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: ENST00000409280
Querying Taster for transcript #2: ENST00000283905
MT speed 0 s - this script 2.744648 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
C7orf31	polymorphism_automatic	1.1074934770372e-06	simple_aae				Y82C	single base exchange	rs2717858		show file
C7orf31	polymorphism_automatic	1.1074934770372e-06	simple_aae				Y82C	single base exchange	rs2717858		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999998892506523 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:25207974T>CN/A show variant in all transcripts IGV

HGNC symbol

C7orf31

Ensembl transcript ID

ENST00000409280

Genbank transcript ID

NM_138811

UniProt peptide

Q8N865

alteration type

single base exchange

alteration region

CDS

DNA changes

c.245A>G
cDNA.554A>G
g.12002A>G

AA changes

Y82C Score: 194 explain score(s)

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

frameshift

known variant

Reference ID: rs2717858

database	homozygous (C/C)	heterozygous	allele carriers
1000G	384	750	1134
ExAC	2841	13569	16410

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.247	0.93
	-0.169	0.916
(flanking)	0.994	0.973

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 marginally increased	11994	wt: 0.9923 / mu: 0.9940 (marginal change - not scored)	wt: CACAGGCCAAAGTAT mu: CACAGGCCAAAGTGT	CAGG\|ccaa

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

not conserved

ENSPTRG00000018997

Mmulatta

not conserved

ENSMMUG00000005701

Fcatus

not conserved

ENSFCAG00000008464

Mmusculus

not conserved

ENSMUSG00000029828

Ggallus

not conserved

ENSGALG00000011021

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1773 / 1773

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

591 / 591

position of stopcodon in wt / mu cDNA

2082 / 2082

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

310 / 310

chromosome

strand

-1

last intron/exon boundary

1261

theoretical NMD boundary in CDS

901

length of CDS

1773

coding sequence (CDS) position

245

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

554

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

12002

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

25207974

original gDNA sequence snippet

CGAGGACCACAGGCCAAAGTATGAGCCTCCTCGTGTCATGG

altered gDNA sequence snippet

CGAGGACCACAGGCCAAAGTGTGAGCCTCCTCGTGTCATGG

original cDNA sequence snippet

CGAGGACCACAGGCCAAAGTATGAGCCTCCTCGTGTCATGG

altered cDNA sequence snippet

CGAGGACCACAGGCCAAAGTGTGAGCCTCCTCGTGTCATGG

wildtype AA sequence

MEVIHGRPYC CRELEGADIL SNTFYSNELH NPLQTVTRPT ASEDRYQELR ESLQQCRLPW
GAEREYGGII PISLPEDHRP KYEPPRVMGK GHQHYGFGGE TWPRKLPVEQ FYYLTQNKKS
DVYGNDSLIP KPPNSTVGEI CLPYPIEHPY HTHICRGAMF PTFTSPEDLY TGIKARTQQP
FPPTVPTKAY DSTVLKTRGN PYRYELIDIP MDSKKKALTW PGQGVYYDFP RGVEKNKPVF
YPKPPKTFAP NTSLNSWDPI CSAKEANIQR NLERSHWLTS YTHDFTGLGP MDPLELDDYH
EKMVAELTRK IGFDPEPQEK FHPVFKPPRP LEGRIARLIQ NRRSLEAIVQ QRPRSCPDCT
PRVLCNFHTF VPSSKEMVAL SDNIPAGVTH KNQDIEEKII EEQSLLSTYE LPSCYPTKDL
TSIYDIKPFP KITDTKKTED LYWRQQSLKT QPTPYCKPDH WIHYENLKSP LRDQYNMCPD
PVSLSKPSVL QNKQDTEAFT LEHFLSKPEE ELFLNMENNE ETRPVLGWIP RAGVTKPQTN
LLELKNSFSK TGAQKRFHKS ILEDHKDLRD NEHSGMKHQF YGHNSYYFYN *

mutated AA sequence

MEVIHGRPYC CRELEGADIL SNTFYSNELH NPLQTVTRPT ASEDRYQELR ESLQQCRLPW
GAEREYGGII PISLPEDHRP KCEPPRVMGK GHQHYGFGGE TWPRKLPVEQ FYYLTQNKKS
DVYGNDSLIP KPPNSTVGEI CLPYPIEHPY HTHICRGAMF PTFTSPEDLY TGIKARTQQP
FPPTVPTKAY DSTVLKTRGN PYRYELIDIP MDSKKKALTW PGQGVYYDFP RGVEKNKPVF
YPKPPKTFAP NTSLNSWDPI CSAKEANIQR NLERSHWLTS YTHDFTGLGP MDPLELDDYH
EKMVAELTRK IGFDPEPQEK FHPVFKPPRP LEGRIARLIQ NRRSLEAIVQ QRPRSCPDCT
PRVLCNFHTF VPSSKEMVAL SDNIPAGVTH KNQDIEEKII EEQSLLSTYE LPSCYPTKDL
TSIYDIKPFP KITDTKKTED LYWRQQSLKT QPTPYCKPDH WIHYENLKSP LRDQYNMCPD
PVSLSKPSVL QNKQDTEAFT LEHFLSKPEE ELFLNMENNE ETRPVLGWIP RAGVTKPQTN
LLELKNSFSK TGAQKRFHKS ILEDHKDLRD NEHSGMKHQF YGHNSYYFYN *

speed

0.36 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: 0.999998892506523 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:25207974T>CN/A show variant in all transcripts IGV

HGNC symbol

C7orf31

Ensembl transcript ID

ENST00000283905

Genbank transcript ID

N/A

UniProt peptide

Q8N865

alteration type

single base exchange

alteration region

CDS

DNA changes

c.245A>G
cDNA.908A>G
g.12002A>G

AA changes

Y82C Score: 194 explain score(s)

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

frameshift

known variant

Reference ID: rs2717858

database	homozygous (C/C)	heterozygous	allele carriers
1000G	384	750	1134
ExAC	2841	13569	16410

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.247	0.93
	-0.169	0.916
(flanking)	0.994	0.973

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 marginally increased	11994	wt: 0.9923 / mu: 0.9940 (marginal change - not scored)	wt: CACAGGCCAAAGTAT mu: CACAGGCCAAAGTGT	CAGG\|ccaa

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

not conserved

ENSPTRG00000018997

Mmulatta

not conserved

ENSMMUG00000005701

Fcatus

not conserved

ENSFCAG00000008464

Mmusculus

not conserved

ENSMUSG00000029828

Ggallus

not conserved

ENSGALG00000011021

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1773 / 1773

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

591 / 591

position of stopcodon in wt / mu cDNA

2436 / 2436

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

664 / 664

chromosome

strand

-1

last intron/exon boundary

1615

theoretical NMD boundary in CDS

901

length of CDS

1773

coding sequence (CDS) position

245

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

908

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

12002

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

25207974

original gDNA sequence snippet

CGAGGACCACAGGCCAAAGTATGAGCCTCCTCGTGTCATGG

altered gDNA sequence snippet

CGAGGACCACAGGCCAAAGTGTGAGCCTCCTCGTGTCATGG

original cDNA sequence snippet

CGAGGACCACAGGCCAAAGTATGAGCCTCCTCGTGTCATGG

altered cDNA sequence snippet

CGAGGACCACAGGCCAAAGTGTGAGCCTCCTCGTGTCATGG

wildtype AA sequence

mutated AA sequence

speed

0.45 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems