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 CM890056)
known disease mutation: rs8632 (pathogenic)

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

ENST00000537449

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.230T>C
g.271215T>C

AA changes

N/A

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

N/A

frameshift

N/A

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

	PhyloP	PhastCons
(flanking)	4.142	1
	4.142	1
(flanking)	1.56	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
Donor marginally increased	271213	wt: 0.4360 / mu: 0.4390 (marginal change - not scored)	wt: TGTTACTTTAATTCA mu: TGTTACTCTAATTCA	TTAC\|ttta

distance from splice site

Kozak consensus sequence altered?

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

451 / 451

chromosome

strand

last intron/exon boundary

835

theoretical NMD boundary in CDS

334

length of CDS

1356

coding sequence (CDS) position

N/A

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

230

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

MVLEYELQYK EVNETKWKMM DPILTTSVPV YSLKVDKEYE VRVRSKQRNS GNYGEFSEVL
YVTLPQMSQF TCEEDFYFPW LLIIIFGIFG LTVMLFVFLF SKQQRIKMLI LPPVPVPKIK
GIDPDLLKEG KLEEVNTILA IHDSYKPEFH SDDSWVEFIE LDIDEPDEKT EESDTDRLLS
SDHEKSHSNL GVKDGDSGRT SCCEPDILET DFNANDIHEG TSEVAQPQRL KGEADLLCLD
QKNQNNSPYH DACPATQQPS VIQAEKNKPQ PLPTEGAEST HQAAHIQLSN PSSLSNIDFY
AQVSDITPAG SVVLSPGQKN KAGMSQCDMH PEMVSLCQEN FLMDNAYFCE ADAKKCIPVA
PHIKVESHIQ PSLNQEDIYI TTESLTTAAG RPGTGEHVPG SEMPVPDYTS IHIVQSPQGL
ILNATALPLP DKEFLSSCGY VSTDQLNKIM P*

mutated AA sequence

N/A

speed

0.85 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