MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000563385
Querying Taster for transcript #2: ENST00000368143
Querying Taster for transcript #3: ENST00000438392
MT speed 0 s - this script 4.32151 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
TMEM244	polymorphism_automatic	0.587020507239122	simple_aae		affected		F111V	single base exchange	rs7776426		show file
TMEM244	polymorphism_automatic	0.587020507239122	simple_aae		affected		F111V	single base exchange	rs7776426		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.412979492760878 (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)

chr6:130152520A>CN/A show variant in all transcripts IGV

HGNC symbol

TMEM244

Ensembl transcript ID

ENST00000368143

Genbank transcript ID

NM_001010876

UniProt peptide

Q5VVB8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.331T>G
cDNA.414T>G
g.30173T>G

AA changes

F111V Score: 50 explain score(s)

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

111

frameshift

known variant

Reference ID: rs7776426

database	homozygous (C/C)	heterozygous	allele carriers
1000G	181	853	1034
ExAC	9361	14045	23406

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.615	1
	1.604	1
(flanking)	0.929	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
Acc marginally increased	30167	wt: 0.2250 / mu: 0.2358 (marginal change - not scored)	wt: TTTTTTCTATTGCAGTTATGTTGGAATTCCCCTTGACATCA mu: TTTTTTCTATTGCAGTTATGTTGGAAGTCCCCTTGACATCA	atgt\|TGGA
Acc increased	30165	wt: 0.65 / mu: 0.81	wt: TTTTTTTTCTATTGCAGTTATGTTGGAATTCCCCTTGACAT mu: TTTTTTTTCTATTGCAGTTATGTTGGAAGTCCCCTTGACAT	ttat\|GTTG
Donor gained	30167	0.97	mu: TTATGTTGGAAGTCC	ATGT\|tgga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

111

mutated

not conserved

111

Ptroglodytes

all identical

ENSPTRG00000029415

111

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

all identical

ENSGALG00000023015

111

Trubripes

no homologue

Drerio

all identical

ENSDARG00000043847

132

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
93	113	TRANSMEM	Helical; (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

387 / 387

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

129 / 129

position of stopcodon in wt / mu cDNA

470 / 470

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

84 / 84

chromosome

strand

-1

last intron/exon boundary

403

theoretical NMD boundary in CDS

269

length of CDS

387

coding sequence (CDS) position

331

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

414

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

30173

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

130152520

original gDNA sequence snippet

CTATTGCAGTTATGTTGGAATTCCCCTTGACATCACATTGG

altered gDNA sequence snippet

CTATTGCAGTTATGTTGGAAGTCCCCTTGACATCACATTGG

original cDNA sequence snippet

CTTCAACTGTTATGTTGGAATTCCCCTTGACATCACATTGG

altered cDNA sequence snippet

CTTCAACTGTTATGTTGGAAGTCCCCTTGACATCACATTGG

wildtype AA sequence

MALQVRVAPS KVVLQKFLLC VILFYTVYYV SLSMGCVMFE VHELNVLAPF DFKTNPSWLN
INYKVLLVST EVTYFVCGLF FVPVVEEWVW DYAISVTILH VAITSTVMLE FPLTSHWWAA
LGISKLLV*

mutated AA sequence

MALQVRVAPS KVVLQKFLLC VILFYTVYYV SLSMGCVMFE VHELNVLAPF DFKTNPSWLN
INYKVLLVST EVTYFVCGLF FVPVVEEWVW DYAISVTILH VAITSTVMLE VPLTSHWWAA
LGISKLLV*

speed

1.19 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: 0.412979492760878 (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)

chr6:130152520A>CN/A show variant in all transcripts IGV

HGNC symbol

TMEM244

Ensembl transcript ID

ENST00000438392

Genbank transcript ID

N/A

UniProt peptide

Q5VVB8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.331T>G
cDNA.512T>G
g.30173T>G

AA changes

F111V Score: 50 explain score(s)

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

111

frameshift

known variant

Reference ID: rs7776426

database	homozygous (C/C)	heterozygous	allele carriers
1000G	181	853	1034
ExAC	9361	14045	23406

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.615	1
	1.604	1
(flanking)	0.929	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
Acc marginally increased	30167	wt: 0.2250 / mu: 0.2358 (marginal change - not scored)	wt: TTTTTTCTATTGCAGTTATGTTGGAATTCCCCTTGACATCA mu: TTTTTTCTATTGCAGTTATGTTGGAAGTCCCCTTGACATCA	atgt\|TGGA
Acc increased	30165	wt: 0.65 / mu: 0.81	wt: TTTTTTTTCTATTGCAGTTATGTTGGAATTCCCCTTGACAT mu: TTTTTTTTCTATTGCAGTTATGTTGGAAGTCCCCTTGACAT	ttat\|GTTG
Donor gained	30167	0.97	mu: TTATGTTGGAAGTCC	ATGT\|tgga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

111

mutated

not conserved

111

Ptroglodytes

all identical

ENSPTRG00000029415

111

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

all identical

ENSGALG00000023015

111

Trubripes

no homologue

Drerio

all identical

ENSDARG00000043847

132

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
93	113	TRANSMEM	Helical; (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

387 / 387

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

129 / 129

position of stopcodon in wt / mu cDNA

568 / 568

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

182 / 182

chromosome

strand

-1

last intron/exon boundary

501

theoretical NMD boundary in CDS

269

length of CDS

387

coding sequence (CDS) position

331

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

512

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

30173

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

130152520

original gDNA sequence snippet

CTATTGCAGTTATGTTGGAATTCCCCTTGACATCACATTGG

altered gDNA sequence snippet

CTATTGCAGTTATGTTGGAAGTCCCCTTGACATCACATTGG

original cDNA sequence snippet

CTTCAACTGTTATGTTGGAATTCCCCTTGACATCACATTGG

altered cDNA sequence snippet

CTTCAACTGTTATGTTGGAAGTCCCCTTGACATCACATTGG

wildtype AA sequence

MALQVRVAPS KVVLQKFLLC VILFYTVYYV SLSMGCVMFE VHELNVLAPF DFKTNPSWLN
INYKVLLVST EVTYFVCGLF FVPVVEEWVW DYAISVTILH VAITSTVMLE FPLTSHWWAA
LGISKLLV*

mutated AA sequence

MALQVRVAPS KVVLQKFLLC VILFYTVYYV SLSMGCVMFE VHELNVLAPF DFKTNPSWLN
INYKVLLVST EVTYFVCGLF FVPVVEEWVW DYAISVTILH VAITSTVMLE VPLTSHWWAA
LGISKLLV*

speed

1.16 s

Problems

data problem

No NCBI gene ID found for this transcript

back to results table