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: ENST00000230882
Querying Taster for transcript #2: ENST00000357703
Querying Taster for transcript #3: ENST00000537449
MT speed 0 s - this script 3.119913 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GHR	disease_causing_automatic	0.999999700239296	simple_aae			0	F92S	single base exchange	rs121909357		show file
GHR	disease_causing_automatic	0.999999933814228	simple_aae			0	F114S	single base exchange	rs121909357		show file
GHR	disease_causing_automatic	1	without_aae			0		single base exchange	rs121909357		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999700239296 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM890056)
known disease mutation: rs8632 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:42695093T>CN/A show variant in all transcripts IGV

HGNC symbol

GHR

Ensembl transcript ID

ENST00000357703

Genbank transcript ID

NM_001242460

UniProt peptide

P10912

alteration type

single base exchange

alteration region

CDS

DNA changes

c.275T>C
cDNA.318T>C
g.271215T>C

AA changes

F92S Score: 155 explain score(s)

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

frameshift

known variant

Reference ID: rs121909357
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs8632 (pathogenic for Laron-type isolated somatotropin defect) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM890056)

known disease mutation at this position, please check HGMD for details (HGMD ID CM890056)
known disease mutation at this position, please check HGMD for details (HGMD ID CM890056)

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.142	1
	4.142	1
(flanking)	1.56	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
Donor marginally increased	271213	wt: 0.4360 / mu: 0.4390 (marginal change - not scored)	wt: TGTTACTTTAATTCA mu: TGTTACTCTAATTCA	TTAC\|ttta

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

ENSPTRG00000016836

114

Mmulatta

all identical

ENSMMUG00000001336

114

Fcatus

not conserved

ENSFCAG00000001689

114

Mmusculus

all identical

ENSMUSG00000055737

122

Ggallus

all identical

ENSGALG00000014855

Trubripes

all identical

ENSTRUG00000015040

119

Drerio

all identical

ENSDARG00000054771

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000005560

protein features

start (aa)	end (aa)	feature	details
19	264	TOPO_DOM	Extracellular (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1851 / 1851

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

617 / 617

position of stopcodon in wt / mu cDNA

1894 / 1894

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

44 / 44

chromosome

strand

last intron/exon boundary

923

theoretical NMD boundary in CDS

829

length of CDS

1851

coding sequence (CDS) position

275

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

318

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

271215

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

42695093

original gDNA sequence snippet

TGGGGAAAACAGCTGTTACTTTAATTCATCGTTTACCTCCA

altered gDNA sequence snippet

TGGGGAAAACAGCTGTTACTCTAATTCATCGTTTACCTCCA

original cDNA sequence snippet

TGGGGAAAACAGCTGTTACTTTAATTCATCGTTTACCTCCA

altered cDNA sequence snippet

TGGGGAAAACAGCTGTTACTCTAATTCATCGTTTACCTCCA

wildtype AA sequence

MDLWQLLLTL ALAGSSDAFS GSEDSSKEPK FTKCRSPERE TFSCHWTDEV HHGTKNLGPI
QLFYTRRNTQ EWTQEWKECP DYVSAGENSC YFNSSFTSIW IPYCIKLTSN GGTVDEKCFS
VDEIVQPDPP IALNWTLLNV SLTGIHADIQ VRWEAPRNAD IQKGWMVLEY ELQYKEVNET
KWKMMDPILT TSVPVYSLKV DKEYEVRVRS KQRNSGNYGE FSEVLYVTLP QMSQFTCEED
FYFPWLLIII FGIFGLTVML FVFLFSKQQR IKMLILPPVP VPKIKGIDPD LLKEGKLEEV
NTILAIHDSY KPEFHSDDSW VEFIELDIDE PDEKTEESDT DRLLSSDHEK SHSNLGVKDG
DSGRTSCCEP DILETDFNAN DIHEGTSEVA QPQRLKGEAD LLCLDQKNQN NSPYHDACPA
TQQPSVIQAE KNKPQPLPTE GAESTHQAAH IQLSNPSSLS NIDFYAQVSD ITPAGSVVLS
PGQKNKAGMS QCDMHPEMVS LCQENFLMDN AYFCEADAKK CIPVAPHIKV ESHIQPSLNQ
EDIYITTESL TTAAGRPGTG EHVPGSEMPV PDYTSIHIVQ SPQGLILNAT ALPLPDKEFL
SSCGYVSTDQ LNKIMP*

mutated AA sequence

MDLWQLLLTL ALAGSSDAFS GSEDSSKEPK FTKCRSPERE TFSCHWTDEV HHGTKNLGPI
QLFYTRRNTQ EWTQEWKECP DYVSAGENSC YSNSSFTSIW IPYCIKLTSN GGTVDEKCFS
VDEIVQPDPP IALNWTLLNV SLTGIHADIQ VRWEAPRNAD IQKGWMVLEY ELQYKEVNET
KWKMMDPILT TSVPVYSLKV DKEYEVRVRS KQRNSGNYGE FSEVLYVTLP QMSQFTCEED
FYFPWLLIII FGIFGLTVML FVFLFSKQQR IKMLILPPVP VPKIKGIDPD LLKEGKLEEV
NTILAIHDSY KPEFHSDDSW VEFIELDIDE PDEKTEESDT DRLLSSDHEK SHSNLGVKDG
DSGRTSCCEP DILETDFNAN DIHEGTSEVA QPQRLKGEAD LLCLDQKNQN NSPYHDACPA
TQQPSVIQAE KNKPQPLPTE GAESTHQAAH IQLSNPSSLS NIDFYAQVSD ITPAGSVVLS
PGQKNKAGMS QCDMHPEMVS LCQENFLMDN AYFCEADAKK CIPVAPHIKV ESHIQPSLNQ
EDIYITTESL TTAAGRPGTG EHVPGSEMPV PDYTSIHIVQ SPQGLILNAT ALPLPDKEFL
SSCGYVSTDQ LNKIMP*

speed

0.44 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: 0.999999933814228 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM890056)
known disease mutation: rs8632 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:42695093T>CN/A show variant in all transcripts IGV

HGNC symbol

GHR

Ensembl transcript ID

ENST00000230882

Genbank transcript ID

NM_000163

UniProt peptide

P10912

alteration type

single base exchange

alteration region

CDS

DNA changes

c.341T>C
cDNA.531T>C
g.271215T>C

AA changes

F114S Score: 155 explain score(s)

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

114

frameshift

known variant

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.142	1
	4.142	1
(flanking)	1.56	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
Donor marginally increased	271213	wt: 0.4360 / mu: 0.4390 (marginal change - not scored)	wt: TGTTACTTTAATTCA mu: TGTTACTCTAATTCA	TTAC\|ttta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

114

mutated

not conserved

114

Ptroglodytes

all identical

ENSPTRG00000016836

114

Mmulatta

all identical

ENSMMUG00000001336

114

Fcatus

not conserved

ENSFCAG00000001689

114

Mmusculus

all identical

ENSMUSG00000055737

122

Ggallus

all identical

ENSGALG00000014855

Trubripes

all identical

ENSTRUG00000015040

121

Drerio

all identical

ENSDARG00000054771

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000005560

protein features

start (aa)	end (aa)	feature	details
19	264	TOPO_DOM	Extracellular (Potential).	lost
111	114	STRAND		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1917 / 1917

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

639 / 639

position of stopcodon in wt / mu cDNA

2107 / 2107

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

191 / 191

chromosome

strand

last intron/exon boundary

1136

theoretical NMD boundary in CDS

895

length of CDS

1917

coding sequence (CDS) position

341

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

531

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

271215

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

42695093

original gDNA sequence snippet

TGGGGAAAACAGCTGTTACTTTAATTCATCGTTTACCTCCA

altered gDNA sequence snippet

TGGGGAAAACAGCTGTTACTCTAATTCATCGTTTACCTCCA

original cDNA sequence snippet

TGGGGAAAACAGCTGTTACTTTAATTCATCGTTTACCTCCA

altered cDNA sequence snippet

TGGGGAAAACAGCTGTTACTCTAATTCATCGTTTACCTCCA

wildtype AA sequence

MDLWQLLLTL ALAGSSDAFS GSEATAAILS RAPWSLQSVN PGLKTNSSKE PKFTKCRSPE
RETFSCHWTD EVHHGTKNLG PIQLFYTRRN TQEWTQEWKE CPDYVSAGEN SCYFNSSFTS
IWIPYCIKLT SNGGTVDEKC FSVDEIVQPD PPIALNWTLL NVSLTGIHAD IQVRWEAPRN
ADIQKGWMVL EYELQYKEVN ETKWKMMDPI LTTSVPVYSL KVDKEYEVRV RSKQRNSGNY
GEFSEVLYVT LPQMSQFTCE EDFYFPWLLI IIFGIFGLTV MLFVFLFSKQ QRIKMLILPP
VPVPKIKGID PDLLKEGKLE EVNTILAIHD SYKPEFHSDD SWVEFIELDI DEPDEKTEES
DTDRLLSSDH EKSHSNLGVK DGDSGRTSCC EPDILETDFN ANDIHEGTSE VAQPQRLKGE
ADLLCLDQKN QNNSPYHDAC PATQQPSVIQ AEKNKPQPLP TEGAESTHQA AHIQLSNPSS
LSNIDFYAQV SDITPAGSVV LSPGQKNKAG MSQCDMHPEM VSLCQENFLM DNAYFCEADA
KKCIPVAPHI KVESHIQPSL NQEDIYITTE SLTTAAGRPG TGEHVPGSEM PVPDYTSIHI
VQSPQGLILN ATALPLPDKE FLSSCGYVST DQLNKIMP*

mutated AA sequence

MDLWQLLLTL ALAGSSDAFS GSEATAAILS RAPWSLQSVN PGLKTNSSKE PKFTKCRSPE
RETFSCHWTD EVHHGTKNLG PIQLFYTRRN TQEWTQEWKE CPDYVSAGEN SCYSNSSFTS
IWIPYCIKLT SNGGTVDEKC FSVDEIVQPD PPIALNWTLL NVSLTGIHAD IQVRWEAPRN
ADIQKGWMVL EYELQYKEVN ETKWKMMDPI LTTSVPVYSL KVDKEYEVRV RSKQRNSGNY
GEFSEVLYVT LPQMSQFTCE EDFYFPWLLI IIFGIFGLTV MLFVFLFSKQ QRIKMLILPP
VPVPKIKGID PDLLKEGKLE EVNTILAIHD SYKPEFHSDD SWVEFIELDI DEPDEKTEES
DTDRLLSSDH EKSHSNLGVK DGDSGRTSCC EPDILETDFN ANDIHEGTSE VAQPQRLKGE
ADLLCLDQKN QNNSPYHDAC PATQQPSVIQ AEKNKPQPLP TEGAESTHQA AHIQLSNPSS
LSNIDFYAQV SDITPAGSVV LSPGQKNKAG MSQCDMHPEM VSLCQENFLM DNAYFCEADA
KKCIPVAPHI KVESHIQPSL NQEDIYITTE SLTTAAGRPG TGEHVPGSEM PVPDYTSIHI
VQSPQGLILN ATALPLPDKE FLSSCGYVST DQLNKIMP*

speed

0.44 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM890056)
known disease mutation: rs8632 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:42695093T>CN/A show variant in all transcripts IGV

HGNC symbol

GHR

Ensembl transcript ID

ENST00000537449

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.230T>C
g.271215T>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.142	1
	4.142	1
(flanking)	1.56	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
Donor marginally increased	271213	wt: 0.4360 / mu: 0.4390 (marginal change - not scored)	wt: TGTTACTTTAATTCA mu: TGTTACTCTAATTCA	TTAC\|ttta

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

451 / 451

chromosome

strand

last intron/exon boundary

835

theoretical NMD boundary in CDS

334

length of CDS

1356

coding sequence (CDS) position

N/A

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

230

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

271215

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

42695093

original gDNA sequence snippet

TGGGGAAAACAGCTGTTACTTTAATTCATCGTTTACCTCCA

altered gDNA sequence snippet

TGGGGAAAACAGCTGTTACTCTAATTCATCGTTTACCTCCA

original cDNA sequence snippet

TGGGGAAAACAGCTGTTACTTTAATTCATCGTTTACCTCCA

altered cDNA sequence snippet

TGGGGAAAACAGCTGTTACTCTAATTCATCGTTTACCTCCA

wildtype AA sequence

MVLEYELQYK EVNETKWKMM DPILTTSVPV YSLKVDKEYE VRVRSKQRNS GNYGEFSEVL
YVTLPQMSQF TCEEDFYFPW LLIIIFGIFG LTVMLFVFLF SKQQRIKMLI LPPVPVPKIK
GIDPDLLKEG KLEEVNTILA IHDSYKPEFH SDDSWVEFIE LDIDEPDEKT EESDTDRLLS
SDHEKSHSNL GVKDGDSGRT SCCEPDILET DFNANDIHEG TSEVAQPQRL KGEADLLCLD
QKNQNNSPYH DACPATQQPS VIQAEKNKPQ PLPTEGAEST HQAAHIQLSN PSSLSNIDFY
AQVSDITPAG SVVLSPGQKN KAGMSQCDMH PEMVSLCQEN FLMDNAYFCE ADAKKCIPVA
PHIKVESHIQ PSLNQEDIYI TTESLTTAAG RPGTGEHVPG SEMPVPDYTS IHIVQSPQGL
ILNATALPLP DKEFLSSCGY VSTDQLNKIM P*

mutated AA sequence

N/A

speed

0.36 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