mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.000259895848801376 (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

ENST00000409233

Genbank transcript ID

N/A

UniProt peptide

Q02643

alteration type

single base exchange

alteration region

CDS

DNA changes

c.347A>G
cDNA.605A>G
g.37771A>G

AA changes

Q116R Score: 43 explain score(s)

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

116

frameshift

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

	PhyloP	PhastCons
(flanking)	1.357	1
	2.143	1
(flanking)	1.379	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
Acc increased	37764	wt: 0.21 / mu: 0.28	wt: ATTTGTCTTTCCTGCAGGCGTCTCTCCAAGTCGACACTTTT mu: ATTTGTCTTTCCTGCAGGCGTCTCTCCGAGTCGACACTTTT	gcgt\|CTCT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

116

mutated

all conserved

116

Ptroglodytes

no alignment

ENSPTRG00000019048

n/a

Mmulatta

no alignment

ENSMMUG00000011764

n/a

Fcatus

all conserved

ENSFCAG00000002543

109

Mmusculus

no alignment

ENSMUSG00000004654

n/a

Ggallus

no alignment

ENSGALG00000005212

n/a

Trubripes

no alignment

ENSTRUG00000017747

n/a

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
23	132	TOPO_DOM	Extracellular (Potential).	lost
116	119	HELIX		lost
133	152	TRANSMEM	Helical; Name=1; (Potential).	might get lost (downstream of altered splice site)
153	162	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
163	181	TRANSMEM	Helical; Name=2; (Potential).	might get lost (downstream of altered splice site)
178	178	CONFLICT	A -> R (in Ref. 1; AAA35890).	might get lost (downstream of altered splice site)
182	204	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
205	227	TRANSMEM	Helical; Name=3; (Potential).	might get lost (downstream of altered splice site)
228	240	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
241	262	TRANSMEM	Helical; Name=4; (Potential).	might get lost (downstream of altered splice site)
263	280	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
281	304	TRANSMEM	Helical; Name=5; (Potential).	might get lost (downstream of altered splice site)
305	329	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
330	348	TRANSMEM	Helical; Name=6; (Potential).	might get lost (downstream of altered splice site)
349	361	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
362	381	TRANSMEM	Helical; Name=7; (Potential).	might get lost (downstream of altered splice site)
382	423	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

519 / 519

position (AA) of stopcodon in wt / mu AA sequence

173 / 173

position of stopcodon in wt / mu cDNA

777 / 777

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

strand

last intron/exon boundary

767

theoretical NMD boundary in CDS

458

length of CDS

519

coding sequence (CDS) position

347

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

605

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 PLELLAEEVL
GPGRHLPLLV DHQRAHCPLG RGELWAFSQY YPHPGEETGA SSGQPPYPVS VLASLQVDTF
PDPTLWNSLH HLQLPARQCW PGHPPPPGAG TGFLPGLHCC HPLLLPQPRG ED*

mutated AA sequence

MVPGTPSPLL GRGKELWLES LACLPGAVKR DCTITGWSEP FPPYPVACPV PLELLAEEVL
GPGRHLPLLV DHQRAHCPLG RGELWAFSQY YPHPGEETGA SSGQPPYPVS VLASLRVDTF
PDPTLWNSLH HLQLPARQCW PGHPPPPGAG TGFLPGLHCC HPLLLPQPRG ED*

speed

0.57 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