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 5 transcript(s)...
Querying Taster for transcript #1: ENST00000326139
Querying Taster for transcript #2: ENST00000409904
Querying Taster for transcript #3: ENST00000409233
Querying Taster for transcript #4: ENST00000409316
Querying Taster for transcript #5: ENST00000337750
MT speed 0 s - this script 4.677612 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GHRHR	disease_causing_automatic	0.999889433225942	simple_aae			0	F242C	single base exchange	rs121918119		show file
GHRHR	disease_causing_automatic	0.999889433225942	simple_aae			0	F178C	single base exchange	rs121918119		show file
GHRHR	disease_causing_automatic	1	without_aae			0		single base exchange	rs121918119		show file
GHRHR	disease_causing_automatic	1	without_aae			0		single base exchange	rs121918119		show file
GHRHR	disease_causing_automatic	1	without_aae			0		single base exchange	rs121918119		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999889433225942 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM010309)
known disease mutation: rs15992 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:31013727T>GN/A show variant in all transcripts IGV

HGNC symbol

GHRHR

Ensembl transcript ID

ENST00000326139

Genbank transcript ID

NM_000823

UniProt peptide

Q02643

alteration type

single base exchange

alteration region

CDS

DNA changes

c.725T>G
cDNA.771T>G
g.35444T>G

AA changes

F242C Score: 205 explain score(s)

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

242

frameshift

known variant

Reference ID: rs121918119
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs15992 (pathogenic for Isolated growth hormone deficiency, type 4) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM010309)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010309)
known disease mutation at this position, please check HGMD for details (HGMD ID CM010309)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.202	0.926
	4.383	1
(flanking)	1.913	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	35434	wt: 0.8379 / mu: 0.8528 (marginal change - not scored)	wt: CCTCCACCTCCCCCAGCTCAAGGAGAGCCTTCTGGTGGCTG mu: CCTCCACCTCCCCCAGCTCAAGGAGAGCCTGCTGGTGGCTG	tcaa\|GGAG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

242

mutated

not conserved

242

Ptroglodytes

all identical

ENSPTRG00000019048

242

Mmulatta

all identical

ENSMMUG00000011764

178

Fcatus

all identical

ENSFCAG00000002543

240

Mmusculus

all identical

ENSMUSG00000004654

242

Ggallus

all identical

ENSGALG00000005212

239

Trubripes

not conserved

ENSTRUG00000017747

245

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
241	262	TRANSMEM	Helical; Name=4; (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1272 / 1272

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

424 / 424

position of stopcodon in wt / mu cDNA

1318 / 1318

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

47 / 47

chromosome

strand

last intron/exon boundary

1193

theoretical NMD boundary in CDS

1096

length of CDS

1272

coding sequence (CDS) position

725

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

771

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

35444

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

31013727

original gDNA sequence snippet

CCCCAGCTCAAGGAGAGCCTTCTGGTGGCTGGTTCTCGCTG

altered gDNA sequence snippet

CCCCAGCTCAAGGAGAGCCTGCTGGTGGCTGGTTCTCGCTG

original cDNA sequence snippet

CCCCAGCTCAAGGAGAGCCTTCTGGTGGCTGGTTCTCGCTG

altered cDNA sequence snippet

CCCCAGCTCAAGGAGAGCCTGCTGGTGGCTGGTTCTCGCTG

wildtype AA sequence

MDRRMWGAHV FCVLSPLPTV LGHMHPECDF ITQLREDESA CLQAAEEMPN TTLGCPATWD
GLLCWPTAGS GEWVTLPCPD FFSHFSSESG AVKRDCTITG WSEPFPPYPV ACPVPLELLA
EEESYFSTVK IIYTVGHSIS IVALFVAITI LVALRRLHCP RNYVHTQLFT TFILKAGAVF
LKDAALFHSD DTDHCSFSTV LCKVSVAASH FATMTNFSWL LAEAVYLNCL LASTSPSSRR
AFWWLVLAGW GLPVLFTGTW VSCKLAFEDI ACWDLDDTSP YWWIIKGPIV LSVGVNFGLF
LNIIRILVRK LEPAQGSLHT QSQYWRLSKS TLFLIPLFGI HYIIFNFLPD NAGLGIRLPL
ELGLGSFQGF IVAILYCFLN QEVRTEISRK WHGHDPELLP AWRTRAKWTT PSRSAAKVLT
SMC*

mutated AA sequence

MDRRMWGAHV FCVLSPLPTV LGHMHPECDF ITQLREDESA CLQAAEEMPN TTLGCPATWD
GLLCWPTAGS GEWVTLPCPD FFSHFSSESG AVKRDCTITG WSEPFPPYPV ACPVPLELLA
EEESYFSTVK IIYTVGHSIS IVALFVAITI LVALRRLHCP RNYVHTQLFT TFILKAGAVF
LKDAALFHSD DTDHCSFSTV LCKVSVAASH FATMTNFSWL LAEAVYLNCL LASTSPSSRR
ACWWLVLAGW GLPVLFTGTW VSCKLAFEDI ACWDLDDTSP YWWIIKGPIV LSVGVNFGLF
LNIIRILVRK LEPAQGSLHT QSQYWRLSKS TLFLIPLFGI HYIIFNFLPD NAGLGIRLPL
ELGLGSFQGF IVAILYCFLN QEVRTEISRK WHGHDPELLP AWRTRAKWTT PSRSAAKVLT
SMC*

speed

0.45 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: 0.999889433225942 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM010309)
known disease mutation: rs15992 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:31013727T>GN/A show variant in all transcripts IGV

HGNC symbol

GHRHR

Ensembl transcript ID

ENST00000409904

Genbank transcript ID

N/A

UniProt peptide

Q02643

alteration type

single base exchange

alteration region

CDS

DNA changes

c.533T>G
cDNA.791T>G
g.35444T>G

AA changes

F178C Score: 205 explain score(s)

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

178

frameshift

known variant

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.202	0.926
	4.383	1
(flanking)	1.913	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	35434	wt: 0.8379 / mu: 0.8528 (marginal change - not scored)	wt: CCTCCACCTCCCCCAGCTCAAGGAGAGCCTTCTGGTGGCTG mu: CCTCCACCTCCCCCAGCTCAAGGAGAGCCTGCTGGTGGCTG	tcaa\|GGAG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

178

mutated

not conserved

178

Ptroglodytes

all identical

ENSPTRG00000019048

242

Mmulatta

all identical

ENSMMUG00000011764

178

Fcatus

all identical

ENSFCAG00000002543

240

Mmusculus

all identical

ENSMUSG00000004654

242

Ggallus

all identical

ENSGALG00000005212

239

Trubripes

not conserved

ENSTRUG00000017747

245

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
163	181	TRANSMEM	Helical; Name=2; (Potential).	lost
178	178	CONFLICT	A -> R (in Ref. 1; AAA35890).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1080 / 1080

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

360 / 360

position of stopcodon in wt / mu cDNA

1338 / 1338

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

259 / 259

chromosome

strand

last intron/exon boundary

1213

theoretical NMD boundary in CDS

904

length of CDS

1080

coding sequence (CDS) position

533

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

791

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

35444

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

31013727

original gDNA sequence snippet

CCCCAGCTCAAGGAGAGCCTTCTGGTGGCTGGTTCTCGCTG

altered gDNA sequence snippet

CCCCAGCTCAAGGAGAGCCTGCTGGTGGCTGGTTCTCGCTG

original cDNA sequence snippet

CCCCAGCTCAAGGAGAGCCTTCTGGTGGCTGGTTCTCGCTG

altered cDNA sequence snippet

CCCCAGCTCAAGGAGAGCCTGCTGGTGGCTGGTTCTCGCTG

wildtype AA sequence

MVPGTPSPLL GRGKELWLES LACLPGAVKR DCTITGWSEP FPPYPVACPV PLELLAEEES
YFSTVKIIYT VGHSISIVAL FVAITILVAL RRLHCPRNYV HTQLFTTFIL KAGAVFLKDA
ALFHSDDTDH CSFSTVLCKV SVAASHFATM TNFSWLLAEA VYLNCLLAST SPSSRRAFWW
LVLAGWGLPV LFTGTWVSCK LAFEDIACWD LDDTSPYWWI IKGPIVLSVG VNFGLFLNII
RILVRKLEPA QGSLHTQSQY WRLSKSTLFL IPLFGIHYII FNFLPDNAGL GIRLPLELGL
GSFQGFIVAI LYCFLNQEVR TEISRKWHGH DPELLPAWRT RAKWTTPSRS AAKVLTSMC*

mutated AA sequence

MVPGTPSPLL GRGKELWLES LACLPGAVKR DCTITGWSEP FPPYPVACPV PLELLAEEES
YFSTVKIIYT VGHSISIVAL FVAITILVAL RRLHCPRNYV HTQLFTTFIL KAGAVFLKDA
ALFHSDDTDH CSFSTVLCKV SVAASHFATM TNFSWLLAEA VYLNCLLAST SPSSRRACWW
LVLAGWGLPV LFTGTWVSCK LAFEDIACWD LDDTSPYWWI IKGPIVLSVG VNFGLFLNII
RILVRKLEPA QGSLHTQSQY WRLSKSTLFL IPLFGIHYII FNFLPDNAGL GIRLPLELGL
GSFQGFIVAI LYCFLNQEVR TEISRKWHGH DPELLPAWRT RAKWTTPSRS AAKVLTSMC*

speed

1.03 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 CM010309)
known disease mutation: rs15992 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:31013727T>GN/A show variant in all transcripts IGV

HGNC symbol

GHRHR

Ensembl transcript ID

ENST00000409233

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.35444T>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.202	0.926
	4.383	1
(flanking)	1.913	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	35434	wt: 0.8379 / mu: 0.8528 (marginal change - not scored)	wt: CCTCCACCTCCCCCAGCTCAAGGAGAGCCTTCTGGTGGCTG mu: CCTCCACCTCCCCCAGCTCAAGGAGAGCCTGCTGGTGGCTG	tcaa\|GGAG

distance from splice site

859

Kozak consensus sequence altered?

N/A

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

259 / 259

chromosome

strand

last intron/exon boundary

767

theoretical NMD boundary in CDS

458

length of CDS

519

coding sequence (CDS) position

N/A

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

N/A

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

35444

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

31013727

original gDNA sequence snippet

CCCCAGCTCAAGGAGAGCCTTCTGGTGGCTGGTTCTCGCTG

altered gDNA sequence snippet

CCCCAGCTCAAGGAGAGCCTGCTGGTGGCTGGTTCTCGCTG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MVPGTPSPLL GRGKELWLES LACLPGAVKR DCTITGWSEP FPPYPVACPV PLELLAEEVL
GPGRHLPLLV DHQRAHCPLG RGELWAFSQY YPHPGEETGA SSGQPPYPVS VLASLQVDTF
PDPTLWNSLH HLQLPARQCW PGHPPPPGAG TGFLPGLHCC HPLLLPQPRG ED*

mutated AA sequence

N/A

speed

1.03 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 CM010309)
known disease mutation: rs15992 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:31013727T>GN/A show variant in all transcripts IGV

HGNC symbol

GHRHR

Ensembl transcript ID

ENST00000409316

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.35444T>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.202	0.926
	4.383	1
(flanking)	1.913	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	35434	wt: 0.8379 / mu: 0.8528 (marginal change - not scored)	wt: CCTCCACCTCCCCCAGCTCAAGGAGAGCCTTCTGGTGGCTG mu: CCTCCACCTCCCCCAGCTCAAGGAGAGCCTGCTGGTGGCTG	tcaa\|GGAG

distance from splice site

317

Kozak consensus sequence altered?

N/A

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

438 / 438

chromosome

strand

last intron/exon boundary

883

theoretical NMD boundary in CDS

395

length of CDS

456

coding sequence (CDS) position

N/A

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

N/A

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

35444

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

31013727

original gDNA sequence snippet

CCCCAGCTCAAGGAGAGCCTTCTGGTGGCTGGTTCTCGCTG

altered gDNA sequence snippet

CCCCAGCTCAAGGAGAGCCTGCTGGTGGCTGGTTCTCGCTG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MLPFSTATTL TTAASPLAAR ALHWHVGELQ TGLRGHRVLG PGRHLPLLVD HQRAHCPLGR
GELWAFSQYY PHPGEETGAS SGQPPYPVSV LASLQVDTFP DPTLWNSLHH LQLPARQCWP
GHPPPPGAGT GFLPGLHCCH PLLLPQPRGE D*

mutated AA sequence

N/A

speed

0.69 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 CM010309)
known disease mutation: rs15992 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:31013727T>GN/A show variant in all transcripts IGV

HGNC symbol

GHRHR

Ensembl transcript ID

ENST00000337750

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.35444T>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.202	0.926
	4.383	1
(flanking)	1.913	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	35434	wt: 0.8379 / mu: 0.8528 (marginal change - not scored)	wt: CCTCCACCTCCCCCAGCTCAAGGAGAGCCTTCTGGTGGCTG mu: CCTCCACCTCCCCCAGCTCAAGGAGAGCCTGCTGGTGGCTG	tcaa\|GGAG

distance from splice site

317

Kozak consensus sequence altered?

N/A

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

259 / 259

chromosome

strand

last intron/exon boundary

828

theoretical NMD boundary in CDS

519

length of CDS

207

coding sequence (CDS) position

N/A

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

N/A

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

35444

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

31013727

original gDNA sequence snippet

CCCCAGCTCAAGGAGAGCCTTCTGGTGGCTGGTTCTCGCTG

altered gDNA sequence snippet

CCCCAGCTCAAGGAGAGCCTGCTGGTGGCTGGTTCTCGCTG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MVPGTPSPLL GRGKELWLES LACLPGAVKR DCTITGWSEP FPPYPVACPV PLELLAEEGC
PCSSLARG*

mutated AA sequence

N/A

speed

1.00 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

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems