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: ENST00000371224
Querying Taster for transcript #2: ENST00000371221
MT speed 0 s - this script 3.427628 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ALDH18A1	disease_causing_automatic	0.999999999530496	simple_aae		affected	0	H784Y	single base exchange	rs121434583		show file
ALDH18A1	disease_causing_automatic	0.999999999530496	simple_aae		affected	0	H782Y	single base exchange	rs121434583		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999530496 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM085228)
known disease mutation: rs16086 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:97366557G>AN/A show variant in all transcripts IGV

HGNC symbol

ALDH18A1

Ensembl transcript ID

ENST00000371224

Genbank transcript ID

NM_002860

UniProt peptide

P54886

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2350C>T
cDNA.2488C>T
g.49907C>T

AA changes

H784Y Score: 83 explain score(s)

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

784

frameshift

known variant

Reference ID: rs121434583
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs16086 (pathogenic for Cutis laxa, autosomal recessive IIIA) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM085228)

known disease mutation at this position, please check HGMD for details (HGMD ID CM085228)
known disease mutation at this position, please check HGMD for details (HGMD ID CM085228)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.146	1
	5.003	1
(flanking)	0.98	1

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 gained	49911	0.46	mu: AAGTTTAAAATATCTTTATGAGAACCTCCCTATTCCTCAGA	atga\|GAAC

distance from splice site

144

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

784

mutated

all conserved

784

Ptroglodytes

all identical

ENSPTRG00000002785

768

Mmulatta

all identical

ENSMMUG00000003102

784

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000025007

784

Ggallus

all identical

ENSGALG00000010522

797

Trubripes

all identical

ENSTRUG00000017580

791

Drerio

all identical

ENSDARG00000061123

768

Dmelanogaster

all identical

FBgn0037146

770

Celegans

all identical

T22H6.2

779

Xtropicalis

all identical

ENSXETG00000022613

786

protein features

start (aa)	end (aa)	feature	details
362	795	REGION	Gamma-glutamyl phosphate reductase.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2388 / 2388

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

796 / 796

position of stopcodon in wt / mu cDNA

2526 / 2526

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

139 / 139

chromosome

strand

-1

last intron/exon boundary

2345

theoretical NMD boundary in CDS

2156

length of CDS

2388

coding sequence (CDS) position

2350

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

2488

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

49907

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

97366557

original gDNA sequence snippet

ATGGAAGTTTAAAATATCTTCATGAGAACCTCCCTATTCCT

altered gDNA sequence snippet

ATGGAAGTTTAAAATATCTTTATGAGAACCTCCCTATTCCT

original cDNA sequence snippet

ATGGAAGTTTAAAATATCTTCATGAGAACCTCCCTATTCCT

altered cDNA sequence snippet

ATGGAAGTTTAAAATATCTTTATGAGAACCTCCCTATTCCT

wildtype AA sequence

MLSQVYRCGF QPFNQHLLPW VKCTTVFRSH CIQPSVIRHV RSWSNIPFIT VPLSRTHGKS
FAHRSELKHA KRIVVKLGSA VVTRGDECGL ALGRLASIVE QVSVLQNQGR EMMLVTSGAV
AFGKQRLRHE ILLSQSVRQA LHSGQNQLKE MAIPVLEARA CAAAGQSGLM ALYEAMFTQY
SICAAQILVT NLDFHDEQKR RNLNGTLHEL LRMNIVPIVN TNDAVVPPAE PNSDLQGVNV
ISVKDNDSLA ARLAVEMKTD LLIVLSDVEG LFDSPPGSDD AKLIDIFYPG DQQSVTFGTK
SRVGMGGMEA KVKAALWALQ GGTSVVIANG THPKVSGHVI TDIVEGKKVG TFFSEVKPAG
PTVEQQGEMA RSGGRMLATL EPEQRAEIIH HLADLLTDQR DEILLANKKD LEEAEGRLAA
PLLKRLSLST SKLNSLAIGL RQIAASSQDS VGRVLRRTRI AKNLELEQVT VPIGVLLVIF
ESRPDCLPQV AALAIASGNG LLLKGGKEAA HSNRILHLLT QEALSIHGVK EAVQLVNTRE
EVEDLCRLDK MIDLIIPRGS SQLVRDIQKA AKGIPVMGHS EGICHMYVDS EASVDKVTRL
VRDSKCEYPA ACNALETLLI HRDLLRTPLF DQIIDMLRVE QVKIHAGPKF ASYLTFSPSE
VKSLRTEYGD LELCIEVVDN VQDAIDHIHK YGSSHTDVIV TEDENTAEFF LQHVDSACVF
WNASTRFSDG YRFGLGAEVG ISTSRIHARG PVGLEGLLTT KWLLRGKDHV VSDFSEHGSL
KYLHENLPIP QRNTN*

mutated AA sequence

speed

0.62 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

disease causing

Model: simple_aae, prob: 0.999999999530496 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM085228)
known disease mutation: rs16086 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:97366557G>AN/A show variant in all transcripts IGV

HGNC symbol

ALDH18A1

Ensembl transcript ID

ENST00000371221

Genbank transcript ID

NM_001017423

UniProt peptide

P54886

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2344C>T
cDNA.2482C>T
g.49907C>T

AA changes

H782Y Score: 83 explain score(s)

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

782

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.146	1
	5.003	1
(flanking)	0.98	1

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 gained	49911	0.46	mu: AAGTTTAAAATATCTTTATGAGAACCTCCCTATTCCTCAGA	atga\|GAAC

distance from splice site

144

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

782

mutated

all conserved

782

Ptroglodytes

all identical

ENSPTRG00000002785

768

Mmulatta

all identical

ENSMMUG00000003102

784

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000025007

784

Ggallus

all identical

ENSGALG00000010522

797

Trubripes

all identical

ENSTRUG00000017580

791

Drerio

all identical

ENSDARG00000061123

768

Dmelanogaster

all identical

FBgn0037146

770

Celegans

all identical

T22H6.2

779

Xtropicalis

all identical

ENSXETG00000022613

786

protein features

start (aa)	end (aa)	feature	details
362	795	REGION	Gamma-glutamyl phosphate reductase.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2382 / 2382

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

794 / 794

position of stopcodon in wt / mu cDNA

2520 / 2520

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

139 / 139

chromosome

strand

-1

last intron/exon boundary

2339

theoretical NMD boundary in CDS

2150

length of CDS

2382

coding sequence (CDS) position

2344

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

2482

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

49907

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

97366557

original gDNA sequence snippet

ATGGAAGTTTAAAATATCTTCATGAGAACCTCCCTATTCCT

altered gDNA sequence snippet

ATGGAAGTTTAAAATATCTTTATGAGAACCTCCCTATTCCT

original cDNA sequence snippet

ATGGAAGTTTAAAATATCTTCATGAGAACCTCCCTATTCCT

altered cDNA sequence snippet

ATGGAAGTTTAAAATATCTTTATGAGAACCTCCCTATTCCT

wildtype AA sequence

MLSQVYRCGF QPFNQHLLPW VKCTTVFRSH CIQPSVIRHV RSWSNIPFIT VPLSRTHGKS
FAHRSELKHA KRIVVKLGSA VVTRGDECGL ALGRLASIVE QVSVLQNQGR EMMLVTSGAV
AFGKQRLRHE ILLSQSVRQA LHSGQNQLKE MAIPVLEARA CAAAGQSGLM ALYEAMFTQY
SICAAQILVT NLDFHDEQKR RNLNGTLHEL LRMNIVPIVN TNDAVVPPAE PNSDLQGVIS
VKDNDSLAAR LAVEMKTDLL IVLSDVEGLF DSPPGSDDAK LIDIFYPGDQ QSVTFGTKSR
VGMGGMEAKV KAALWALQGG TSVVIANGTH PKVSGHVITD IVEGKKVGTF FSEVKPAGPT
VEQQGEMARS GGRMLATLEP EQRAEIIHHL ADLLTDQRDE ILLANKKDLE EAEGRLAAPL
LKRLSLSTSK LNSLAIGLRQ IAASSQDSVG RVLRRTRIAK NLELEQVTVP IGVLLVIFES
RPDCLPQVAA LAIASGNGLL LKGGKEAAHS NRILHLLTQE ALSIHGVKEA VQLVNTREEV
EDLCRLDKMI DLIIPRGSSQ LVRDIQKAAK GIPVMGHSEG ICHMYVDSEA SVDKVTRLVR
DSKCEYPAAC NALETLLIHR DLLRTPLFDQ IIDMLRVEQV KIHAGPKFAS YLTFSPSEVK
SLRTEYGDLE LCIEVVDNVQ DAIDHIHKYG SSHTDVIVTE DENTAEFFLQ HVDSACVFWN
ASTRFSDGYR FGLGAEVGIS TSRIHARGPV GLEGLLTTKW LLRGKDHVVS DFSEHGSLKY
LHENLPIPQR NTN*

mutated AA sequence

MLSQVYRCGF QPFNQHLLPW VKCTTVFRSH CIQPSVIRHV RSWSNIPFIT VPLSRTHGKS
FAHRSELKHA KRIVVKLGSA VVTRGDECGL ALGRLASIVE QVSVLQNQGR EMMLVTSGAV
AFGKQRLRHE ILLSQSVRQA LHSGQNQLKE MAIPVLEARA CAAAGQSGLM ALYEAMFTQY
SICAAQILVT NLDFHDEQKR RNLNGTLHEL LRMNIVPIVN TNDAVVPPAE PNSDLQGVIS
VKDNDSLAAR LAVEMKTDLL IVLSDVEGLF DSPPGSDDAK LIDIFYPGDQ QSVTFGTKSR
VGMGGMEAKV KAALWALQGG TSVVIANGTH PKVSGHVITD IVEGKKVGTF FSEVKPAGPT
VEQQGEMARS GGRMLATLEP EQRAEIIHHL ADLLTDQRDE ILLANKKDLE EAEGRLAAPL
LKRLSLSTSK LNSLAIGLRQ IAASSQDSVG RVLRRTRIAK NLELEQVTVP IGVLLVIFES
RPDCLPQVAA LAIASGNGLL LKGGKEAAHS NRILHLLTQE ALSIHGVKEA VQLVNTREEV
EDLCRLDKMI DLIIPRGSSQ LVRDIQKAAK GIPVMGHSEG ICHMYVDSEA SVDKVTRLVR
DSKCEYPAAC NALETLLIHR DLLRTPLFDQ IIDMLRVEQV KIHAGPKFAS YLTFSPSEVK
SLRTEYGDLE LCIEVVDNVQ DAIDHIHKYG SSHTDVIVTE DENTAEFFLQ HVDSACVFWN
ASTRFSDGYR FGLGAEVGIS TSRIHARGPV GLEGLLTTKW LLRGKDHVVS DFSEHGSLKY
LYENLPIPQR NTN*

speed

0.82 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems