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: ENST00000515037
Querying Taster for transcript #2: ENST00000358869
MT speed 0 s - this script 3.51097 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FAM114A1	polymorphism_automatic	0.051554209986308	simple_aae		affected		G84R	single base exchange	rs11096964		show file
FAM114A1	polymorphism_automatic	0.927445185355182	without_aae		affected			single base exchange	rs11096964		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.948445790013692 (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)

chr4:38879949G>AN/A show variant in all transcripts IGV

HGNC symbol

FAM114A1

Ensembl transcript ID

ENST00000358869

Genbank transcript ID

NM_138389

UniProt peptide

Q8IWE2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.250G>A
cDNA.426G>A
g.10652G>A

AA changes

G84R Score: 125 explain score(s)

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

frameshift

known variant

Reference ID: rs11096964

database	homozygous (A/A)	heterozygous	allele carriers
1000G	124	770	894
ExAC	4092	21824	25916

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.397	0.143
	0.593	0.52
(flanking)	1.098	0.817

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	10653	wt: 0.5736 / mu: 0.5981 (marginal change - not scored)	wt: CCTGGAGCCCCCTCTCAATGGAGACGTGACTGAGGATACAC mu: CCTGGAGCCCCCTCTCAATAGAGACGTGACTGAGGATACAC	atgg\|AGAC
Acc increased	10649	wt: 0.53 / mu: 0.63	wt: ACGCCCTGGAGCCCCCTCTCAATGGAGACGTGACTGAGGAT mu: ACGCCCTGGAGCCCCCTCTCAATAGAGACGTGACTGAGGAT	ctca\|ATGG
Donor marginally increased	10652	wt: 0.9956 / mu: 0.9982 (marginal change - not scored)	wt: TCAATGGAGACGTGA mu: TCAATAGAGACGTGA	AATG\|gaga
Donor increased	10654	wt: 0.79 / mu: 0.96	wt: AATGGAGACGTGACT mu: AATAGAGACGTGACT	TGGA\|gacg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000023549

Mmulatta

all identical

ENSMMUG00000004471

Fcatus

no alignment

ENSFCAG00000005987

n/a

Mmusculus

all identical

ENSMUSG00000029185

Ggallus

all identical

ENSGALG00000013583

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000008287

Dmelanogaster

no alignment

FBgn0038360

n/a

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000018498

n/a

protein features

start (aa)	end (aa)	feature	details
196	196	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
199	199	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
343	367	COILED	Potential.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1692 / 1692

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

564 / 564

position of stopcodon in wt / mu cDNA

1868 / 1868

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

177 / 177

chromosome

strand

last intron/exon boundary

1767

theoretical NMD boundary in CDS

1540

length of CDS

1692

coding sequence (CDS) position

250

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

426

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

10652

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

38879949

original gDNA sequence snippet

CCCTGGAGCCCCCTCTCAATGGAGACGTGACTGAGGATACA

altered gDNA sequence snippet

CCCTGGAGCCCCCTCTCAATAGAGACGTGACTGAGGATACA

original cDNA sequence snippet

CCCTGGAGCCCCCTCTCAATGGAGACGTGACTGAGGATACA

altered cDNA sequence snippet

CCCTGGAGCCCCCTCTCAATAGAGACGTGACTGAGGATACA

wildtype AA sequence

MSDDAGDTLA TGDKAEVTEM PNSDSLPEDA EVHCDSAAVS HEPTPADPRG EGHENAAVQG
AGAAAIGPPV QPQDANALEP PLNGDVTEDT LAECIDSVSL EAEPRSEIPL QEQNYLAVDS
PPSGGGWAGW GSWGKSLLSS ASATVGHGLT AVKEKAGATL RIHGVNSGSS EGAQPNTENG
VPEITDAATD QGPAESPPTS PSSASRGMLS AITNVVQNTG KSVLTGGLDA LEFIGKKTMN
VLAESDPGFK RTKTLMERTV SLSQMLREAK EKEKQRLAQQ LTMERTAHYG MLFDEYQGLS
HLEALEILSN ESESKVQSFL ASLDGEKLEL LKNDLISIKD IFAAKELENE ENQEEQGLEE
KGEEFARMLT ELLFELHVAA TPDKLNKAMK RAHDWVEEDQ TVVSVDVAKV SEEETKKEEK
EEKSQDPQED KKEEKKTKTI EEVYMSSIES LAEVTARCIE QLHKVAELIL HGQEEEKPAQ
DQAKVLIKLT TAMCNEVASL SKKFTNSLTT VGSNKKAEVL NPMISSVLLE GCNSTTYIQD
AFQLLLPVLQ VSHIQTSCLK AQP*

mutated AA sequence

MSDDAGDTLA TGDKAEVTEM PNSDSLPEDA EVHCDSAAVS HEPTPADPRG EGHENAAVQG
AGAAAIGPPV QPQDANALEP PLNRDVTEDT LAECIDSVSL EAEPRSEIPL QEQNYLAVDS
PPSGGGWAGW GSWGKSLLSS ASATVGHGLT AVKEKAGATL RIHGVNSGSS EGAQPNTENG
VPEITDAATD QGPAESPPTS PSSASRGMLS AITNVVQNTG KSVLTGGLDA LEFIGKKTMN
VLAESDPGFK RTKTLMERTV SLSQMLREAK EKEKQRLAQQ LTMERTAHYG MLFDEYQGLS
HLEALEILSN ESESKVQSFL ASLDGEKLEL LKNDLISIKD IFAAKELENE ENQEEQGLEE
KGEEFARMLT ELLFELHVAA TPDKLNKAMK RAHDWVEEDQ TVVSVDVAKV SEEETKKEEK
EEKSQDPQED KKEEKKTKTI EEVYMSSIES LAEVTARCIE QLHKVAELIL HGQEEEKPAQ
DQAKVLIKLT TAMCNEVASL SKKFTNSLTT VGSNKKAEVL NPMISSVLLE GCNSTTYIQD
AFQLLLPVLQ VSHIQTSCLK AQP*

speed

0.84 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: 0.0725548146448178 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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)

chr4:38879949G>AN/A show variant in all transcripts IGV

HGNC symbol

FAM114A1

Ensembl transcript ID

ENST00000515037

Genbank transcript ID

N/A

UniProt peptide

Q8IWE2

alteration type

single base exchange

alteration region

intron

DNA changes

g.10652G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs11096964

database	homozygous (A/A)	heterozygous	allele carriers
1000G	124	770	894
ExAC	4092	21824	25916

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.397	0.143
	0.593	0.52
(flanking)	1.098	0.817

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

splice sites

splice site change before start ATG (at aa -90) |

effect	gDNA position	score	detection sequence	exon-intron border
Acc marginally increased	10653	wt: 0.5736 / mu: 0.5981 (marginal change - not scored)	wt: CCTGGAGCCCCCTCTCAATGGAGACGTGACTGAGGATACAC mu: CCTGGAGCCCCCTCTCAATAGAGACGTGACTGAGGATACAC	atgg\|AGAC
Acc increased	10649	wt: 0.53 / mu: 0.63	wt: ACGCCCTGGAGCCCCCTCTCAATGGAGACGTGACTGAGGAT mu: ACGCCCTGGAGCCCCCTCTCAATAGAGACGTGACTGAGGAT	ctca\|ATGG
Donor marginally increased	10652	wt: 0.9956 / mu: 0.9982 (marginal change - not scored)	wt: TCAATGGAGACGTGA mu: TCAATAGAGACGTGA	AATG\|gaga
Donor increased	10654	wt: 0.79 / mu: 0.96	wt: AATGGAGACGTGACT mu: AATAGAGACGTGACT	TGGA\|gacg

distance from splice site

10494

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
196	196	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
199	199	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
343	367	COILED	Potential.	might get lost (downstream of altered splice site)

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

358 / 358

chromosome

strand

last intron/exon boundary

1327

theoretical NMD boundary in CDS

919

length of CDS

1071

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)

10652

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

38879949

original gDNA sequence snippet

CCCTGGAGCCCCCTCTCAATGGAGACGTGACTGAGGATACA

altered gDNA sequence snippet

CCCTGGAGCCCCCTCTCAATAGAGACGTGACTGAGGATACA

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MLSAITNVVQ NTGKSVLTGG LDALEFIGKK TMNVLAESDP GFKRTKTLME RTVSLSQMLR
EAKEKEKQRL AQQLTMERTA HYGMLFDEYQ GLSHLEALEI LSNESESKVQ SFLASLDGEK
LELLKNDLIS IKDIFAAKEL ENEENQEEQG LEEKGEEFAR MLTELLFELH VAATPDKLNK
AMKRAHDWVE EDQTVVSVDV AKVSEEETKK EEKEEKSQDP QEDKKEEKKT KTIEEVYMSS
IESLAEVTAR CIEQLHKVAE LILHGQEEEK PAQDQAKVLI KLTTAMCNEV ASLSKKFTNS
LTTVGSNKKA EVLNPMISSV LLEGCNSTTY IQDAFQLLLP VLQVSHIQTS CLKAQP*

mutated AA sequence

N/A

speed

0.68 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems