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: ENST00000391945
Querying Taster for transcript #2: ENST00000391944
MT speed 0 s - this script 3.744511 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ERCC2	disease_causing_automatic	0.999999999963764	simple_aae		affected	0	L407P	single base exchange	rs121913025		show file
ERCC2	disease_causing_automatic	0.99999999997217	simple_aae		affected	0	L485P	single base exchange	rs121913025		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999963764 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM013388)
known disease mutation: rs16791 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:45860553A>GN/A show variant in all transcripts IGV

HGNC symbol

ERCC2

Ensembl transcript ID

ENST00000391944

Genbank transcript ID

N/A

UniProt peptide

P18074

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1220T>C
cDNA.1248T>C
g.13624T>C

AA changes

L407P Score: 98 explain score(s)

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

407

frameshift

known variant

Reference ID: rs121913025
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs16791 (pathogenic for Xeroderma pigmentosum, group D) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM013388)

known disease mutation at this position, please check HGMD for details (HGMD ID CM013388)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013388)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.074	1
	3.836	1
(flanking)	1.531	0.946

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	13618	wt: 0.53 / mu: 0.63	wt: CACCATGGCAACCTTCACCATGACGCTGGCACGGGTCTGCC mu: CACCATGGCAACCTTCACCATGACGCCGGCACGGGTCTGCC	ccat\|GACG
Donor increased	13624	wt: 0.73 / mu: 0.83	wt: GACGCTGGCACGGGT mu: GACGCCGGCACGGGT	CGCT\|ggca
Donor increased	13616	wt: 0.65 / mu: 0.88	wt: TTCACCATGACGCTG mu: TTCACCATGACGCCG	CACC\|atga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

407

mutated

not conserved

407

Ptroglodytes

all identical

ENSPTRG00000011149

485

Mmulatta

all identical

ENSMMUG00000014419

483

Fcatus

all identical

ENSFCAG00000002679

497

Mmusculus

all identical

ENSMUSG00000030400

485

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000007303

485

Drerio

all identical

ENSDARG00000021985

485

Dmelanogaster

all identical

FBgn0261850

485

Celegans

no alignment

Y50D7A.11

n/a

Xtropicalis

not conserved

ENSXETG00000018229

483

protein features

start (aa)	end (aa)	feature	details
438	637	REGION	Mediates interaction with MMS19.	might get lost (downstream of altered splice site)
682	695	MOTIF	Nuclear localization signal (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2049 / 2049

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

683 / 683

position of stopcodon in wt / mu cDNA

2077 / 2077

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

29 / 29

chromosome

strand

-1

last intron/exon boundary

1985

theoretical NMD boundary in CDS

1906

length of CDS

2049

coding sequence (CDS) position

1220

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

1248

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

13624

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

45860553

original gDNA sequence snippet

GGCAACCTTCACCATGACGCTGGCACGGGTCTGCCTCTGCC

altered gDNA sequence snippet

GGCAACCTTCACCATGACGCCGGCACGGGTCTGCCTCTGCC

original cDNA sequence snippet

GGCAACCTTCACCATGACGCTGGCACGGGTCTGCCTCTGCC

altered cDNA sequence snippet

GGCAACCTTCACCATGACGCCGGCACGGGTCTGCCTCTGCC

wildtype AA sequence

MKLNVDGLLV YFPYDYIYPE QFSYMRELKR TLDAKGHGVL EMPSGTGKTV SLLALIMAYQ
RAYPLEVTKL IYCSRTVPEI EKVIEELRKL LNFYEKQEGE KLPFLGLALS SRKNLCIHPE
ILHANVVVYS YHYLLDPKIA DLVSKELARK AVVVFDEAHN IDNVCIDSMS VNLTRRTLDR
CQGNLETLQK TVLRIKETDE QRLRDEYRRL VEGLREASAA RETDAHLANP VLPDEVLQEA
VPGSIRTAEH FLGFLRRLLE YVKWRLRVQH VVQESPPAFL SGLAQRVCIQ RKPLRFCAER
LRSLLHTLEI TDLADFSPLT LLANFATLVS TYAKGFTIII EPFDDRTPTI ANPILHFSCM
DASLAIKPVF ERFQSVIITS GTLSPLDIYP KILDFHPVTM ATFTMTLARV CLCPMIIGRG
NDQVAISSKF ETREDIAVIR NYGNLLLEMS AVVPDGIVAF FTSYQYMEST VASWYEQGIL
ENIQRNKLLF IETQDGAETS VALEKYQEAC ENGRGAILLS VARGKVSEGI DFVHHYGRAV
IMFGVPYVYT QSRILKARLE YLRDQFQIRE NDFLTFDAMR HAAQCVGRAI RGKTDYGLMV
FADKRFARGD KRGKLPRWIQ EHLTDANLNL TVDEGVQVAK YFLRQMAQPF HREDQLGLSL
LSLEQLESEE TLKRIEQIAQ QL*

mutated AA sequence

MKLNVDGLLV YFPYDYIYPE QFSYMRELKR TLDAKGHGVL EMPSGTGKTV SLLALIMAYQ
RAYPLEVTKL IYCSRTVPEI EKVIEELRKL LNFYEKQEGE KLPFLGLALS SRKNLCIHPE
ILHANVVVYS YHYLLDPKIA DLVSKELARK AVVVFDEAHN IDNVCIDSMS VNLTRRTLDR
CQGNLETLQK TVLRIKETDE QRLRDEYRRL VEGLREASAA RETDAHLANP VLPDEVLQEA
VPGSIRTAEH FLGFLRRLLE YVKWRLRVQH VVQESPPAFL SGLAQRVCIQ RKPLRFCAER
LRSLLHTLEI TDLADFSPLT LLANFATLVS TYAKGFTIII EPFDDRTPTI ANPILHFSCM
DASLAIKPVF ERFQSVIITS GTLSPLDIYP KILDFHPVTM ATFTMTPARV CLCPMIIGRG
NDQVAISSKF ETREDIAVIR NYGNLLLEMS AVVPDGIVAF FTSYQYMEST VASWYEQGIL
ENIQRNKLLF IETQDGAETS VALEKYQEAC ENGRGAILLS VARGKVSEGI DFVHHYGRAV
IMFGVPYVYT QSRILKARLE YLRDQFQIRE NDFLTFDAMR HAAQCVGRAI RGKTDYGLMV
FADKRFARGD KRGKLPRWIQ EHLTDANLNL TVDEGVQVAK YFLRQMAQPF HREDQLGLSL
LSLEQLESEE TLKRIEQIAQ QL*

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

disease causing

Model: simple_aae, prob: 0.99999999997217 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM013388)
known disease mutation: rs16791 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:45860553A>GN/A show variant in all transcripts IGV

HGNC symbol

ERCC2

Ensembl transcript ID

ENST00000391945

Genbank transcript ID

NM_000400

UniProt peptide

P18074

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1454T>C
cDNA.1532T>C
g.13624T>C

AA changes

L485P Score: 98 explain score(s)

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

485

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.074	1
	3.836	1
(flanking)	1.531	0.946

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	13618	wt: 0.53 / mu: 0.63	wt: CACCATGGCAACCTTCACCATGACGCTGGCACGGGTCTGCC mu: CACCATGGCAACCTTCACCATGACGCCGGCACGGGTCTGCC	ccat\|GACG
Donor increased	13624	wt: 0.73 / mu: 0.83	wt: GACGCTGGCACGGGT mu: GACGCCGGCACGGGT	CGCT\|ggca
Donor increased	13616	wt: 0.65 / mu: 0.88	wt: TTCACCATGACGCTG mu: TTCACCATGACGCCG	CACC\|atga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

485

mutated

not conserved

485

Ptroglodytes

all identical

ENSPTRG00000011149

485

Mmulatta

all identical

ENSMMUG00000014419

483

Fcatus

all identical

ENSFCAG00000002679

497

Mmusculus

all identical

ENSMUSG00000030400

485

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000007303

485

Drerio

all identical

ENSDARG00000021985

485

Dmelanogaster

all identical

FBgn0261850

485

Celegans

no alignment

Y50D7A.11

n/a

Xtropicalis

not conserved

ENSXETG00000018229

483

protein features

start (aa)	end (aa)	feature	details
438	637	REGION	Mediates interaction with MMS19.	lost
682	695	MOTIF	Nuclear localization signal (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2283 / 2283

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

761 / 761

position of stopcodon in wt / mu cDNA

2361 / 2361

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

79 / 79

chromosome

strand

-1

last intron/exon boundary

2269

theoretical NMD boundary in CDS

2140

length of CDS

2283

coding sequence (CDS) position

1454

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

1532

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

13624

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

45860553

original gDNA sequence snippet

GGCAACCTTCACCATGACGCTGGCACGGGTCTGCCTCTGCC

altered gDNA sequence snippet

GGCAACCTTCACCATGACGCCGGCACGGGTCTGCCTCTGCC

original cDNA sequence snippet

GGCAACCTTCACCATGACGCTGGCACGGGTCTGCCTCTGCC

altered cDNA sequence snippet

GGCAACCTTCACCATGACGCCGGCACGGGTCTGCCTCTGCC

wildtype AA sequence

MKLNVDGLLV YFPYDYIYPE QFSYMRELKR TLDAKGHGVL EMPSGTGKTV SLLALIMAYQ
RAYPLEVTKL IYCSRTVPEI EKVIEELRKL LNFYEKQEGE KLPFLGLALS SRKNLCIHPE
VTPLRFGKDV DGKCHSLTAS YVRAQYQHDT SLPHCRFYEE FDAHGREVPL PAGIYNLDDL
KALGRRQGWC PYFLARYSIL HANVVVYSYH YLLDPKIADL VSKELARKAV VVFDEAHNID
NVCIDSMSVN LTRRTLDRCQ GNLETLQKTV LRIKETDEQR LRDEYRRLVE GLREASAARE
TDAHLANPVL PDEVLQEAVP GSIRTAEHFL GFLRRLLEYV KWRLRVQHVV QESPPAFLSG
LAQRVCIQRK PLRFCAERLR SLLHTLEITD LADFSPLTLL ANFATLVSTY AKGFTIIIEP
FDDRTPTIAN PILHFSCMDA SLAIKPVFER FQSVIITSGT LSPLDIYPKI LDFHPVTMAT
FTMTLARVCL CPMIIGRGND QVAISSKFET REDIAVIRNY GNLLLEMSAV VPDGIVAFFT
SYQYMESTVA SWYEQGILEN IQRNKLLFIE TQDGAETSVA LEKYQEACEN GRGAILLSVA
RGKVSEGIDF VHHYGRAVIM FGVPYVYTQS RILKARLEYL RDQFQIREND FLTFDAMRHA
AQCVGRAIRG KTDYGLMVFA DKRFARGDKR GKLPRWIQEH LTDANLNLTV DEGVQVAKYF
LRQMAQPFHR EDQLGLSLLS LEQLESEETL KRIEQIAQQL *

mutated AA sequence

MKLNVDGLLV YFPYDYIYPE QFSYMRELKR TLDAKGHGVL EMPSGTGKTV SLLALIMAYQ
RAYPLEVTKL IYCSRTVPEI EKVIEELRKL LNFYEKQEGE KLPFLGLALS SRKNLCIHPE
VTPLRFGKDV DGKCHSLTAS YVRAQYQHDT SLPHCRFYEE FDAHGREVPL PAGIYNLDDL
KALGRRQGWC PYFLARYSIL HANVVVYSYH YLLDPKIADL VSKELARKAV VVFDEAHNID
NVCIDSMSVN LTRRTLDRCQ GNLETLQKTV LRIKETDEQR LRDEYRRLVE GLREASAARE
TDAHLANPVL PDEVLQEAVP GSIRTAEHFL GFLRRLLEYV KWRLRVQHVV QESPPAFLSG
LAQRVCIQRK PLRFCAERLR SLLHTLEITD LADFSPLTLL ANFATLVSTY AKGFTIIIEP
FDDRTPTIAN PILHFSCMDA SLAIKPVFER FQSVIITSGT LSPLDIYPKI LDFHPVTMAT
FTMTPARVCL CPMIIGRGND QVAISSKFET REDIAVIRNY GNLLLEMSAV VPDGIVAFFT
SYQYMESTVA SWYEQGILEN IQRNKLLFIE TQDGAETSVA LEKYQEACEN GRGAILLSVA
RGKVSEGIDF VHHYGRAVIM FGVPYVYTQS RILKARLEYL RDQFQIREND FLTFDAMRHA
AQCVGRAIRG KTDYGLMVFA DKRFARGDKR GKLPRWIQEH LTDANLNLTV DEGVQVAKYF
LRQMAQPFHR EDQLGLSLLS LEQLESEETL KRIEQIAQQL *

speed

0.49 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems