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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000254122
Querying Taster for transcript #2: ENST00000417547
Querying Taster for transcript #3: ENST00000533718
MT speed 0 s - this script 2.743675 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FSHB	disease_causing_automatic	0.999999999905254	simple_aae		affected	0	C69G	single base exchange	rs5030776		show file
FSHB	disease_causing_automatic	0.999999999905254	simple_aae		affected	0	C69G	single base exchange	rs5030776		show file
FSHB	disease_causing_automatic	0.999999999905254	simple_aae		affected	0	C69G	single base exchange	rs5030776		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999905254 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM970535)
known disease mutation: rs16241 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:30255162T>GN/A show variant in all transcripts IGV

HGNC symbol

FSHB

Ensembl transcript ID

ENST00000254122

Genbank transcript ID

N/A

UniProt peptide

P01225

alteration type

single base exchange

alteration region

CDS

DNA changes

c.205T>G
cDNA.274T>G
g.2600T>G

AA changes

C69G Score: 159 explain score(s)

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

frameshift

known variant

Reference ID: rs5030776
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs16241 (pathogenic for Hypogonadotropic hypogonadism 24 without anosmia) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970535)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970535)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970535)

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.387	0.006
	4.229	0.993
(flanking)	5.103	0.998

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	2592	wt: 0.9516 / mu: 0.9718 (marginal change - not scored)	wt: AATCCAGAAAACATG mu: AATCCAGAAAACAGG	TCCA\|gaaa
Donor increased	2591	wt: 0.29 / mu: 0.35	wt: AAATCCAGAAAACAT mu: AAATCCAGAAAACAG	ATCC\|agaa
Donor increased	2599	wt: 0.21 / mu: 0.94	wt: AAAACATGTACCTTC mu: AAAACAGGTACCTTC	AACA\|tgta

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

ENSPTRG00000003463

Mmulatta

all identical

ENSMMUG00000018882

Fcatus

all identical

ENSFCAG00000014631

Mmusculus

all identical

ENSMUSG00000027120

Ggallus

all identical

ENSGALG00000012140

Trubripes

no homologue

Drerio

all identical

ENSDARG00000010841

Dmelanogaster

all identical

FBgn0063368

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000018246

protein features

start (aa)	end (aa)	feature	details
68	81	STRAND		lost
69	69	DISULFID		lost
84	84	DISULFID		might get lost (downstream of altered splice site)
90	103	STRAND		might get lost (downstream of altered splice site)
100	100	DISULFID		might get lost (downstream of altered splice site)
102	102	DISULFID		might get lost (downstream of altered splice site)
105	105	DISULFID		might get lost (downstream of altered splice site)
107	109	TURN		might get lost (downstream of altered splice site)
110	114	STRAND		might get lost (downstream of altered splice site)
112	112	DISULFID		might get lost (downstream of altered splice site)
122	122	DISULFID		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

390 / 390

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

130 / 130

position of stopcodon in wt / mu cDNA

459 / 459

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

70 / 70

chromosome

strand

last intron/exon boundary

229

theoretical NMD boundary in CDS

109

length of CDS

390

coding sequence (CDS) position

205

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

274

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

2600

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

30255162

original gDNA sequence snippet

GGCCCAAAATCCAGAAAACATGTACCTTCAAGGAACTGGTA

altered gDNA sequence snippet

GGCCCAAAATCCAGAAAACAGGTACCTTCAAGGAACTGGTA

original cDNA sequence snippet

GGCCCAAAATCCAGAAAACATGTACCTTCAAGGAACTGGTA

altered cDNA sequence snippet

GGCCCAAAATCCAGAAAACAGGTACCTTCAAGGAACTGGTA

wildtype AA sequence

MKTLQFFFLF CCWKAICCNS CELTNITIAI EKEECRFCIS INTTWCAGYC YTRDLVYKDP
ARPKIQKTCT FKELVYETVR VPGCAHHADS LYTYPVATQC HCGKCDSDST DCTVRGLGPS
YCSFGEMKE*

mutated AA sequence

MKTLQFFFLF CCWKAICCNS CELTNITIAI EKEECRFCIS INTTWCAGYC YTRDLVYKDP
ARPKIQKTGT FKELVYETVR VPGCAHHADS LYTYPVATQC HCGKCDSDST DCTVRGLGPS
YCSFGEMKE*

speed

0.42 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

disease causing

Model: simple_aae, prob: 0.999999999905254 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM970535)
known disease mutation: rs16241 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:30255162T>GN/A show variant in all transcripts IGV

HGNC symbol

FSHB

Ensembl transcript ID

ENST00000417547

Genbank transcript ID

NM_000510

UniProt peptide

P01225

alteration type

single base exchange

alteration region

CDS

DNA changes

c.205T>G
cDNA.244T>G
g.2600T>G

AA changes

C69G Score: 159 explain score(s)

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

frameshift

known variant

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.387	0.006
	4.229	0.993
(flanking)	5.103	0.998

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	2592	wt: 0.9516 / mu: 0.9718 (marginal change - not scored)	wt: AATCCAGAAAACATG mu: AATCCAGAAAACAGG	TCCA\|gaaa
Donor increased	2591	wt: 0.29 / mu: 0.35	wt: AAATCCAGAAAACAT mu: AAATCCAGAAAACAG	ATCC\|agaa
Donor increased	2599	wt: 0.21 / mu: 0.94	wt: AAAACATGTACCTTC mu: AAAACAGGTACCTTC	AACA\|tgta

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

ENSPTRG00000003463

Mmulatta

all identical

ENSMMUG00000018882

Fcatus

all identical

ENSFCAG00000014631

Mmusculus

all identical

ENSMUSG00000027120

Ggallus

all identical

ENSGALG00000012140

Trubripes

no homologue

Drerio

all identical

ENSDARG00000010841

Dmelanogaster

all identical

FBgn0063368

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000018246

protein features

start (aa)	end (aa)	feature	details
68	81	STRAND		lost
69	69	DISULFID		lost
84	84	DISULFID		might get lost (downstream of altered splice site)
90	103	STRAND		might get lost (downstream of altered splice site)
100	100	DISULFID		might get lost (downstream of altered splice site)
102	102	DISULFID		might get lost (downstream of altered splice site)
105	105	DISULFID		might get lost (downstream of altered splice site)
107	109	TURN		might get lost (downstream of altered splice site)
110	114	STRAND		might get lost (downstream of altered splice site)
112	112	DISULFID		might get lost (downstream of altered splice site)
122	122	DISULFID		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

390 / 390

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

130 / 130

position of stopcodon in wt / mu cDNA

429 / 429

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

40 / 40

chromosome

strand

last intron/exon boundary

199

theoretical NMD boundary in CDS

109

length of CDS

390

coding sequence (CDS) position

205

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

244

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

2600

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

30255162

original gDNA sequence snippet

GGCCCAAAATCCAGAAAACATGTACCTTCAAGGAACTGGTA

altered gDNA sequence snippet

GGCCCAAAATCCAGAAAACAGGTACCTTCAAGGAACTGGTA

original cDNA sequence snippet

GGCCCAAAATCCAGAAAACATGTACCTTCAAGGAACTGGTA

altered cDNA sequence snippet

GGCCCAAAATCCAGAAAACAGGTACCTTCAAGGAACTGGTA

wildtype AA sequence

MKTLQFFFLF CCWKAICCNS CELTNITIAI EKEECRFCIS INTTWCAGYC YTRDLVYKDP
ARPKIQKTCT FKELVYETVR VPGCAHHADS LYTYPVATQC HCGKCDSDST DCTVRGLGPS
YCSFGEMKE*

mutated AA sequence

MKTLQFFFLF CCWKAICCNS CELTNITIAI EKEECRFCIS INTTWCAGYC YTRDLVYKDP
ARPKIQKTGT FKELVYETVR VPGCAHHADS LYTYPVATQC HCGKCDSDST DCTVRGLGPS
YCSFGEMKE*

speed

0.28 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999905254 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM970535)
known disease mutation: rs16241 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:30255162T>GN/A show variant in all transcripts IGV

HGNC symbol

FSHB

Ensembl transcript ID

ENST00000533718

Genbank transcript ID

N/A

UniProt peptide

P01225

alteration type

single base exchange

alteration region

CDS

DNA changes

c.205T>G
cDNA.235T>G
g.2600T>G

AA changes

C69G Score: 159 explain score(s)

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

frameshift

known variant

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.387	0.006
	4.229	0.993
(flanking)	5.103	0.998

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	2592	wt: 0.9516 / mu: 0.9718 (marginal change - not scored)	wt: AATCCAGAAAACATG mu: AATCCAGAAAACAGG	TCCA\|gaaa
Donor increased	2591	wt: 0.29 / mu: 0.35	wt: AAATCCAGAAAACAT mu: AAATCCAGAAAACAG	ATCC\|agaa
Donor increased	2599	wt: 0.21 / mu: 0.94	wt: AAAACATGTACCTTC mu: AAAACAGGTACCTTC	AACA\|tgta

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

ENSPTRG00000003463

Mmulatta

all identical

ENSMMUG00000018882

Fcatus

all identical

ENSFCAG00000014631

Mmusculus

all identical

ENSMUSG00000027120

Ggallus

all identical

ENSGALG00000012140

Trubripes

no homologue

Drerio

all identical

ENSDARG00000010841

Dmelanogaster

all identical

FBgn0063368

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000018246

protein features

start (aa)	end (aa)	feature	details
68	81	STRAND		lost
69	69	DISULFID		lost
84	84	DISULFID		might get lost (downstream of altered splice site)
90	103	STRAND		might get lost (downstream of altered splice site)
100	100	DISULFID		might get lost (downstream of altered splice site)
102	102	DISULFID		might get lost (downstream of altered splice site)
105	105	DISULFID		might get lost (downstream of altered splice site)
107	109	TURN		might get lost (downstream of altered splice site)
110	114	STRAND		might get lost (downstream of altered splice site)
112	112	DISULFID		might get lost (downstream of altered splice site)
122	122	DISULFID		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

390 / 390

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

130 / 130

position of stopcodon in wt / mu cDNA

420 / 420

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

31 / 31

chromosome

strand

last intron/exon boundary

190

theoretical NMD boundary in CDS

109

length of CDS

390

coding sequence (CDS) position

205

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

235

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

2600

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

30255162

original gDNA sequence snippet

GGCCCAAAATCCAGAAAACATGTACCTTCAAGGAACTGGTA

altered gDNA sequence snippet

GGCCCAAAATCCAGAAAACAGGTACCTTCAAGGAACTGGTA

original cDNA sequence snippet

GGCCCAAAATCCAGAAAACATGTACCTTCAAGGAACTGGTA

altered cDNA sequence snippet

GGCCCAAAATCCAGAAAACAGGTACCTTCAAGGAACTGGTA

wildtype AA sequence

MKTLQFFFLF CCWKAICCNS CELTNITIAI EKEECRFCIS INTTWCAGYC YTRDLVYKDP
ARPKIQKTCT FKELVYETVR VPGCAHHADS LYTYPVATQC HCGKCDSDST DCTVRGLGPS
YCSFGEMKE*

mutated AA sequence

MKTLQFFFLF CCWKAICCNS CELTNITIAI EKEECRFCIS INTTWCAGYC YTRDLVYKDP
ARPKIQKTGT FKELVYETVR VPGCAHHADS LYTYPVATQC HCGKCDSDST DCTVRGLGPS
YCSFGEMKE*

speed

0.28 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems