MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000291744
Querying Taster for transcript #2: ENST00000350339
MT speed 0 s - this script 4.096328 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FCN2	polymorphism_automatic	0.00269583497581705	simple_aae				T198M	single base exchange	rs17549193		show file
FCN2	polymorphism_automatic	0.016207183575693	simple_aae				T236M	single base exchange	rs17549193		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.997304165024183 (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 CM051922)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:137779026C>TN/A show variant in all transcripts IGV

HGNC symbol

FCN2

Ensembl transcript ID

ENST00000350339

Genbank transcript ID

NM_015837

UniProt peptide

Q15485

alteration type

single base exchange

alteration region

CDS

DNA changes

c.593C>T
cDNA.607C>T
g.6373C>T

AA changes

T198M Score: 81 explain score(s)

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

198

frameshift

known variant

Reference ID: rs17549193

database	homozygous (T/T)	heterozygous	allele carriers
1000G	181	884	1065
ExAC	4441	22960	27401

known disease mutation at this position, please check HGMD for details (HGMD ID CM051922)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.503	0.654
	0.666	0.377
(flanking)	-3.945	0

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

198

mutated

not conserved

198

Ptroglodytes

all identical

ENSPTRG00000021530

236

Mmulatta

all identical

ENSMMUG00000014403

236

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000026835

237

Ggallus

all conserved

ENSGALG00000009151

237

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0033312

255

Celegans

all identical

D1009.3

355

NGVDPF

Xtropicalis

not conserved

ENSXETG00000008638

244

protein features

start (aa)	end (aa)	feature	details
96	313	DOMAIN	Fibrinogen C-terminal.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

828 / 828

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

276 / 276

position of stopcodon in wt / mu cDNA

842 / 842

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

15 / 15

chromosome

strand

last intron/exon boundary

595

theoretical NMD boundary in CDS

530

length of CDS

828

coding sequence (CDS) position

593

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

607

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

6373

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

137779026

original gDNA sequence snippet

CTGCACAGGAGATTCCCTGACGTTCCACAACAACCAGTCCT

altered gDNA sequence snippet

CTGCACAGGAGATTCCCTGATGTTCCACAACAACCAGTCCT

original cDNA sequence snippet

CAGTGCGGGAGATTCCCTGACGTTCCACAACAACCAGTCCT

altered cDNA sequence snippet

CAGTGCGGGAGATTCCCTGATGTTCCACAACAACCAGTCCT

wildtype AA sequence

MELDRAVGVL GAATLLLSFL GMAWALQAAD TCPGERGPPG PPGKAGPPGP NGAPGEPQPC
LTGPRTCKDL LDRGHFLSGW HTIYLPDCRP LTVLCDMDTD GGGWTVFQRR VDGSVDFYRD
WATYKQGFGS RLGEFWLGND NIHALTAQGT SELRVDLVDF EDNYQFAKYR SFKVADEAEK
YNLVLGAFVE GSAGDSLTFH NNQSFSTKDQ DNDLNTGNCA VMFQGAWWYK NCHVSNLNGR
YLRGTHGSFA NGINWKSGKG YNYSYKVSEM KVRPA*

mutated AA sequence

MELDRAVGVL GAATLLLSFL GMAWALQAAD TCPGERGPPG PPGKAGPPGP NGAPGEPQPC
LTGPRTCKDL LDRGHFLSGW HTIYLPDCRP LTVLCDMDTD GGGWTVFQRR VDGSVDFYRD
WATYKQGFGS RLGEFWLGND NIHALTAQGT SELRVDLVDF EDNYQFAKYR SFKVADEAEK
YNLVLGAFVE GSAGDSLMFH NNQSFSTKDQ DNDLNTGNCA VMFQGAWWYK NCHVSNLNGR
YLRGTHGSFA NGINWKSGKG YNYSYKVSEM KVRPA*

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: 0.983792816424307 (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 CM051922)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:137779026C>TN/A show variant in all transcripts IGV

HGNC symbol

FCN2

Ensembl transcript ID

ENST00000291744

Genbank transcript ID

NM_004108

UniProt peptide

Q15485

alteration type

single base exchange

alteration region

CDS

DNA changes

c.707C>T
cDNA.717C>T
g.6373C>T

AA changes

T236M Score: 81 explain score(s)

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

236

frameshift

known variant

Reference ID: rs17549193

database	homozygous (T/T)	heterozygous	allele carriers
1000G	181	884	1065
ExAC	4441	22960	27401

known disease mutation at this position, please check HGMD for details (HGMD ID CM051922)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.503	0.654
	0.666	0.377
(flanking)	-3.945	0

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

236

mutated

not conserved

236

Ptroglodytes

all identical

ENSPTRG00000021530

236

Mmulatta

all identical

ENSMMUG00000014403

236

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000026835

237

Ggallus

all conserved

ENSGALG00000009151

237

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0033312

255

Celegans

all identical

D1009.3

355

NGVDPF

Xtropicalis

not conserved

ENSXETG00000008638

244

protein features

start (aa)	end (aa)	feature	details
96	313	DOMAIN	Fibrinogen C-terminal.	lost
236	238	HELIX		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

942 / 942

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

314 / 314

position of stopcodon in wt / mu cDNA

952 / 952

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

11 / 11

chromosome

strand

last intron/exon boundary

705

theoretical NMD boundary in CDS

644

length of CDS

942

coding sequence (CDS) position

707

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

717

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

6373

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

137779026

original gDNA sequence snippet

CTGCACAGGAGATTCCCTGACGTTCCACAACAACCAGTCCT

altered gDNA sequence snippet

CTGCACAGGAGATTCCCTGATGTTCCACAACAACCAGTCCT

original cDNA sequence snippet

CAGTGCGGGAGATTCCCTGACGTTCCACAACAACCAGTCCT

altered cDNA sequence snippet

CAGTGCGGGAGATTCCCTGATGTTCCACAACAACCAGTCCT

wildtype AA sequence

MELDRAVGVL GAATLLLSFL GMAWALQAAD TCPEVKMVGL EGSDKLTILR GCPGLPGAPG
PKGEAGTNGK RGERGPPGPP GKAGPPGPNG APGEPQPCLT GPRTCKDLLD RGHFLSGWHT
IYLPDCRPLT VLCDMDTDGG GWTVFQRRVD GSVDFYRDWA TYKQGFGSRL GEFWLGNDNI
HALTAQGTSE LRVDLVDFED NYQFAKYRSF KVADEAEKYN LVLGAFVEGS AGDSLTFHNN
QSFSTKDQDN DLNTGNCAVM FQGAWWYKNC HVSNLNGRYL RGTHGSFANG INWKSGKGYN
YSYKVSEMKV RPA*

mutated AA sequence

MELDRAVGVL GAATLLLSFL GMAWALQAAD TCPEVKMVGL EGSDKLTILR GCPGLPGAPG
PKGEAGTNGK RGERGPPGPP GKAGPPGPNG APGEPQPCLT GPRTCKDLLD RGHFLSGWHT
IYLPDCRPLT VLCDMDTDGG GWTVFQRRVD GSVDFYRDWA TYKQGFGSRL GEFWLGNDNI
HALTAQGTSE LRVDLVDFED NYQFAKYRSF KVADEAEKYN LVLGAFVEGS AGDSLMFHNN
QSFSTKDQDN DLNTGNCAVM FQGAWWYKNC HVSNLNGRYL RGTHGSFANG INWKSGKGYN
YSYKVSEMKV RPA*

speed

1.17 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems