon in wt / mu cDNA

1323 / 1323

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

220 / 220

chromosome

strand

last intron/exon boundary

979

theoretical NMD boundary in CDS

709

length of CDS

1104

coding sequence (CDS) position

767

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

986

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

7671

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

186338382

original gDNA sequence snippet

GTCCTTTTTCCAGCCCGTGAGCTCACAGCCCCAACCAGAAG

altered gDNA sequence snippet

GTCCTTTTTCCAGCCCGTGACCTCACAGCCCCAACCAGAAG

original cDNA sequence snippet

GTTCCAAACACAGCCCGTGAGCTCACAGCCCCAACCAGAAG

altered cDNA sequence snippet

GTTCCAAACACAGCCCGTGACCTCACAGCCCCAACCAGAAG

wildtype AA sequence

MKSLVLLLCL AQLWGCHSAP HGPGLIYRQP NCDDPETEEA ALVAIDYINQ NLPWGYKHTL
NQIDEVKVWP QQPSGELFEI EIDTLETTCH VLDPTPVARC SVRQLKEHAV EGDCDFQLLK
LDGKFSVVYA KCDSSPDSAE DVRKVCQDCP LLAPLNDTRV VHAAKAALAA FNAQNNGSNF
QLEEISRAQL VPLPPSTYVE FTVSGTDCVA KEATEAAKCN LLAEKQYGFC KATLSEKLGG
AEVAVTCMVF QTQPVSSQPQ PEGANEAVPT PVVDPDAPPS PPLGAPGLPP AGSPPDSHVL
LAAPPGHQLH RAHYDLRHTF MGVVSLGSPS GEVSHPRKTR TVVQPSVGAA AGPVVPPCPG
RIRHFKV*

mutated AA sequence

MKSLVLLLCL AQLWGCHSAP HGPGLIYRQP NCDDPETEEA ALVAIDYINQ NLPWGYKHTL
NQIDEVKVWP QQPSGELFEI EIDTLETTCH VLDPTPVARC SVRQLKEHAV EGDCDFQLLK
LDGKFSVVYA KCDSSPDSAE DVRKVCQDCP LLAPLNDTRV VHAAKAALAA FNAQNNGSNF
QLEEISRAQL VPLPPSTYVE FTVSGTDCVA KEATEAAKCN LLAEKQYGFC KATLSEKLGG
AEVAVTCMVF QTQPVTSQPQ PEGANEAVPT PVVDPDAPPS PPLGAPGLPP AGSPPDSHVL
LAAPPGHQLH RAHYDLRHTF MGVVSLGSPS GEVSHPRKTR TVVQPSVGAA AGPVVPPCPG
RIRHFKV*

speed

1.31 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: 0.999999999999999 (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 CM052828)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:186338382G>CN/A show variant in all transcripts IGV

HGNC symbol

AHSG

Ensembl transcript ID

ENST00000273784

Genbank transcript ID

N/A

UniProt peptide

P02765

alteration type

single base exchange

alteration region

CDS

DNA changes

c.770G>C
cDNA.846G>C
g.7671G>C

AA changes

S257T Score: 58 explain score(s)

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

257

frameshift

known variant

Reference ID: rs4918

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1289	996	2285
ExAC	27901	-23035	4866

known disease mutation at this position, please check HGMD for details (HGMD ID CM052828)

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.55	0
	-0.699	0
(flanking)	-0.491	0

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 decreased	7663	wt: 0.68 / mu: 0.53	wt: AGGAAATGGTCCTTTTTCCAGCCCGTGAGCTCACAGCCCCA mu: AGGAAATGGTCCTTTTTCCAGCCCGTGACCTCACAGCCCCA	ccag\|CCCG
Acc marginally increased	7668	wt: 0.8268 / mu: 0.8827 (marginal change - not scored)	wt: ATGGTCCTTTTTCCAGCCCGTGAGCTCACAGCCCCAACCAG mu: ATGGTCCTTTTTCCAGCCCGTGACCTCACAGCCCCAACCAG	ccgt\|GAGC
Acc marginally increased	7666	wt: 0.9684 / mu: 0.9717 (marginal change - not scored)	wt: AAATGGTCCTTTTTCCAGCCCGTGAGCTCACAGCCCCAACC mu: AAATGGTCCTTTTTCCAGCCCGTGACCTCACAGCCCCAACC	gccc\|GTGA
Acc marginally increased	7661	wt: 0.6992 / mu: 0.7279 (marginal change - not scored)	wt: GAAGGAAATGGTCCTTTTTCCAGCCCGTGAGCTCACAGCCC mu: GAAGGAAATGGTCCTTTTTCCAGCCCGTGACCTCACAGCCC	ttcc\|AGCC
Acc marginally increased	7662	wt: 0.6581 / mu: 0.6846 (marginal change - not scored)	wt: AAGGAAATGGTCCTTTTTCCAGCCCGTGAGCTCACAGCCCC mu: AAGGAAATGGTCCTTTTTCCAGCCCGTGACCTCACAGCCCC	tcca\|GCCC
Donor increased	7666	wt: 0.22 / mu: 0.76	wt: CAGCCCGTGAGCTCA mu: CAGCCCGTGACCTCA	GCCC\|gtga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

257

mutated

all conserved

257

Ptroglodytes

all conserved

ENSPTRG00000015714

256

Mmulatta

all conserved

ENSMMUG00000017567

256

Fcatus

not conserved

ENSFCAG00000012056

256

Mmusculus

not conserved

ENSMUSG00000022868

256

Ggallus

not conserved

ENSGALG00000008601

257

Trubripes

not conserved

ENSTRUG00000009139

261

Drerio

not conserved

ENSDARG00000069293

285

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000019385

253

protein features

start (aa)	end (aa)	feature	details
144	255	DOMAIN	Cystatin fetuin-A-type 2.	might get lost (downstream of altered splice site)
256	256	CARBOHYD	O-linked (GalNAc...). /FTId=CAR_000066.	might get lost (downstream of altered splice site)
270	270	CARBOHYD	O-linked (GalNAc...). /FTId=CAR_000067.	might get lost (downstream of altered splice site)
301	340	PROPEP	Connecting peptide. /FTId=PRO_0000008888.	might get lost (downstream of altered splice site)
325	325	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
328	328	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
330	330	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
334	334	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
346	346	CARBOHYD	O-linked (GalNAc...). /FTId=CAR_000068.	might get lost (downstream of altered splice site)
358	358	DISULFID	Interchain (between A and B chains).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1107 / 1107

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

369 / 369

position of stopcodon in wt / mu cDNA

1183 / 1183

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

77 / 77

chromosome

strand

last intron/exon boundary

839

theoretical NMD boundary in CDS

712

length of CDS

1107

coding sequence (CDS) position

770

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

846

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

7671

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

186338382

original gDNA sequence snippet

GTCCTTTTTCCAGCCCGTGAGCTCACAGCCCCAACCAGAAG

altered gDNA sequence snippet

GTCCTTTTTCCAGCCCGTGACCTCACAGCCCCAACCAGAAG

original cDNA sequence snippet

GTTCCAAACACAGCCCGTGAGCTCACAGCCCCAACCAGAAG

altered cDNA sequence snippet

GTTCCAAACACAGCCCGTGACCTCACAGCCCCAACCAGAAG

wildtype AA sequence

MKSLVLLLCL AQLWGCHSAP HGPGLIYRQP NCDDPETEEA ALVAIDYINQ NLPWGYKHTL
NQIDEVKVWP QQPSGELFEI EIDTLETTCH VLDPTPVARC SVRQLKEHAV EGDCDFQLLK
LDGKFSVVYA KCDSSPADSA EDVRKVCQDC PLLAPLNDTR VVHAAKAALA AFNAQNNGSN
FQLEEISRAQ LVPLPPSTYV EFTVSGTDCV AKEATEAAKC NLLAEKQYGF CKATLSEKLG
GAEVAVTCMV FQTQPVSSQP QPEGANEAVP TPVVDPDAPP SPPLGAPGLP PAGSPPDSHV
LLAAPPGHQL HRAHYDLRHT FMGVVSLGSP SGEVSHPRKT RTVVQPSVGA AAGPVVPPCP
GRIRHFKV*

mutated AA sequence

MKSLVLLLCL AQLWGCHSAP HGPGLIYRQP NCDDPETEEA ALVAIDYINQ NLPWGYKHTL
NQIDEVKVWP QQPSGELFEI EIDTLETTCH VLDPTPVARC SVRQLKEHAV EGDCDFQLLK
LDGKFSVVYA KCDSSPADSA EDVRKVCQDC PLLAPLNDTR VVHAAKAALA AFNAQNNGSN
FQLEEISRAQ LVPLPPSTYV EFTVSGTDCV AKEATEAAKC NLLAEKQYGF CKATLSEKLG
GAEVAVTCMV FQTQPVTSQP QPEGANEAVP TPVVDPDAPP SPPLGAPGLP PAGSPPDSHV
LLAAPPGHQL HRAHYDLRHT FMGVVSLGSP SGEVSHPRKT RTVVQPSVGA AAGPVVPPCP
GRIRHFKV*

speed

1.29 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems