Yum, tasty mutations...

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 no
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
PhyloPPhastCons
(flanking)1.2020.926
4.3831
(flanking)1.9131
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased35434wt: 0.8379 / mu: 0.8528 (marginal change - not scored)wt: CCTCCACCTCCCCCAGCTCAAGGAGAGCCTTCTGGTGGCTG
mu: CCTCCACCTCCCCCAGCTCAAGGAGAGCCTGCTGGTGGCTG		 tcaa|GGAG
distance from splice site 27
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      178LASTSPSSRRAFWWLVLAGWGLPV
mutated  not conserved    178LASTSPSSRRACWW
Ptroglodytes  all identical  ENSPTRG00000019048  242LASTSPSSRRAFWWLVLAGWGLP
Mmulatta  all identical  ENSMMUG00000011764  178LASTSPSSRRAFWW
Fcatus  all identical  ENSFCAG00000002543  240LASKSPSTRRAFWWL
Mmusculus  all identical  ENSMUSG00000004654  242LASTSPRSKPAFWWLVLAGWGLP
Ggallus  all identical  ENSGALG00000005212  239LLSSLSHGRRYFWWLVLFGWGFP
Trubripes  not conserved  ENSTRUG00000017747  245LVSSFCHARRCVWGFSLLGWGVP
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
163181TRANSMEMHelical; Name=2; (Potential).lost
178178CONFLICTA -> 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 7
strand 1
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 1.28 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