MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000448498
Querying Taster for transcript #2: ENST00000423219
Querying Taster for transcript #3: ENST00000273173
MT speed 0 s - this script 3.530814 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SLC22A14	polymorphism_automatic	4.18546221014893e-07	simple_aae		affected		P560R	single base exchange	rs240033		show file
SLC22A14	polymorphism_automatic	4.18546221014893e-07	simple_aae		affected		P560R	single base exchange	rs240033		show file
SLC22A14	polymorphism_automatic	7.36938618017824e-07	simple_aae		affected		P545R	single base exchange	rs240033		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999581453779 (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)

chr3:38357961C>GN/A show variant in all transcripts IGV

HGNC symbol

SLC22A14

Ensembl transcript ID

ENST00000448498

Genbank transcript ID

N/A

UniProt peptide

Q9Y267

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1679C>G
cDNA.1721C>G
g.34177C>G

AA changes

P560R Score: 103 explain score(s)

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

560

frameshift

known variant

Reference ID: rs240033

database	homozygous (G/G)	heterozygous	allele carriers
1000G	163	956	1119
ExAC	4561	23645	28206

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.351	0.009
	0.701	0.007
(flanking)	-1.921	0.001

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 marginally increased	34176	wt: 0.9149 / mu: 0.9793 (marginal change - not scored)	wt: TTTCCCTCTCCTCCCTGCTGCCGGAAACGCGAGATCAGCCC mu: TTTCCCTCTCCTCCCTGCTGCGGGAAACGCGAGATCAGCCC	ctgc\|CGGA
Acc marginally increased	34167	wt: 0.9779 / mu: 0.9837 (marginal change - not scored)	wt: TCGTGGCCTTTTCCCTCTCCTCCCTGCTGCCGGAAACGCGA mu: TCGTGGCCTTTTCCCTCTCCTCCCTGCTGCGGGAAACGCGA	tcct\|CCCT
Acc marginally increased	34170	wt: 0.9860 / mu: 0.9896 (marginal change - not scored)	wt: TGGCCTTTTCCCTCTCCTCCCTGCTGCCGGAAACGCGAGAT mu: TGGCCTTTTCCCTCTCCTCCCTGCTGCGGGAAACGCGAGAT	tccc\|TGCT
Acc marginally increased	34173	wt: 0.9849 / mu: 0.9890 (marginal change - not scored)	wt: CCTTTTCCCTCTCCTCCCTGCTGCCGGAAACGCGAGATCAG mu: CCTTTTCCCTCTCCTCCCTGCTGCGGGAAACGCGAGATCAG	ctgc\|TGCC
Acc marginally increased	34169	wt: 0.9759 / mu: 0.9802 (marginal change - not scored)	wt: GTGGCCTTTTCCCTCTCCTCCCTGCTGCCGGAAACGCGAGA mu: GTGGCCTTTTCCCTCTCCTCCCTGCTGCGGGAAACGCGAGA	ctcc\|CTGC
Acc marginally increased	34171	wt: 0.9941 / mu: 0.9948 (marginal change - not scored)	wt: GGCCTTTTCCCTCTCCTCCCTGCTGCCGGAAACGCGAGATC mu: GGCCTTTTCCCTCTCCTCCCTGCTGCGGGAAACGCGAGATC	ccct\|GCTG
Donor gained	34176	0.90	mu: TGCTGCGGGAAACGC	CTGC\|ggga
Donor gained	34171	0.55	mu: CTCCCTGCTGCGGGA	CCCT\|gctg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

560

mutated

not conserved

560

Ptroglodytes

all identical

ENSPTRG00000014757

560

Mmulatta

all identical

ENSMMUG00000004842

582

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000070280

544

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000091222

456

Dmelanogaster

all identical

FBgn0035645

507

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
539	559	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
560	594	TOPO_DOM	Cytoplasmic (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1785 / 1785

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

595 / 595

position of stopcodon in wt / mu cDNA

1827 / 1827

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

43 / 43

chromosome

strand

last intron/exon boundary

1776

theoretical NMD boundary in CDS

1683

length of CDS

1785

coding sequence (CDS) position

1679

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

1721

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

34177

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

38357961

original gDNA sequence snippet

TTCCCTCTCCTCCCTGCTGCCGGAAACGCGAGATCAGCCCC

altered gDNA sequence snippet

TTCCCTCTCCTCCCTGCTGCGGGAAACGCGAGATCAGCCCC

original cDNA sequence snippet

TTCCCTCTCCTCCCTGCTGCCGGAAACGCGAGATCAGCCCC

altered cDNA sequence snippet

TTCCCTCTCCTCCCTGCTGCGGGAAACGCGAGATCAGCCCC

wildtype AA sequence

MAGEENFKEE LRSQDASRNL NQHEVAGHPH SWSLEMLLRR LRAVHTKQDD KFANLLDAVG
EFGTFQQRLV ALTFIPSIMS AFFMFADHFV FTAQKPYCNT SWILAVGPHL SKAEQLNLTI
PQAPNGSFLT CFMYLPVPWN LDSIIQFGLN DTDTCQDGWI YPDAKKRSLI NEFDLVCGME
TKKDTAQIMF MAGLPIGSLI FRLITDKMGR YPAILLSLLG LIIFGFGTAF MNSFHLYLFF
RFGISQSVVG YAISSISLAT EWLVGEHRAH AIILGHCFFA VGAVLLTGIA YSLPHWQLLF
LVGGILVIPF ISYIWILPES PRWLMMKGKV KEAKQVLCYA ASVNKKTIPS NLLDELQLPR
KKVTRASVLD FCKNRQLCKV TLVMSCVWFT VSYTYFTLSL RMRELGVSVH FRHVVPSIME
VPARLCCIFL LQQIGRKWSL AVTLLQAIIW CLLLLFLPEG EDGLRLKWPR CPATELKSMT
ILVLMLREFS LAATVTVFFL YTAELLPTVL RATGLGLVSL ASVAGAILSL TIISQTPSLL
PIFLCCVLAI VAFSLSSLLP ETRDQPLSES LNHSSQIRNK VKDMKTKETS SDDV*

mutated AA sequence

speed

0.68 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: 0.999999581453779 (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)

chr3:38357961C>GN/A show variant in all transcripts IGV

HGNC symbol

SLC22A14

Ensembl transcript ID

ENST00000273173

Genbank transcript ID

NM_004803

UniProt peptide

Q9Y267

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1679C>G
cDNA.1770C>G
g.34177C>G

AA changes

P560R Score: 103 explain score(s)

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

560

frameshift

known variant

Reference ID: rs240033

database	homozygous (G/G)	heterozygous	allele carriers
1000G	163	956	1119
ExAC	4561	23645	28206

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.351	0.009
	0.701	0.007
(flanking)	-1.921	0.001

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 marginally increased	34176	wt: 0.9149 / mu: 0.9793 (marginal change - not scored)	wt: TTTCCCTCTCCTCCCTGCTGCCGGAAACGCGAGATCAGCCC mu: TTTCCCTCTCCTCCCTGCTGCGGGAAACGCGAGATCAGCCC	ctgc\|CGGA
Acc marginally increased	34167	wt: 0.9779 / mu: 0.9837 (marginal change - not scored)	wt: TCGTGGCCTTTTCCCTCTCCTCCCTGCTGCCGGAAACGCGA mu: TCGTGGCCTTTTCCCTCTCCTCCCTGCTGCGGGAAACGCGA	tcct\|CCCT
Acc marginally increased	34170	wt: 0.9860 / mu: 0.9896 (marginal change - not scored)	wt: TGGCCTTTTCCCTCTCCTCCCTGCTGCCGGAAACGCGAGAT mu: TGGCCTTTTCCCTCTCCTCCCTGCTGCGGGAAACGCGAGAT	tccc\|TGCT
Acc marginally increased	34173	wt: 0.9849 / mu: 0.9890 (marginal change - not scored)	wt: CCTTTTCCCTCTCCTCCCTGCTGCCGGAAACGCGAGATCAG mu: CCTTTTCCCTCTCCTCCCTGCTGCGGGAAACGCGAGATCAG	ctgc\|TGCC
Acc marginally increased	34169	wt: 0.9759 / mu: 0.9802 (marginal change - not scored)	wt: GTGGCCTTTTCCCTCTCCTCCCTGCTGCCGGAAACGCGAGA mu: GTGGCCTTTTCCCTCTCCTCCCTGCTGCGGGAAACGCGAGA	ctcc\|CTGC
Acc marginally increased	34171	wt: 0.9941 / mu: 0.9948 (marginal change - not scored)	wt: GGCCTTTTCCCTCTCCTCCCTGCTGCCGGAAACGCGAGATC mu: GGCCTTTTCCCTCTCCTCCCTGCTGCGGGAAACGCGAGATC	ccct\|GCTG
Donor gained	34176	0.90	mu: TGCTGCGGGAAACGC	CTGC\|ggga
Donor gained	34171	0.55	mu: CTCCCTGCTGCGGGA	CCCT\|gctg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

560

mutated

not conserved

560

Ptroglodytes

all identical

ENSPTRG00000014757

560

Mmulatta

all identical

ENSMMUG00000004842

582

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000070280

544

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000091222

456

Dmelanogaster

all identical

FBgn0035645

507

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
539	559	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
560	594	TOPO_DOM	Cytoplasmic (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1785 / 1785

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

595 / 595

position of stopcodon in wt / mu cDNA

1876 / 1876

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

92 / 92

chromosome

strand

last intron/exon boundary

1825

theoretical NMD boundary in CDS

1683

length of CDS

1785

coding sequence (CDS) position

1679

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

1770

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

34177

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

38357961

original gDNA sequence snippet

TTCCCTCTCCTCCCTGCTGCCGGAAACGCGAGATCAGCCCC

altered gDNA sequence snippet

TTCCCTCTCCTCCCTGCTGCGGGAAACGCGAGATCAGCCCC

original cDNA sequence snippet

TTCCCTCTCCTCCCTGCTGCCGGAAACGCGAGATCAGCCCC

altered cDNA sequence snippet

TTCCCTCTCCTCCCTGCTGCGGGAAACGCGAGATCAGCCCC

wildtype AA sequence

mutated AA sequence

speed

0.76 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999263061382 (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)

chr3:38357961C>GN/A show variant in all transcripts IGV

HGNC symbol

SLC22A14

Ensembl transcript ID

ENST00000423219

Genbank transcript ID

N/A

UniProt peptide

Q9Y267

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1634C>G
cDNA.1676C>G
g.34177C>G

AA changes

P545R Score: 103 explain score(s)

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

545

frameshift

known variant

Reference ID: rs240033

database	homozygous (G/G)	heterozygous	allele carriers
1000G	163	956	1119
ExAC	4561	23645	28206

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.351	0.009
	0.701	0.007
(flanking)	-1.921	0.001

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 marginally increased	34176	wt: 0.9149 / mu: 0.9793 (marginal change - not scored)	wt: TTTCCCTCTCCTCCCTGCTGCCGGAAACGCGAGATCAGCCC mu: TTTCCCTCTCCTCCCTGCTGCGGGAAACGCGAGATCAGCCC	ctgc\|CGGA
Acc marginally increased	34167	wt: 0.9779 / mu: 0.9837 (marginal change - not scored)	wt: TCGTGGCCTTTTCCCTCTCCTCCCTGCTGCCGGAAACGCGA mu: TCGTGGCCTTTTCCCTCTCCTCCCTGCTGCGGGAAACGCGA	tcct\|CCCT
Acc marginally increased	34170	wt: 0.9860 / mu: 0.9896 (marginal change - not scored)	wt: TGGCCTTTTCCCTCTCCTCCCTGCTGCCGGAAACGCGAGAT mu: TGGCCTTTTCCCTCTCCTCCCTGCTGCGGGAAACGCGAGAT	tccc\|TGCT
Acc marginally increased	34173	wt: 0.9849 / mu: 0.9890 (marginal change - not scored)	wt: CCTTTTCCCTCTCCTCCCTGCTGCCGGAAACGCGAGATCAG mu: CCTTTTCCCTCTCCTCCCTGCTGCGGGAAACGCGAGATCAG	ctgc\|TGCC
Acc marginally increased	34169	wt: 0.9759 / mu: 0.9802 (marginal change - not scored)	wt: GTGGCCTTTTCCCTCTCCTCCCTGCTGCCGGAAACGCGAGA mu: GTGGCCTTTTCCCTCTCCTCCCTGCTGCGGGAAACGCGAGA	ctcc\|CTGC
Acc marginally increased	34171	wt: 0.9941 / mu: 0.9948 (marginal change - not scored)	wt: GGCCTTTTCCCTCTCCTCCCTGCTGCCGGAAACGCGAGATC mu: GGCCTTTTCCCTCTCCTCCCTGCTGCGGGAAACGCGAGATC	ccct\|GCTG
Donor gained	34176	0.90	mu: TGCTGCGGGAAACGC	CTGC\|ggga
Donor gained	34171	0.55	mu: CTCCCTGCTGCGGGA	CCCT\|gctg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

545

mutated

not conserved

545

Ptroglodytes

all identical

ENSPTRG00000014757

560

Mmulatta

all identical

ENSMMUG00000004842

582

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000070280

544

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000091222

457

Dmelanogaster

all identical

FBgn0035645

507

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
539	559	TRANSMEM	Helical; (Potential).	lost
560	594	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1740 / 1740

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

580 / 580

position of stopcodon in wt / mu cDNA

1782 / 1782

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

43 / 43

chromosome

strand

last intron/exon boundary

1731

theoretical NMD boundary in CDS

1638

length of CDS

1740

coding sequence (CDS) position

1634

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

1676

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

34177

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

38357961

original gDNA sequence snippet

TTCCCTCTCCTCCCTGCTGCCGGAAACGCGAGATCAGCCCC

altered gDNA sequence snippet

TTCCCTCTCCTCCCTGCTGCGGGAAACGCGAGATCAGCCCC

original cDNA sequence snippet

TTCCCTCTCCTCCCTGCTGCCGGAAACGCGAGATCAGCCCC

altered cDNA sequence snippet

TTCCCTCTCCTCCCTGCTGCGGGAAACGCGAGATCAGCCCC

wildtype AA sequence

MAGEENFKEE LRSQDASRNL NQHEVAGHPH SWSLEMLLRR LRAVHTKQDD KFANLLDAVG
EFGTFQQRLV ALTFIPSIMS AFFMFADHFV FTAQKPYCNT SWILAVGPHL SKAEQLNLTI
PQAPNGSFLT CFMYLPVPWN LDSIIQFGLN DTDTCQDGWI YPDAKKRSLI NEFDLVCGME
TKKDTAQIMF MAGLPIGSLI FRLITDKMGR YPAILLSLLG LIIFGFGTAF MNSFHLYLFF
RFGISQSVVG YAISSISLAT EWLVGEHRAH AIILGHCFFA VGAVLLTGIA YSLPHWQLLF
LVGGILVIPF ISYIWILPES PRWLMMKGKV KEAKQVLCYA ASVNKKTIPS NLLDELQLPR
KKVTRASVLD FCKNRQLCKV TLVMSCVWFT VSYTYFTLSL RMRELGVSVH FRHVVPSIME
VPARLCCIFL LQQIGRKWSL AVTLLQAIIW CLLLLFLPEE LKSMTILVLM LREFSLAATV
TVFFLYTAEL LPTVLRATGL GLVSLASVAG AILSLTIISQ TPSLLPIFLC CVLAIVAFSL
SSLLPETRDQ PLSESLNHSS QIRNKVKDMK TKETSSDDV*

mutated AA sequence

MAGEENFKEE LRSQDASRNL NQHEVAGHPH SWSLEMLLRR LRAVHTKQDD KFANLLDAVG
EFGTFQQRLV ALTFIPSIMS AFFMFADHFV FTAQKPYCNT SWILAVGPHL SKAEQLNLTI
PQAPNGSFLT CFMYLPVPWN LDSIIQFGLN DTDTCQDGWI YPDAKKRSLI NEFDLVCGME
TKKDTAQIMF MAGLPIGSLI FRLITDKMGR YPAILLSLLG LIIFGFGTAF MNSFHLYLFF
RFGISQSVVG YAISSISLAT EWLVGEHRAH AIILGHCFFA VGAVLLTGIA YSLPHWQLLF
LVGGILVIPF ISYIWILPES PRWLMMKGKV KEAKQVLCYA ASVNKKTIPS NLLDELQLPR
KKVTRASVLD FCKNRQLCKV TLVMSCVWFT VSYTYFTLSL RMRELGVSVH FRHVVPSIME
VPARLCCIFL LQQIGRKWSL AVTLLQAIIW CLLLLFLPEE LKSMTILVLM LREFSLAATV
TVFFLYTAEL LPTVLRATGL GLVSLASVAG AILSLTIISQ TPSLLPIFLC CVLAIVAFSL
SSLLRETRDQ PLSESLNHSS QIRNKVKDMK TKETSSDDV*

speed

0.67 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems