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 7 transcript(s)...
Querying Taster for transcript #1: ENST00000251343
Querying Taster for transcript #2: ENST00000399395
Querying Taster for transcript #3: ENST00000553930
Querying Taster for transcript #4: ENST00000538105
Querying Taster for transcript #5: ENST00000554698
Querying Taster for transcript #6: ENST00000555365
Querying Taster for transcript #7: ENST00000399390
MT speed 0 s - this script 5.203088 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SDR39U1	polymorphism_automatic	0.999979921104036	simple_aae		affected		L232F	single base exchange	rs3211056		show file
SDR39U1	polymorphism_automatic	0.999979921104036	simple_aae		affected		L107F	single base exchange	rs3211056		show file
SDR39U1	polymorphism_automatic	0.999979921104036	simple_aae		affected		L150F	single base exchange	rs3211056		show file
SDR39U1	polymorphism_automatic	0.999979921104036	simple_aae		affected		L124F	single base exchange	rs3211056		show file
SDR39U1	polymorphism_automatic	0.999979921104036	simple_aae		affected		L65F	single base exchange	rs3211056		show file
SDR39U1	polymorphism_automatic	0.999979921104036	simple_aae		affected		L137F	single base exchange	rs3211056		show file
KHNYN	polymorphism_automatic	1	without_aae		affected			single base exchange	rs3211056		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 2.00788959640649e-05 (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)

chr14:24909475C>GN/A show variant in all transcripts IGV

HGNC symbol

SDR39U1

Ensembl transcript ID

ENST00000399395

Genbank transcript ID

NM_020195

UniProt peptide

Q9NRG7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.696G>C
cDNA.730G>C
g.2637G>C

AA changes

L232F Score: 22 explain score(s)

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

232

frameshift

known variant

Reference ID: rs3211056

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1542	748	2290
ExAC	-	-	-

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.034	1
	2.149	1
(flanking)	2.357	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 increased	2648	wt: 0.45 / mu: 0.78	wt: CCAGACCTTGGGTGCTGCCCTGGGCCGCCGAGCCTTCATCC mu: CCAGACCTTCGGTGCTGCCCTGGGCCGCCGAGCCTTCATCC	ccct\|GGGC
Acc marginally increased	2638	wt: 0.5307 / mu: 0.5743 (marginal change - not scored)	wt: CTGAGTTTGCCCAGACCTTGGGTGCTGCCCTGGGCCGCCGA mu: CTGAGTTTGCCCAGACCTTCGGTGCTGCCCTGGGCCGCCGA	ttgg\|GTGC

distance from splice site

224

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

232

mutated

not conserved

232

Ptroglodytes

all identical

ENSPTRG00000006222

258

Mmulatta

all identical

ENSMMUG00000009517

256

Fcatus

all identical

ENSFCAG00000005606

253

Mmusculus

all identical

ENSMUSG00000022223

232

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000006828

235

Drerio

all identical

ENSDARG00000068215

235

Dmelanogaster

not conserved

FBgn0033769

240

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000016929

236

VKD

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

882 / 882

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

294 / 294

position of stopcodon in wt / mu cDNA

916 / 916

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

35 / 35

chromosome

strand

-1

last intron/exon boundary

507

theoretical NMD boundary in CDS

422

length of CDS

882

coding sequence (CDS) position

696

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

730

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

2637

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

24909475

original gDNA sequence snippet

GCTGAGTTTGCCCAGACCTTGGGTGCTGCCCTGGGCCGCCG

altered gDNA sequence snippet

GCTGAGTTTGCCCAGACCTTCGGTGCTGCCCTGGGCCGCCG

original cDNA sequence snippet

GCTGAGTTTGCCCAGACCTTGGGTGCTGCCCTGGGCCGCCG

altered cDNA sequence snippet

GCTGAGTTTGCCCAGACCTTCGGTGCTGCCCTGGGCCGCCG

wildtype AA sequence

MRVLVGGGTG FIGTALTQLL NARGHEVTLV SRKPGPGRIT WDELAASGLP SCDAAVNLAG
ENILNPLRRW NETFQKEVIG SRLETTQLLA KAITKAPQPP KAWVLVTGVA YYQPSLTAEY
DEDSPGGDFD FFSNLVTKWE AAARLPGDST RQVVVRSGVV LGRGGGAMGH MLLPFRLGLG
GPIGSGHQFF PWIHIGDLAG ILTHALEANH VHGVLNGVAP SSATNAEFAQ TLGAALGRRA
FIPLPSAVVQ AVFGRQRAIM LLEGQKVIPQ RTLATGYQYS FPELGAALKE IVA*

mutated AA sequence

MRVLVGGGTG FIGTALTQLL NARGHEVTLV SRKPGPGRIT WDELAASGLP SCDAAVNLAG
ENILNPLRRW NETFQKEVIG SRLETTQLLA KAITKAPQPP KAWVLVTGVA YYQPSLTAEY
DEDSPGGDFD FFSNLVTKWE AAARLPGDST RQVVVRSGVV LGRGGGAMGH MLLPFRLGLG
GPIGSGHQFF PWIHIGDLAG ILTHALEANH VHGVLNGVAP SSATNAEFAQ TFGAALGRRA
FIPLPSAVVQ AVFGRQRAIM LLEGQKVIPQ RTLATGYQYS FPELGAALKE IVA*

speed

0.93 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: 2.00788959640649e-05 (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)

chr14:24909475C>GN/A show variant in all transcripts IGV

HGNC symbol

SDR39U1

Ensembl transcript ID

ENST00000553930

Genbank transcript ID

N/A

UniProt peptide

Q9NRG7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.321G>C
cDNA.835G>C
g.2637G>C

AA changes

L107F Score: 22 explain score(s)

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

107

frameshift

known variant

Reference ID: rs3211056

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1542	748	2290
ExAC	-	-	-

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.034	1
	2.149	1
(flanking)	2.357	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 increased	2648	wt: 0.45 / mu: 0.78	wt: CCAGACCTTGGGTGCTGCCCTGGGCCGCCGAGCCTTCATCC mu: CCAGACCTTCGGTGCTGCCCTGGGCCGCCGAGCCTTCATCC	ccct\|GGGC
Acc marginally increased	2638	wt: 0.5307 / mu: 0.5743 (marginal change - not scored)	wt: CTGAGTTTGCCCAGACCTTGGGTGCTGCCCTGGGCCGCCGA mu: CTGAGTTTGCCCAGACCTTCGGTGCTGCCCTGGGCCGCCGA	ttgg\|GTGC

distance from splice site

333

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

107

mutated

not conserved

107

Ptroglodytes

all identical

ENSPTRG00000006222

258

Mmulatta

all identical

ENSMMUG00000009517

256

Fcatus

all identical

ENSFCAG00000005606

252

Mmusculus

all identical

ENSMUSG00000022223

232

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000006828

240

Drerio

all identical

ENSDARG00000068215

240

Dmelanogaster

not conserved

FBgn0033769

239

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000016929

237

VKD

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

507 / 507

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

169 / 169

position of stopcodon in wt / mu cDNA

1021 / 1021

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

515 / 515

chromosome

strand

-1

last intron/exon boundary

503

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

507

coding sequence (CDS) position

321

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

835

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

2637

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

24909475

original gDNA sequence snippet

GCTGAGTTTGCCCAGACCTTGGGTGCTGCCCTGGGCCGCCG

altered gDNA sequence snippet

GCTGAGTTTGCCCAGACCTTCGGTGCTGCCCTGGGCCGCCG

original cDNA sequence snippet

GCTGAGTTTGCCCAGACCTTGGGTGCTGCCCTGGGCCGCCG

altered cDNA sequence snippet

GCTGAGTTTGCCCAGACCTTCGGTGCTGCCCTGGGCCGCCG

wildtype AA sequence

MGRVRKGKQK PGGAVGSFKA ERTPVPSLFP ALGVVLGRGG GAMGHMLLPF RLGLGGPIGS
GHQFFPWIHI GDLAGILTHA LEANHVHGVL NGVAPSSATN AEFAQTLGAA LGRRAFIPLP
SAVVQAVFGR QRAIMLLEGQ KVIPQRTLAT GYQYSFPELG AALKEIVA*

mutated AA sequence

MGRVRKGKQK PGGAVGSFKA ERTPVPSLFP ALGVVLGRGG GAMGHMLLPF RLGLGGPIGS
GHQFFPWIHI GDLAGILTHA LEANHVHGVL NGVAPSSATN AEFAQTFGAA LGRRAFIPLP
SAVVQAVFGR QRAIMLLEGQ KVIPQRTLAT GYQYSFPELG AALKEIVA*

speed

0.95 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 2.00788959640649e-05 (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)

chr14:24909475C>GN/A show variant in all transcripts IGV

HGNC symbol

SDR39U1

Ensembl transcript ID

ENST00000538105

Genbank transcript ID

N/A

UniProt peptide

Q9NRG7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.450G>C
cDNA.554G>C
g.2637G>C

AA changes

L150F Score: 22 explain score(s)

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

150

frameshift

known variant

Reference ID: rs3211056

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1542	748	2290
ExAC	-	-	-

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.034	1
	2.149	1
(flanking)	2.357	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 increased	2648	wt: 0.45 / mu: 0.78	wt: CCAGACCTTGGGTGCTGCCCTGGGCCGCCGAGCCTTCATCC mu: CCAGACCTTCGGTGCTGCCCTGGGCCGCCGAGCCTTCATCC	ccct\|GGGC
Acc marginally increased	2638	wt: 0.5307 / mu: 0.5743 (marginal change - not scored)	wt: CTGAGTTTGCCCAGACCTTGGGTGCTGCCCTGGGCCGCCGA mu: CTGAGTTTGCCCAGACCTTCGGTGCTGCCCTGGGCCGCCGA	ttgg\|GTGC

distance from splice site

224

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

150

mutated

not conserved

150

Ptroglodytes

all identical

ENSPTRG00000006222

258

Mmulatta

all identical

ENSMMUG00000009517

256

Fcatus

all identical

ENSFCAG00000005606

253

Mmusculus

all identical

ENSMUSG00000022223

232

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000006828

239

Drerio

all identical

ENSDARG00000068215

235

Dmelanogaster

not conserved

FBgn0033769

239

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000016929

236

VKD

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

636 / 636

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

212 / 212

position of stopcodon in wt / mu cDNA

740 / 740

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

105 / 105

chromosome

strand

-1

last intron/exon boundary

331

theoretical NMD boundary in CDS

176

length of CDS

636

coding sequence (CDS) position

450

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

554

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

2637

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

24909475

original gDNA sequence snippet

GCTGAGTTTGCCCAGACCTTGGGTGCTGCCCTGGGCCGCCG

altered gDNA sequence snippet

GCTGAGTTTGCCCAGACCTTCGGTGCTGCCCTGGGCCGCCG

original cDNA sequence snippet

GCTGAGTTTGCCCAGACCTTGGGTGCTGCCCTGGGCCGCCG

altered cDNA sequence snippet

GCTGAGTTTGCCCAGACCTTCGGTGCTGCCCTGGGCCGCCG

wildtype AA sequence

MSSLHRGCRA AMPPSTWPER TSSTLSEAYY QPSLTAEYDE DSPGGDFDFF SNLVTKWEAA
ARLPGDSTRQ VVVRSGVVLG RGGGAMGHML LPFRLGLGGP IGSGHQFFPW IHIGDLAGIL
THALEANHVH GVLNGVAPSS ATNAEFAQTL GAALGRRAFI PLPSAVVQAV FGRQRAIMLL
EGQKVIPQRT LATGYQYSFP ELGAALKEIV A*

mutated AA sequence

MSSLHRGCRA AMPPSTWPER TSSTLSEAYY QPSLTAEYDE DSPGGDFDFF SNLVTKWEAA
ARLPGDSTRQ VVVRSGVVLG RGGGAMGHML LPFRLGLGGP IGSGHQFFPW IHIGDLAGIL
THALEANHVH GVLNGVAPSS ATNAEFAQTF GAALGRRAFI PLPSAVVQAV FGRQRAIMLL
EGQKVIPQRT LATGYQYSFP ELGAALKEIV A*

speed

0.85 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 2.00788959640649e-05 (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)

chr14:24909475C>GN/A show variant in all transcripts IGV

HGNC symbol

SDR39U1

Ensembl transcript ID

ENST00000554698

Genbank transcript ID

N/A

UniProt peptide

Q9NRG7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.372G>C
cDNA.880G>C
g.2637G>C

AA changes

L124F Score: 22 explain score(s)

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

124

frameshift

known variant

Reference ID: rs3211056

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1542	748	2290
ExAC	-	-	-

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.034	1
	2.149	1
(flanking)	2.357	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 increased	2648	wt: 0.45 / mu: 0.78	wt: CCAGACCTTGGGTGCTGCCCTGGGCCGCCGAGCCTTCATCC mu: CCAGACCTTCGGTGCTGCCCTGGGCCGCCGAGCCTTCATCC	ccct\|GGGC
Acc marginally increased	2638	wt: 0.5307 / mu: 0.5743 (marginal change - not scored)	wt: CTGAGTTTGCCCAGACCTTGGGTGCTGCCCTGGGCCGCCGA mu: CTGAGTTTGCCCAGACCTTCGGTGCTGCCCTGGGCCGCCGA	ttgg\|GTGC

distance from splice site

224

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

124

mutated

not conserved

124

Ptroglodytes

all identical

ENSPTRG00000006222

258

Mmulatta

all identical

ENSMMUG00000009517

256

Fcatus

all identical

ENSFCAG00000005606

253

Mmusculus

all identical

ENSMUSG00000022223

233

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000006828

240

Drerio

all identical

ENSDARG00000068215

240

Dmelanogaster

not conserved

FBgn0033769

239

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000016929

237

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

558 / 558

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

186 / 186

position of stopcodon in wt / mu cDNA

1066 / 1066

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

509 / 509

chromosome

strand

-1

last intron/exon boundary

657

theoretical NMD boundary in CDS

length of CDS

558

coding sequence (CDS) position

372

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

880

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

2637

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

24909475

original gDNA sequence snippet

GCTGAGTTTGCCCAGACCTTGGGTGCTGCCCTGGGCCGCCG

altered gDNA sequence snippet

GCTGAGTTTGCCCAGACCTTCGGTGCTGCCCTGGGCCGCCG

original cDNA sequence snippet

GCTGAGTTTGCCCAGACCTTGGGTGCTGCCCTGGGCCGCCG

altered cDNA sequence snippet

GCTGAGTTTGCCCAGACCTTCGGTGCTGCCCTGGGCCGCCG

wildtype AA sequence

MAYYQPSLTA EYDEDSPGGD FDFFSNLVTK WEAAARLPGD STRQVVVRSG VVLGRGGGAM
GHMLLPFRLG LGGPIGSGHQ FFPWIHIGDL AGILTHALEA NHVHGVLNGV APSSATNAEF
AQTLGAALGR RAFIPLPSAV VQAVFGRQRA IMLLEGQKVI PQRTLATGYQ YSFPELGAAL
KEIVA*

mutated AA sequence

MAYYQPSLTA EYDEDSPGGD FDFFSNLVTK WEAAARLPGD STRQVVVRSG VVLGRGGGAM
GHMLLPFRLG LGGPIGSGHQ FFPWIHIGDL AGILTHALEA NHVHGVLNGV APSSATNAEF
AQTFGAALGR RAFIPLPSAV VQAVFGRQRA IMLLEGQKVI PQRTLATGYQ YSFPELGAAL
KEIVA*

speed

0.69 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 2.00788959640649e-05 (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)

chr14:24909475C>GN/A show variant in all transcripts IGV

HGNC symbol

SDR39U1

Ensembl transcript ID

ENST00000555365

Genbank transcript ID

N/A

UniProt peptide

Q9NRG7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.195G>C
cDNA.609G>C
g.2637G>C

AA changes

L65F Score: 22 explain score(s)

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

frameshift

known variant

Reference ID: rs3211056

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1542	748	2290
ExAC	-	-	-

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.034	1
	2.149	1
(flanking)	2.357	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 increased	2648	wt: 0.45 / mu: 0.78	wt: CCAGACCTTGGGTGCTGCCCTGGGCCGCCGAGCCTTCATCC mu: CCAGACCTTCGGTGCTGCCCTGGGCCGCCGAGCCTTCATCC	ccct\|GGGC
Acc marginally increased	2638	wt: 0.5307 / mu: 0.5743 (marginal change - not scored)	wt: CTGAGTTTGCCCAGACCTTGGGTGCTGCCCTGGGCCGCCGA mu: CTGAGTTTGCCCAGACCTTCGGTGCTGCCCTGGGCCGCCGA	ttgg\|GTGC

distance from splice site

224

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000006222

258

Mmulatta

all identical

ENSMMUG00000009517

256

Fcatus

all identical

ENSFCAG00000005606

253

Mmusculus

all identical

ENSMUSG00000022223

233

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000006828

240

Drerio

all identical

ENSDARG00000068215

240

Dmelanogaster

not conserved

FBgn0033769

239

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000016929

239

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

381 / 381

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

127 / 127

position of stopcodon in wt / mu cDNA

795 / 795

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

415 / 415

chromosome

strand

-1

last intron/exon boundary

386

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

381

coding sequence (CDS) position

195

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

609

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

2637

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

24909475

original gDNA sequence snippet

GCTGAGTTTGCCCAGACCTTGGGTGCTGCCCTGGGCCGCCG

altered gDNA sequence snippet

GCTGAGTTTGCCCAGACCTTCGGTGCTGCCCTGGGCCGCCG

original cDNA sequence snippet

GCTGAGTTTGCCCAGACCTTGGGTGCTGCCCTGGGCCGCCG

altered cDNA sequence snippet

GCTGAGTTTGCCCAGACCTTCGGTGCTGCCCTGGGCCGCCG

wildtype AA sequence

MGHMLLPFRL GLGGPIGSGH QFFPWIHIGD LAGILTHALE ANHVHGVLNG VAPSSATNAE
FAQTLGAALG RRAFIPLPSA VVQAVFGRQR AIMLLEGQKV IPQRTLATGY QYSFPELGAA
LKEIVA*

mutated AA sequence

MGHMLLPFRL GLGGPIGSGH QFFPWIHIGD LAGILTHALE ANHVHGVLNG VAPSSATNAE
FAQTFGAALG RRAFIPLPSA VVQAVFGRQR AIMLLEGQKV IPQRTLATGY QYSFPELGAA
LKEIVA*

speed

0.67 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 2.00788959640649e-05 (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)

chr14:24909475C>GN/A show variant in all transcripts IGV

HGNC symbol

SDR39U1

Ensembl transcript ID

ENST00000399390

Genbank transcript ID

N/A

UniProt peptide

Q9NRG7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.411G>C
cDNA.411G>C
g.2637G>C

AA changes

L137F Score: 22 explain score(s)

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

137

frameshift

known variant

Reference ID: rs3211056

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1542	748	2290
ExAC	-	-	-

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.034	1
	2.149	1
(flanking)	2.357	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 increased	2648	wt: 0.45 / mu: 0.78	wt: CCAGACCTTGGGTGCTGCCCTGGGCCGCCGAGCCTTCATCC mu: CCAGACCTTCGGTGCTGCCCTGGGCCGCCGAGCCTTCATCC	ccct\|GGGC
Acc marginally increased	2638	wt: 0.5307 / mu: 0.5743 (marginal change - not scored)	wt: CTGAGTTTGCCCAGACCTTGGGTGCTGCCCTGGGCCGCCGA mu: CTGAGTTTGCCCAGACCTTCGGTGCTGCCCTGGGCCGCCGA	ttgg\|GTGC

distance from splice site

224

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

137

mutated

not conserved

137

Ptroglodytes

all identical

ENSPTRG00000006222

258

Mmulatta

all identical

ENSMMUG00000009517

256

Fcatus

all identical

ENSFCAG00000005606

253

Mmusculus

all identical

ENSMUSG00000022223

232

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000006828

240

Drerio

all identical

ENSDARG00000068215

240

Dmelanogaster

not conserved

FBgn0033769

239

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000016929

237

VKD

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

597 / 597

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

199 / 199

position of stopcodon in wt / mu cDNA

597 / 597

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

1 / 1

chromosome

strand

-1

last intron/exon boundary

188

theoretical NMD boundary in CDS

137

length of CDS

597

coding sequence (CDS) position

411

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

411

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

2637

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

24909475

original gDNA sequence snippet

GCTGAGTTTGCCCAGACCTTGGGTGCTGCCCTGGGCCGCCG

altered gDNA sequence snippet

GCTGAGTTTGCCCAGACCTTCGGTGCTGCCCTGGGCCGCCG

original cDNA sequence snippet

GCTGAGTTTGCCCAGACCTTGGGTGCTGCCCTGGGCCGCCG

altered cDNA sequence snippet

GCTGAGTTTGCCCAGACCTTCGGTGCTGCCCTGGGCCGCCG

wildtype AA sequence

MALSPNGEIL RAREAYYQPS LTAEYDEDSP GGDFDFFSNL VTKWEAAARL PGDSTRQVVV
RSGVVLGRGG GAMGHMLLPF RLGLGGPIGS GHQFFPWIHI GDLAGILTHA LEANHVHGVL
NGVAPSSATN AEFAQTLGAA LGRRAFIPLP SAVVQAVFGR QRAIMLLEGQ KVIPQRTLAT
GYQYSFPELG AALKEIVA*

mutated AA sequence

MALSPNGEIL RAREAYYQPS LTAEYDEDSP GGDFDFFSNL VTKWEAAARL PGDSTRQVVV
RSGVVLGRGG GAMGHMLLPF RLGLGGPIGS GHQFFPWIHI GDLAGILTHA LEANHVHGVL
NGVAPSSATN AEFAQTFGAA LGRRAFIPLP SAVVQAVFGR QRAIMLLEGQ KVIPQRTLAT
GYQYSFPELG AALKEIVA*

speed

0.60 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 6.71190891345765e-19 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:24909475C>GN/A show variant in all transcripts IGV

HGNC symbol

KHNYN

Ensembl transcript ID

ENST00000251343

Genbank transcript ID

NM_015299

UniProt peptide

N/A

alteration type

single base exchange

alteration region

3'UTR

DNA changes

cDNA.5160C>G
g.10984C>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs3211056

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1542	748	2290
ExAC	-	-	-

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.034	1
	2.149	1
(flanking)	2.357	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

splice site change occurs after stopcodon (at aa 1671)

effect	gDNA position	score	detection sequence	exon-intron border
Donor marginally increased	10981	wt: 0.9950 / mu: 0.9959 (marginal change - not scored)	wt: GCAGCACCCAAGGTC mu: GCAGCACCGAAGGTC	AGCA\|ccca
Donor gained	10978	0.52	mu: AGGGCAGCACCGAAG	GGCA\|gcac

distance from splice site

1066

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

poly(A) signal

signal is predicted to be ok

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

140 / 140

chromosome

strand

last intron/exon boundary

1927

theoretical NMD boundary in CDS

1737

length of CDS

2037

coding sequence (CDS) position

N/A

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

5160

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

10984

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

24909475

original gDNA sequence snippet

CGGCGGCCCAGGGCAGCACCCAAGGTCTGGGCAAACTCAGC

altered gDNA sequence snippet

CGGCGGCCCAGGGCAGCACCGAAGGTCTGGGCAAACTCAGC

original cDNA sequence snippet

CGGCGGCCCAGGGCAGCACCCAAGGTCTGGGCAAACTCAGC

altered cDNA sequence snippet

CGGCGGCCCAGGGCAGCACCGAAGGTCTGGGCAAACTCAGC

wildtype AA sequence

MPTWGARPAS PDRFAVSAEA ENKVREQQPH VERIFSVGVS VLPKDCPDNP HIWLQLEGPK
ENASRAKEYL KGLCSPELQD EIHYPPKLHC IFLGAQGFFL DCLAWSTSAH LVPRAPGSLM
ISGLTEAFVM AQSRVEELAE RLSWDFTPGP SSGASQCTGV LRDFSALLQS PGDAHREALL
QLPLAVQEEL LSLVQEASSG QGPGALASWE GRSSALLGAQ CQGVRAPPSD GRESLDTGSM
GPGDCRGARG DTYAVEKEGG KQGGPREMDW GWKELPGEEA WEREVALRPQ SVGGGARESA
PLKGKALGKE EIALGGGGFC VHREPPGAHG SCHRAAQSRG ASLLQRLHNG NASPPRVPSP
PPAPEPPWHC GDRGDCGDRG DVGDRGDKQQ GMARGRGPQW KRGARGGNLV TGTQRFKEAL
QDPFTLCLAN VPGQPDLRHI VIDGSNVAMV HGLQHYFSSR GIAIAVQYFW DRGHRDITVF
VPQWRFSKDA KVRESHFLQK LYSLSLLSLT PSRVMDGKRI SSYDDRFMVK LAEETDGIIV
SNDQFRDLAE ESEKWMAIIR ERLLPFTFVG NLFMVPDDPL GRNGPTLDEF LKKPARTQGS
SKAQHPSRGF AEHGKQQQGR EEEKGSGGIR KTRETERLRR QLLEVFWGQD HKVDFILQRE
PYCRDINQLS EALLSLNF*

mutated AA sequence

N/A

speed

0.83 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems