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: ENST00000230449
Querying Taster for transcript #2: ENST00000448181
Querying Taster for transcript #3: ENST00000380907
MT speed 0 s - this script 4.188781 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
EXOC2	polymorphism_automatic	0.996469203415928	without_aae					single base exchange	rs1211554		show file
EXOC2	polymorphism_automatic	0.996469203415928	without_aae					single base exchange	rs1211554		show file
HUS1B	polymorphism_automatic	0.999984327646553	simple_aae				D268Y	single base exchange	rs1211554		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.00353079658407157 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM062777)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:656143C>AN/A show variant in all transcripts IGV

HGNC symbol

EXOC2

Ensembl transcript ID

ENST00000230449

Genbank transcript ID

NM_018303

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.36975G>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs1211554

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1472	762	2234
ExAC	-	-	-

known disease mutation at this position, please check HGMD for details (HGMD ID CM062777)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.745	0.775
	0.264	0.774
(flanking)	0.073	0.784

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	36971	wt: 0.9678 / mu: 0.9719 (marginal change - not scored)	wt: CTTCAGCTTGTTTTGGTTCAAGAAGATGTCTCTCTTCAGTA mu: CTTCAGCTTGTTTTGGTTCAAGAATATGTCTCTCTTCAGTA	tcaa\|GAAG
Acc marginally increased	36966	wt: 0.7158 / mu: 0.7523 (marginal change - not scored)	wt: CTCTTCTTCAGCTTGTTTTGGTTCAAGAAGATGTCTCTCTT mu: CTCTTCTTCAGCTTGTTTTGGTTCAAGAATATGTCTCTCTT	ttgg\|TTCA
Acc marginally increased	36965	wt: 0.9703 / mu: 0.9732 (marginal change - not scored)	wt: ACTCTTCTTCAGCTTGTTTTGGTTCAAGAAGATGTCTCTCT mu: ACTCTTCTTCAGCTTGTTTTGGTTCAAGAATATGTCTCTCT	tttg\|GTTC

distance from splice site

18282

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

N/A

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

N/A

position of start ATG in wt / mu cDNA

137 / 137

chromosome

strand

-1

last intron/exon boundary

2818

theoretical NMD boundary in CDS

2631

length of CDS

2775

coding sequence (CDS) position

N/A

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

N/A

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

36975

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

656143

original gDNA sequence snippet

AGCTTGTTTTGGTTCAAGAAGATGTCTCTCTTCAGTATTTC

altered gDNA sequence snippet

AGCTTGTTTTGGTTCAAGAATATGTCTCTCTTCAGTATTTC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MSRSRQPPLV TGISPNEGIP WTKVTIRGEN LGTGPTDLIG LTICGHNCLL TAEWMSASKI
VCRVGQAKND KGDIIVTTKS GGRGTSTVSF KLLKPEKIGI LDQSAVWVDE MNYYDMRTDR
NKGIPPLSLR PANPLGIEIE KSKFSQKDLE MLFHGMSADF TSENFSAAWY LIENHSNTSF
EQLKMAVTNL KRQANKKSEG SLAYVKGGLS TFFEAQDALS AIHQKLEADG TEKVEGSMTQ
KLENVLNRAS NTADTLFQEV LGRKDKADST RNALNVLQRF KFLFNLPLNI ERNIQKGDYD
VVINDYEKAK SLFGKTEVQV FKKYYAEVET RIEALRELLL DKLLETPSTL HDQKRYIRYL
SDLHASGDPA WQCIGAQHKW ILQLMHSCKE GYVKDLKGNP GLHSPMLDLD NDTRPSVLGH
LSQTASLKRG SSFQSGRDDT WRYKTPHRVA FVEKLTKLVL SQLPNFWKLW ISYVNGSLFS
ETAEKSGQIE RSKNVRQRQN DFKKMIQEVM HSLVKLTRGA LLPLSIRDGE AKQYGGWEVK
CELSGQWLAH AIQTVRLTHE SLTALEIPND LLQTIQDLIL DLRVRCVMAT LQHTAEEIKR
LAEKEDWIVD NEGLTSLPCQ FEQCIVCSLQ SLKGVLECKP GEASVFQQPK TQEEVCQLSI
NIMQVFIYCL EQLSTKPDAD IDTTHLSVDV SSPDLFGSIH EDFSLTSEQR LLIVLSNCCY
LERHTFLNIA EHFEKHNFQG IEKITQVSMA SLKELDQRLF ENYIELKADP IVGSLEPGIY
AGYFDWKDCL PPTGVRNYLK EALVNIIAVH AEVFTISKEL VPRVLSKVIE AVSEELSRLM
QCVSSFSKNG ALQARLEICA LRDTVAVYLT PESKSSFKQA LEALPQLSSG ADKKLLEELL
NKFKSSMHLQ LTCFQAASST MMKT*

mutated AA sequence

N/A

speed

0.91 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: without_aae, prob: 0.00353079658407157 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM062777)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:656143C>AN/A show variant in all transcripts IGV

HGNC symbol

EXOC2

Ensembl transcript ID

ENST00000448181

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.36975G>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs1211554

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1472	762	2234
ExAC	-	-	-

known disease mutation at this position, please check HGMD for details (HGMD ID CM062777)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.745	0.775
	0.264	0.774
(flanking)	0.073	0.784

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	36971	wt: 0.9678 / mu: 0.9719 (marginal change - not scored)	wt: CTTCAGCTTGTTTTGGTTCAAGAAGATGTCTCTCTTCAGTA mu: CTTCAGCTTGTTTTGGTTCAAGAATATGTCTCTCTTCAGTA	tcaa\|GAAG
Acc marginally increased	36966	wt: 0.7158 / mu: 0.7523 (marginal change - not scored)	wt: CTCTTCTTCAGCTTGTTTTGGTTCAAGAAGATGTCTCTCTT mu: CTCTTCTTCAGCTTGTTTTGGTTCAAGAATATGTCTCTCTT	ttgg\|TTCA
Acc marginally increased	36965	wt: 0.9703 / mu: 0.9732 (marginal change - not scored)	wt: ACTCTTCTTCAGCTTGTTTTGGTTCAAGAAGATGTCTCTCT mu: ACTCTTCTTCAGCTTGTTTTGGTTCAAGAATATGTCTCTCT	tttg\|GTTC

distance from splice site

36876

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

N/A

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

N/A

position of start ATG in wt / mu cDNA

123 / 123

chromosome

strand

-1

last intron/exon boundary

1589

theoretical NMD boundary in CDS

1416

length of CDS

1560

coding sequence (CDS) position

N/A

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

N/A

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

36975

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

656143

original gDNA sequence snippet

AGCTTGTTTTGGTTCAAGAAGATGTCTCTCTTCAGTATTTC

altered gDNA sequence snippet

AGCTTGTTTTGGTTCAAGAATATGTCTCTCTTCAGTATTTC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MLDLDNDTRP SVLGHLSQTA SLKRGSSFQS GRDDTWRYKT PHRVAFVEKL TKLVLSQLPN
FWKLWISYVN GSLFSETAEK SGQIERSKNV RQRQNDFKKM IQEVMHSLVK LTRGALLPLS
IRDGEAKQYG GWEVKCELSG QWLAHAIQTV RLTHESLTAL EIPNDLLQTI QDLILDLRVR
CVMATLQHTA EEIKRLAEKE DWIVDNEGLT SLPCQFEQCI VCSLQSLKGV LECKPGEASV
FQQPKTQEEV CQLSINIMQV FIYCLEQLST KPDADIDTTH LSVDVSSPDL FGSIHEDFSL
TSEQRLLIVL SNCCYLERHT FLNIAEHFEK HNFQGIEKIT QVSMASLKEL DQRLFENYIE
LKADPIVGSL EPGIYAGYFD WKDCLPPTGV RNYLKEALVN IIAVHAEVFT ISKELVPRVL
SKVIEAVSEE LSRLMQCVSS FSKNGALQAR LEICALRDTV AVYLTPESKS SFKQALEALP
QLSSGADKKL LEELLNKFKS SMHLQLTCFQ AASSTMMKT*

mutated AA sequence

N/A

speed

0.88 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1.56723534466806e-05 (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 CM062777)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:656143C>AN/A show variant in all transcripts IGV

HGNC symbol

HUS1B

Ensembl transcript ID

ENST00000380907

Genbank transcript ID

NM_148959

UniProt peptide

Q8NHY5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.802G>T
cDNA.821G>T
g.821G>T

AA changes

D268Y Score: 160 explain score(s)

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

268

frameshift

known variant

Reference ID: rs1211554

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1472	762	2234
ExAC	-	-	-

known disease mutation at this position, please check HGMD for details (HGMD ID CM062777)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.745	0.775
	0.264	0.774
(flanking)	0.073	0.784

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	817	wt: 0.9678 / mu: 0.9719 (marginal change - not scored)	wt: CTTCAGCTTGTTTTGGTTCAAGAAGATGTCTCTCTTCAGTA mu: CTTCAGCTTGTTTTGGTTCAAGAATATGTCTCTCTTCAGTA	tcaa\|GAAG
Acc marginally increased	811	wt: 0.9703 / mu: 0.9732 (marginal change - not scored)	wt: ACTCTTCTTCAGCTTGTTTTGGTTCAAGAAGATGTCTCTCT mu: ACTCTTCTTCAGCTTGTTTTGGTTCAAGAATATGTCTCTCT	tttg\|GTTC
Acc marginally increased	812	wt: 0.7158 / mu: 0.7523 (marginal change - not scored)	wt: CTCTTCTTCAGCTTGTTTTGGTTCAAGAAGATGTCTCTCTT mu: CTCTTCTTCAGCTTGTTTTGGTTCAAGAATATGTCTCTCTT	ttgg\|TTCA

distance from splice site

205

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

268

mutated

not conserved

268

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000023562

268

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000076430

266

Ggallus

all identical

ENSGALG00000012450

273

Trubripes

all identical

ENSTRUG00000005081

274

Drerio

all identical

ENSDARG00000061380

273

Dmelanogaster

all identical

FBgn0026417

265

Celegans

all identical

H26D21.1

265

Xtropicalis

all identical

ENSXETG00000015679

271

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

837 / 837

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

279 / 279

position of stopcodon in wt / mu cDNA

856 / 856

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

20 / 20

chromosome

strand

-1

last intron/exon boundary

theoretical NMD boundary in CDS

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

length of CDS

837

coding sequence (CDS) position

802

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

821

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

821

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

656143

original gDNA sequence snippet

AGCTTGTTTTGGTTCAAGAAGATGTCTCTCTTCAGTATTTC

altered gDNA sequence snippet

AGCTTGTTTTGGTTCAAGAATATGTCTCTCTTCAGTATTTC

original cDNA sequence snippet

AGCTTGTTTTGGTTCAAGAAGATGTCTCTCTTCAGTATTTC

altered cDNA sequence snippet

AGCTTGTTTTGGTTCAAGAATATGTCTCTCTTCAGTATTTC

wildtype AA sequence

MKFRAKITGK GCLELFIHVS GTVARLAKVC VLRVRPDSLC FGPAGSGGLH EARLWCEVRQ
GAFQQFRMEG VSEDLDEIHL ELTAEHLSRA ARSAAGASSL KLQLTHKRRP SLTVAVELVS
SLGRARSVVH DLPVRVLPRR VWRDCLPPSL RASDASIRLP RWRTLRSIVE RMANVGSHVL
VEANLSGRMT LSIETEVVSI QSYFKNLGNP PQSAVGVPEN RDLESMVQVR VDNRKLLQFL
EGQQIHPTTA LCNIWDNTLL QLVLVQEDVS LQYFIPAL*

mutated AA sequence

speed

1.11 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