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: ENST00000354370
Querying Taster for transcript #2: ENST00000396423
MT speed 0 s - this script 2.986189 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
HNF4G	polymorphism_automatic	0.154526031444148	simple_aae		affected		M190I	single base exchange	rs1805098		show file
HNF4G	polymorphism_automatic	0.526936960460124	simple_aae		affected		M227I	single base exchange	rs1805098		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.845473968555852 (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)

chr8:76468282G>AN/A show variant in all transcripts IGV

HGNC symbol

HNF4G

Ensembl transcript ID

ENST00000354370

Genbank transcript ID

N/A

UniProt peptide

Q14541

alteration type

single base exchange

alteration region

CDS

DNA changes

c.570G>A
cDNA.840G>A
g.148134G>A

AA changes

M190I Score: 10 explain score(s)

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

190

frameshift

known variant

Reference ID: rs1805098

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1067	945	2012
ExAC	21377	-9987	11390

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.772	0.865
	-0.051	0.85
(flanking)	4.958	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
Donor increased	148135	wt: 0.80 / mu: 0.95	wt: TGATGTATAAAGATA mu: TGATATATAAAGATA	ATGT\|ataa
Donor gained	148130	0.34	mu: ATCCATGATATATAA	CCAT\|gata

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

190

mutated

all conserved

190

Ptroglodytes

all identical

ENSPTRG00000020357

227

Mmulatta

all identical

ENSMMUG00000002774

190

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000017688

244

Ggallus

not conserved

ENSGALG00000015670

237

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000071565

240

Dmelanogaster

not conserved

FBgn0004914

354

Celegans

not conserved

T23H4.2

196

SIC

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
176	188	HELIX		might get lost (downstream of altered splice site)
191	196	STRAND		might get lost (downstream of altered splice site)
202	204	STRAND		might get lost (downstream of altered splice site)
210	212	TURN		might get lost (downstream of altered splice site)
213	222	HELIX		might get lost (downstream of altered splice site)
224	230	HELIX		might get lost (downstream of altered splice site)
234	245	HELIX		might get lost (downstream of altered splice site)
256	275	HELIX		might get lost (downstream of altered splice site)
277	280	STRAND		might get lost (downstream of altered splice site)
281	283	TURN		might get lost (downstream of altered splice site)
284	289	HELIX		might get lost (downstream of altered splice site)
292	311	HELIX		might get lost (downstream of altered splice site)
319	324	HELIX		might get lost (downstream of altered splice site)
325	327	TURN		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1227 / 1227

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

409 / 409

position of stopcodon in wt / mu cDNA

1497 / 1497

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

271 / 271

chromosome

strand

last intron/exon boundary

1376

theoretical NMD boundary in CDS

1055

length of CDS

1227

coding sequence (CDS) position

570

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

840

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

148134

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

76468282

original gDNA sequence snippet

GCTACAAAGAGATCCATGATGTATAAAGATATTTTGCTTTT

altered gDNA sequence snippet

GCTACAAAGAGATCCATGATATATAAAGATATTTTGCTTTT

original cDNA sequence snippet

GCTACAAAGAGATCCATGATGTATAAAGATATTTTGCTTTT

altered cDNA sequence snippet

GCTACAAAGAGATCCATGATATATAAAGATATTTTGCTTTT

wildtype AA sequence

MNTTDNGVNC LCAICGDRAT GKHYGASSCD GCKGFFRRSI RKSHVYSCRF SRQCVVDKDK
RNQCRYCRLR KCFRAGMKKE AVQNERDRIS TRRSTFDGSN IPSINTLAQA EVRSRQISVS
SPGSSTDINV KKIASIGDVC ESMKQQLLVL VEWAKYIPAF CELPLDDQVA LLRAHAGEHL
LLGATKRSMM YKDILLLGNN YVIHRNSCEV EISRVANRVL DELVRPFQEI QIDDNEYACL
KAIVFFDPDA KGLSDPVKIK NMRFQVQIGL EDYINDRQYD SRGRFGELLL LLPTLQSITW
QMIEQIQFVK LFGMVKIDNL LQEMLLGGAS NDGSHLHHPM HPHLSQDPLT GQTILLGPMS
TLVHADQIST PETPLPSPPQ GSGQEQYKIA ANQASVISHQ HLSKQKQL*

mutated AA sequence

MNTTDNGVNC LCAICGDRAT GKHYGASSCD GCKGFFRRSI RKSHVYSCRF SRQCVVDKDK
RNQCRYCRLR KCFRAGMKKE AVQNERDRIS TRRSTFDGSN IPSINTLAQA EVRSRQISVS
SPGSSTDINV KKIASIGDVC ESMKQQLLVL VEWAKYIPAF CELPLDDQVA LLRAHAGEHL
LLGATKRSMI YKDILLLGNN YVIHRNSCEV EISRVANRVL DELVRPFQEI QIDDNEYACL
KAIVFFDPDA KGLSDPVKIK NMRFQVQIGL EDYINDRQYD SRGRFGELLL LLPTLQSITW
QMIEQIQFVK LFGMVKIDNL LQEMLLGGAS NDGSHLHHPM HPHLSQDPLT GQTILLGPMS
TLVHADQIST PETPLPSPPQ GSGQEQYKIA ANQASVISHQ HLSKQKQL*

speed

0.52 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: 0.473063039539876 (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)

chr8:76468282G>AN/A show variant in all transcripts IGV

HGNC symbol

HNF4G

Ensembl transcript ID

ENST00000396423

Genbank transcript ID

NM_004133

UniProt peptide

Q14541

alteration type

single base exchange

alteration region

CDS

DNA changes

c.681G>A
cDNA.805G>A
g.148134G>A

AA changes

M227I Score: 10 explain score(s)

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

227

frameshift

known variant

Reference ID: rs1805098

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1067	945	2012
ExAC	21377	-9987	11390

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.772	0.865
	-0.051	0.85
(flanking)	4.958	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
Donor increased	148135	wt: 0.80 / mu: 0.95	wt: TGATGTATAAAGATA mu: TGATATATAAAGATA	ATGT\|ataa
Donor gained	148130	0.34	mu: ATCCATGATATATAA	CCAT\|gata

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

227

mutated

all conserved

227

Ptroglodytes

all identical

ENSPTRG00000020357

227

Mmulatta

all identical

ENSMMUG00000002774

190

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000017688

244

Ggallus

not conserved

ENSGALG00000015670

237

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000071565

240

Dmelanogaster

not conserved

FBgn0004914

354

Celegans

not conserved

T23H4.2

196

SIC

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
224	230	HELIX		lost
234	245	HELIX		might get lost (downstream of altered splice site)
256	275	HELIX		might get lost (downstream of altered splice site)
277	280	STRAND		might get lost (downstream of altered splice site)
281	283	TURN		might get lost (downstream of altered splice site)
284	289	HELIX		might get lost (downstream of altered splice site)
292	311	HELIX		might get lost (downstream of altered splice site)
319	324	HELIX		might get lost (downstream of altered splice site)
325	327	TURN		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1338 / 1338

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

446 / 446

position of stopcodon in wt / mu cDNA

1462 / 1462

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

125 / 125

chromosome

strand

last intron/exon boundary

1341

theoretical NMD boundary in CDS

1166

length of CDS

1338

coding sequence (CDS) position

681

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

805

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

148134

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

76468282

original gDNA sequence snippet

GCTACAAAGAGATCCATGATGTATAAAGATATTTTGCTTTT

altered gDNA sequence snippet

GCTACAAAGAGATCCATGATATATAAAGATATTTTGCTTTT

original cDNA sequence snippet

GCTACAAAGAGATCCATGATGTATAAAGATATTTTGCTTTT

altered cDNA sequence snippet

GCTACAAAGAGATCCATGATATATAAAGATATTTTGCTTTT

wildtype AA sequence

MDMANYSEVL DPTYTTLEFE TMQILYNSSD SSAPETSMNT TDNGVNCLCA ICGDRATGKH
YGASSCDGCK GFFRRSIRKS HVYSCRFSRQ CVVDKDKRNQ CRYCRLRKCF RAGMKKEAVQ
NERDRISTRR STFDGSNIPS INTLAQAEVR SRQISVSSPG SSTDINVKKI ASIGDVCESM
KQQLLVLVEW AKYIPAFCEL PLDDQVALLR AHAGEHLLLG ATKRSMMYKD ILLLGNNYVI
HRNSCEVEIS RVANRVLDEL VRPFQEIQID DNEYACLKAI VFFDPDAKGL SDPVKIKNMR
FQVQIGLEDY INDRQYDSRG RFGELLLLLP TLQSITWQMI EQIQFVKLFG MVKIDNLLQE
MLLGGASNDG SHLHHPMHPH LSQDPLTGQT ILLGPMSTLV HADQISTPET PLPSPPQGSG
QEQYKIAANQ ASVISHQHLS KQKQL*

mutated AA sequence

MDMANYSEVL DPTYTTLEFE TMQILYNSSD SSAPETSMNT TDNGVNCLCA ICGDRATGKH
YGASSCDGCK GFFRRSIRKS HVYSCRFSRQ CVVDKDKRNQ CRYCRLRKCF RAGMKKEAVQ
NERDRISTRR STFDGSNIPS INTLAQAEVR SRQISVSSPG SSTDINVKKI ASIGDVCESM
KQQLLVLVEW AKYIPAFCEL PLDDQVALLR AHAGEHLLLG ATKRSMIYKD ILLLGNNYVI
HRNSCEVEIS RVANRVLDEL VRPFQEIQID DNEYACLKAI VFFDPDAKGL SDPVKIKNMR
FQVQIGLEDY INDRQYDSRG RFGELLLLLP TLQSITWQMI EQIQFVKLFG MVKIDNLLQE
MLLGGASNDG SHLHHPMHPH LSQDPLTGQT ILLGPMSTLV HADQISTPET PLPSPPQGSG
QEQYKIAANQ ASVISHQHLS KQKQL*

speed

0.46 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems