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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000264560
Querying Taster for transcript #2: ENST00000338448
MT speed 0 s - this script 3.712365 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PALM	polymorphism_automatic	2.80997447532627e-13	simple_aae		affected		T107A	single base exchange	rs1050457		show file
PALM	polymorphism_automatic	2.80997447532627e-13	simple_aae		affected		T107A	single base exchange	rs1050457		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999719 (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)

chr19:731144A>GN/A show variant in all transcripts IGV

HGNC symbol

PALM

Ensembl transcript ID

ENST00000264560

Genbank transcript ID

NM_001040134

UniProt peptide

O75781

alteration type

single base exchange

alteration region

CDS

DNA changes

c.319A>G
cDNA.513A>G
g.22192A>G

AA changes

T107A Score: 58 explain score(s)

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

107

frameshift

known variant

Reference ID: rs1050457

database	homozygous (G/G)	heterozygous	allele carriers
1000G	795	1146	1941
ExAC	11005	10757	21762

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.24	0
	-0.124	0
(flanking)	0.451	0.001

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	22199	wt: 0.25 / mu: 0.47	wt: CTCCGCCCCAGCCACTGCCAAGGAGAACGCGGCGGCCCCGA mu: CTCCGCCCCAGCCGCTGCCAAGGAGAACGCGGCGGCCCCGA	ccaa\|GGAG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

107

mutated

not conserved

107

Ptroglodytes

not conserved

ENSPTRG00000010163

105

Mmulatta

not conserved

ENSMMUG00000022877

102

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000035863

107

Ggallus

all identical

ENSGALG00000001846

174

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000014639

105

protein features

start (aa)	end (aa)	feature	details
116	116	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
124	124	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
141	141	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
145	145	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
152	152	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
154	154	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
158	158	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
162	162	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
346	346	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
367	367	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
369	369	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
381	381	LIPID	S-palmitoyl cysteine (Potential).	might get lost (downstream of altered splice site)
381	383	MUTAGEN	CKC->SKS: Inhibits axonal and dendritic filopodia formation and reduces axonal and dendritic branching.	might get lost (downstream of altered splice site)
383	383	LIPID	S-palmitoyl cysteine (Potential).	might get lost (downstream of altered splice site)
384	384	MOD_RES	Cysteine methyl ester (Potential).	might get lost (downstream of altered splice site)
384	384	LIPID	S-farnesyl cysteine (Potential).	might get lost (downstream of altered splice site)
385	387	PROPEP	Removed in mature form (Potential). /FTId=PRO_0000396689.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1032 / 1032

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

344 / 344

position of stopcodon in wt / mu cDNA

1226 / 1226

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

195 / 195

chromosome

strand

last intron/exon boundary

697

theoretical NMD boundary in CDS

452

length of CDS

1032

coding sequence (CDS) position

319

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

513

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

22192

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

731144

original gDNA sequence snippet

GTGGAGACTCCGCCCCAGCCACTGCCAAGGAGAACGCGGCG

altered gDNA sequence snippet

GTGGAGACTCCGCCCCAGCCGCTGCCAAGGAGAACGCGGCG

original cDNA sequence snippet

GTGGAGACTCCGCCCCAGCCACTGCCAAGGAGAACGCGGCG

altered cDNA sequence snippet

GTGGAGACTCCGCCCCAGCCGCTGCCAAGGAGAACGCGGCG

wildtype AA sequence

MEVLAAETTS QQERLQAIAE KRKRQAEIEN KRRQLEDERR QLQHLKSKAL RERWLLEGTP
SSASEGDEDL RRQMQDDEQK TRLLEDSVSR LEKEIEVLER GDSAPATAKE NAAAPSPVRA
PAPSPAKEER KTEVVMNSQQ TPVGTPKDKR VSNTPLRTVD GSPMMKAVVH AVDGTAENGI
HPLSSSEVDE LIHKADEVTL SEAGSTAGAA ETRGAVEGAA RTTPSRREIT GVQAQPGEAT
SGPPGIQPGQ EPPVTMIFMG YQNVEDEAET KKVLGLQDTI TAELVVIEDA AEPKEPAPPN
GSAAEPPTEA ASREENQAGP EATTSDPQDL DMKKHRCKCC SIM*

mutated AA sequence

MEVLAAETTS QQERLQAIAE KRKRQAEIEN KRRQLEDERR QLQHLKSKAL RERWLLEGTP
SSASEGDEDL RRQMQDDEQK TRLLEDSVSR LEKEIEVLER GDSAPAAAKE NAAAPSPVRA
PAPSPAKEER KTEVVMNSQQ TPVGTPKDKR VSNTPLRTVD GSPMMKAVVH AVDGTAENGI
HPLSSSEVDE LIHKADEVTL SEAGSTAGAA ETRGAVEGAA RTTPSRREIT GVQAQPGEAT
SGPPGIQPGQ EPPVTMIFMG YQNVEDEAET KKVLGLQDTI TAELVVIEDA AEPKEPAPPN
GSAAEPPTEA ASREENQAGP EATTSDPQDL DMKKHRCKCC SIM*

speed

0.90 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: 0.999999999999719 (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)

chr19:731144A>GN/A show variant in all transcripts IGV

HGNC symbol

PALM

Ensembl transcript ID

ENST00000338448

Genbank transcript ID

NM_002579

UniProt peptide

O75781

alteration type

single base exchange

alteration region

CDS

DNA changes

c.319A>G
cDNA.365A>G
g.22192A>G

AA changes

T107A Score: 58 explain score(s)

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

107

frameshift

known variant

Reference ID: rs1050457

database	homozygous (G/G)	heterozygous	allele carriers
1000G	795	1146	1941
ExAC	11005	10757	21762

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.24	0
	-0.124	0
(flanking)	0.451	0.001

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	22199	wt: 0.25 / mu: 0.47	wt: CTCCGCCCCAGCCACTGCCAAGGAGAACGCGGCGGCCCCGA mu: CTCCGCCCCAGCCGCTGCCAAGGAGAACGCGGCGGCCCCGA	ccaa\|GGAG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

107

mutated

not conserved

107

Ptroglodytes

not conserved

ENSPTRG00000010163

105

Mmulatta

not conserved

ENSMMUG00000022877

102

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000035863

107

Ggallus

all identical

ENSGALG00000001846

174

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000014639

105

protein features

start (aa)	end (aa)	feature	details
116	116	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
124	124	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
141	141	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
145	145	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
152	152	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
154	154	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
158	158	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
162	162	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
346	346	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
367	367	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
369	369	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
381	381	LIPID	S-palmitoyl cysteine (Potential).	might get lost (downstream of altered splice site)
381	383	MUTAGEN	CKC->SKS: Inhibits axonal and dendritic filopodia formation and reduces axonal and dendritic branching.	might get lost (downstream of altered splice site)
383	383	LIPID	S-palmitoyl cysteine (Potential).	might get lost (downstream of altered splice site)
384	384	MOD_RES	Cysteine methyl ester (Potential).	might get lost (downstream of altered splice site)
384	384	LIPID	S-farnesyl cysteine (Potential).	might get lost (downstream of altered splice site)
385	387	PROPEP	Removed in mature form (Potential). /FTId=PRO_0000396689.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1164 / 1164

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

388 / 388

position of stopcodon in wt / mu cDNA

1210 / 1210

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

47 / 47

chromosome

strand

last intron/exon boundary

681

theoretical NMD boundary in CDS

584

length of CDS

1164

coding sequence (CDS) position

319

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

365

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

22192

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

731144

original gDNA sequence snippet

GTGGAGACTCCGCCCCAGCCACTGCCAAGGAGAACGCGGCG

altered gDNA sequence snippet

GTGGAGACTCCGCCCCAGCCGCTGCCAAGGAGAACGCGGCG

original cDNA sequence snippet

GTGGAGACTCCGCCCCAGCCACTGCCAAGGAGAACGCGGCG

altered cDNA sequence snippet

GTGGAGACTCCGCCCCAGCCGCTGCCAAGGAGAACGCGGCG

wildtype AA sequence

MEVLAAETTS QQERLQAIAE KRKRQAEIEN KRRQLEDERR QLQHLKSKAL RERWLLEGTP
SSASEGDEDL RRQMQDDEQK TRLLEDSVSR LEKEIEVLER GDSAPATAKE NAAAPSPVRA
PAPSPAKEER KTEVVMNSQQ TPVGTPKDKR VSNTPLRTVD GSPMMKAAMY SVEITVEKDK
VTGETRVLSS TTLLPRQPLP LGIKVYEDET KVVHAVDGTA ENGIHPLSSS EVDELIHKAD
EVTLSEAGST AGAAETRGAV EGAARTTPSR REITGVQAQP GEATSGPPGI QPGQEPPVTM
IFMGYQNVED EAETKKVLGL QDTITAELVV IEDAAEPKEP APPNGSAAEP PTEAASREEN
QAGPEATTSD PQDLDMKKHR CKCCSIM*

mutated AA sequence

MEVLAAETTS QQERLQAIAE KRKRQAEIEN KRRQLEDERR QLQHLKSKAL RERWLLEGTP
SSASEGDEDL RRQMQDDEQK TRLLEDSVSR LEKEIEVLER GDSAPAAAKE NAAAPSPVRA
PAPSPAKEER KTEVVMNSQQ TPVGTPKDKR VSNTPLRTVD GSPMMKAAMY SVEITVEKDK
VTGETRVLSS TTLLPRQPLP LGIKVYEDET KVVHAVDGTA ENGIHPLSSS EVDELIHKAD
EVTLSEAGST AGAAETRGAV EGAARTTPSR REITGVQAQP GEATSGPPGI QPGQEPPVTM
IFMGYQNVED EAETKKVLGL QDTITAELVV IEDAAEPKEP APPNGSAAEP PTEAASREEN
QAGPEATTSD PQDLDMKKHR CKCCSIM*

speed

0.82 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems