Yum, tasty mutations...

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 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      114DYVSAGENSCYFNSSFTSIWIPYC
mutated  not conserved    114DYVSAGENSCYSNSSFTS
Ptroglodytes  all identical  ENSPTRG00000016836  114DYVSAGENSCYFNSSFTS
Mmulatta  all identical  ENSMMUG00000001336  114DYVSAGENSCYFNSSFTS
Fcatus  not conserved  ENSFCAG00000001689  114XXXXXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000055737  122YFNSSYTSIWIPY
Ggallus  all identical  ENSGALG00000014855  88SCYFNTSYTSIWIPY
Trubripes  all identical  ENSTRUG00000015040  121KYIHSNRE-CFFDKNHTSVWTNY
Drerio  all identical  ENSDARG00000054771  99TQTVKNECYFNKTFTRIWTSY
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000005560  60SCYFSKTYTSIWVSY
protein features
start (aa)end (aa)featuredetails 
19264TOPO_DOMExtracellular (Potential).lost
111114STRANDlost
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 5
strand 1
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 1.19 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