Yum, tasty mutations...

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		 92
frameshift no
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
PhyloPPhastCons
(flanking)4.1421
4.1421
(flanking)1.561
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased271213wt: 0.4360 / mu: 0.4390 (marginal change - not scored)wt: TGTTACTTTAATTCA
mu: TGTTACTCTAATTCA		 TTAC|ttta
distance from splice site 75
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      92DYVSAGENSCYFNSSFTSIWIPYC
mutated  not conserved    92DYVSAGENSCYSNSSFTSIWIPY
Ptroglodytes  all identical  ENSPTRG00000016836  114DYVSAGENSCYFNSSFTS
Mmulatta  all identical  ENSMMUG00000001336  114DYVSAGENSCYFNSSFTS
Fcatus  not conserved  ENSFCAG00000001689  114XXXXXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000055737  122YFNSSYTSIWIPY
Ggallus  all identical  ENSGALG00000014855  92DYITAGENSCYFNTSYTSIWIPY
Trubripes  all identical  ENSTRUG00000015040  119E-CFFDKNHTSVWTNY
Drerio  all identical  ENSDARG00000054771  99DYTQTVKNECYFNKTFTRIWTSY
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000005560  60SCYFSKTYTSIWVSY
protein features
start (aa)end (aa)featuredetails 
19264TOPO_DOMExtracellular (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 5
strand 1
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 1.25 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