Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.306504992715146 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM020716)
  • known disease mutation: rs15994 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:31016054A>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.793A>G
cDNA.1051A>G
g.37771A>G
AA changes K265E Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 265
frameshift no
known variant Reference ID: rs121918121
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs15994 (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 CM020716)

known disease mutation at this position, please check HGMD for details (HGMD ID CM020716)
known disease mutation at this position, please check HGMD for details (HGMD ID CM020716)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.3571
2.1431
(flanking)1.3791
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased37764wt: 0.21 / mu: 0.28wt: ATTTGTCTTTCCTGCAGGCGTCTCTCCAAGTCGACACTTTT
mu: ATTTGTCTTTCCTGCAGGCGTCTCTCCGAGTCGACACTTTT		 gcgt|CTCT
distance from splice site 11
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      265LHTQSQYWRLSKSTLFLIPLFGIH
mutated  all conserved    265LHTQSQYWRLSESTLFLIPLFGI
Ptroglodytes  all identical  ENSPTRG00000019048  329LHTQSQYWRLSKSTLFLIPLFGI
Mmulatta  not conserved  ENSMMUG00000011764  263LKTGLQPRSATDSLILLVKPEGW
Fcatus  all identical  ENSFCAG00000002543  327LHPQSQYRRLSKSTLLLIPLFGI
Mmusculus  all identical  ENSMUSG00000004654  329LHTRAQYWRLSKSTLLLIPLFGI
Ggallus  all conserved  ENSGALG00000005212  326FNNSSQYRRLSRSTLLLIPLFGT
Trubripes  all identical  ENSTRUG00000017747  332FNNSSQYRRLAKSTLLLIPLFGT
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
241262TRANSMEMHelical; Name=4; (Potential).might get lost (downstream of altered splice site)
263280TOPO_DOMExtracellular (Potential).lost
281304TRANSMEMHelical; Name=5; (Potential).might get lost (downstream of altered splice site)
305329TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
330348TRANSMEMHelical; Name=6; (Potential).might get lost (downstream of altered splice site)
349361TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
362381TRANSMEMHelical; Name=7; (Potential).might get lost (downstream of altered splice site)
382423TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
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 7
strand 1
last intron/exon boundary 1213
theoretical NMD boundary in CDS 904
length of CDS 1080
coding sequence (CDS) position 793
cDNA position
(for ins/del: last normal base / first normal base)		 1051
gDNA position
(for ins/del: last normal base / first normal base)		 37771
chromosomal position
(for ins/del: last normal base / first normal base)		 31016054
original gDNA sequence snippet TTTCCTGCAGGCGTCTCTCCAAGTCGACACTTTTCCTGATC
altered gDNA sequence snippet TTTCCTGCAGGCGTCTCTCCGAGTCGACACTTTTCCTGATC
original cDNA sequence snippet CTCAGTATTGGCGTCTCTCCAAGTCGACACTTTTCCTGATC
altered cDNA sequence snippet CTCAGTATTGGCGTCTCTCCGAGTCGACACTTTTCCTGATC
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 SPSSRRAFWW
LVLAGWGLPV LFTGTWVSCK LAFEDIACWD LDDTSPYWWI IKGPIVLSVG VNFGLFLNII
RILVRKLEPA QGSLHTQSQY WRLSESTLFL IPLFGIHYII FNFLPDNAGL GIRLPLELGL
GSFQGFIVAI LYCFLNQEVR TEISRKWHGH DPELLPAWRT RAKWTTPSRS AAKVLTSMC*
speed 1.05 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