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: ENST00000454765
Querying Taster for transcript #2: ENST00000287773
MT speed 2.18 s - this script 4.215971 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
TMEM171	polymorphism_automatic	0.000206154810251991	simple_aae		affected		N139K	single base exchange	rs636926		show file
TMEM171	polymorphism_automatic	0.000206154810251991	simple_aae		affected		N139K	single base exchange	rs636926		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999793845189748 (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)

chr5:72419617C>AN/A show variant in all transcripts IGV

HGNC symbol

TMEM171

Ensembl transcript ID

ENST00000454765

Genbank transcript ID

NM_173490

UniProt peptide

Q8WVE6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.417C>A
cDNA.890C>A
g.3499C>A

AA changes

N139K Score: 94 explain score(s)

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

139

frameshift

known variant

Reference ID: rs636926

database	homozygous (A/A)	heterozygous	allele carriers
1000G	561	1123	1684
ExAC	7186	18395	25581

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.044	0.726
	0.058	0.744
(flanking)	3.48	0.996

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	3502	wt: 0.50 / mu: 0.58	wt: AACTGGGCGCAGGAA mu: AAATGGGCGCAGGAA	CTGG\|gcgc
Donor gained	3499	0.31	mu: TCCAAATGGGCGCAG	CAAA\|tggg

distance from splice site

224

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

139

mutated

not conserved

139

Ptroglodytes

all identical

ENSPTRG00000016977

139

Mmulatta

all conserved

ENSMMUG00000015433

139

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000052485

138

Ggallus

no alignment

ENSGALG00000015020

n/a

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000026182

139

protein features

start (aa)	end (aa)	feature	details
160	180	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
323	323	CONFLICT	P -> S (in Ref. 2; AAH35310).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

975 / 975

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

325 / 325

position of stopcodon in wt / mu cDNA

1448 / 1448

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

474 / 474

chromosome

strand

last intron/exon boundary

1256

theoretical NMD boundary in CDS

732

length of CDS

975

coding sequence (CDS) position

417

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

890

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

3499

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

72419617

original gDNA sequence snippet

GTCCCTGGATGTGGCTCCAACTGGGCGCAGGAACCGCTAAA

altered gDNA sequence snippet

GTCCCTGGATGTGGCTCCAAATGGGCGCAGGAACCGCTAAA

original cDNA sequence snippet

GTCCCTGGATGTGGCTCCAACTGGGCGCAGGAACCGCTAAA

altered cDNA sequence snippet

GTCCCTGGATGTGGCTCCAAATGGGCGCAGGAACCGCTAAA

wildtype AA sequence

MSPAAAAEPD GDQQDRHVSK LIFCFFVFGA VLLCVGVLLS IFGFQACQYK PLPDCPMVLK
VAGPACAVVG LGAVILARSR AQLQLRAGLQ RGQQMDPDRA FICGESRQFA QCLIFGFLFL
TSGMLISVLG IWVPGCGSNW AQEPLNETDT GDSEPRMCGF LSLQIMGPLI VLVGLCFFVV
AHVKKRNTLN AGQDASEREE GQIQIMEPVQ VTVGDSVIIF PPPPPPYFPE SSASAVAESP
GTNSLLPNEN PPSYYSIFNY GRTPTSEGAA SERDCESIYT ISGTNSSSEA SHTPHLPSEL
PPRYEEKENA AATFLPLSSE PSPP*

mutated AA sequence

MSPAAAAEPD GDQQDRHVSK LIFCFFVFGA VLLCVGVLLS IFGFQACQYK PLPDCPMVLK
VAGPACAVVG LGAVILARSR AQLQLRAGLQ RGQQMDPDRA FICGESRQFA QCLIFGFLFL
TSGMLISVLG IWVPGCGSKW AQEPLNETDT GDSEPRMCGF LSLQIMGPLI VLVGLCFFVV
AHVKKRNTLN AGQDASEREE GQIQIMEPVQ VTVGDSVIIF PPPPPPYFPE SSASAVAESP
GTNSLLPNEN PPSYYSIFNY GRTPTSEGAA SERDCESIYT ISGTNSSSEA SHTPHLPSEL
PPRYEEKENA AATFLPLSSE PSPP*

speed

1.27 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: 0.999793845189748 (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)

chr5:72419617C>AN/A show variant in all transcripts IGV

HGNC symbol

TMEM171

Ensembl transcript ID

ENST00000287773

Genbank transcript ID

NM_001161342

UniProt peptide

Q8WVE6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.417C>A
cDNA.613C>A
g.3499C>A

AA changes

N139K Score: 94 explain score(s)

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

139

frameshift

known variant

Reference ID: rs636926

database	homozygous (A/A)	heterozygous	allele carriers
1000G	561	1123	1684
ExAC	7186	18395	25581

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.044	0.726
	0.058	0.744
(flanking)	3.48	0.996

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	3502	wt: 0.50 / mu: 0.58	wt: AACTGGGCGCAGGAA mu: AAATGGGCGCAGGAA	CTGG\|gcgc
Donor gained	3499	0.31	mu: TCCAAATGGGCGCAG	CAAA\|tggg

distance from splice site

224

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

139

mutated

not conserved

139

Ptroglodytes

all identical

ENSPTRG00000016977

139

Mmulatta

all conserved

ENSMMUG00000015433

139

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000052485

138

Ggallus

no alignment

ENSGALG00000015020

n/a

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000026182

139

protein features

start (aa)	end (aa)	feature	details
160	180	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
323	323	CONFLICT	P -> S (in Ref. 2; AAH35310).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

972 / 972

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

324 / 324

position of stopcodon in wt / mu cDNA

1168 / 1168

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

197 / 197

chromosome

strand

last intron/exon boundary

979

theoretical NMD boundary in CDS

732

length of CDS

972

coding sequence (CDS) position

417

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

613

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

3499

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

72419617

original gDNA sequence snippet

GTCCCTGGATGTGGCTCCAACTGGGCGCAGGAACCGCTAAA

altered gDNA sequence snippet

GTCCCTGGATGTGGCTCCAAATGGGCGCAGGAACCGCTAAA

original cDNA sequence snippet

GTCCCTGGATGTGGCTCCAACTGGGCGCAGGAACCGCTAAA

altered cDNA sequence snippet

GTCCCTGGATGTGGCTCCAAATGGGCGCAGGAACCGCTAAA

wildtype AA sequence

MSPAAAAEPD GDQQDRHVSK LIFCFFVFGA VLLCVGVLLS IFGFQACQYK PLPDCPMVLK
VAGPACAVVG LGAVILARSR AQLQLRAGLQ RGQQMDPDRA FICGESRQFA QCLIFGFLFL
TSGMLISVLG IWVPGCGSNW AQEPLNETDT GDSEPRMCGF LSLQIMGPLI VLVGLCFFVV
AHVKKRNTLN AGQDASEREE GQIQIMEPVQ VTVGDSVIIF PPPPPPYFPE SSASAVAESP
GTNSLLPNEN PPSYYSIFNY GTPTSEGAAS ERDCESIYTI SGTNSSSEAS HTPHLPSELP
PRYEEKENAA ATFLPLSSEP SPP*

mutated AA sequence

MSPAAAAEPD GDQQDRHVSK LIFCFFVFGA VLLCVGVLLS IFGFQACQYK PLPDCPMVLK
VAGPACAVVG LGAVILARSR AQLQLRAGLQ RGQQMDPDRA FICGESRQFA QCLIFGFLFL
TSGMLISVLG IWVPGCGSKW AQEPLNETDT GDSEPRMCGF LSLQIMGPLI VLVGLCFFVV
AHVKKRNTLN AGQDASEREE GQIQIMEPVQ VTVGDSVIIF PPPPPPYFPE SSASAVAESP
GTNSLLPNEN PPSYYSIFNY GTPTSEGAAS ERDCESIYTI SGTNSSSEAS HTPHLPSELP
PRYEEKENAA ATFLPLSSEP SPP*

speed

0.91 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems