mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.516154909129738 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM010308)
known disease mutation: rs15993 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:31013667C>AN/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.473C>A
cDNA.731C>A
g.35384C>A

AA changes

A158E Score: 107 explain score(s)

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

158

frameshift

known variant

Reference ID: rs121918120

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	4	4

known disease mutation: rs15993 (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 CM010308)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010308)
known disease mutation at this position, please check HGMD for details (HGMD ID CM010308)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.31	1
	0.671	0.898
(flanking)	-0.765	0.797

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 gained	35380	0.31	mu: GGCTGTTGGAAGAAG	CTGT\|tgga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

158

mutated

not conserved

158

Ptroglodytes

all identical

ENSPTRG00000019048

222

Mmulatta

all identical

ENSMMUG00000011764

158

Fcatus

not conserved

ENSFCAG00000002543

220

Mmusculus

all identical

ENSMUSG00000004654

222

Ggallus

not conserved

ENSGALG00000005212

219

Trubripes

not conserved

ENSTRUG00000017747

225

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
153	162	TOPO_DOM	Cytoplasmic (Potential).	lost
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

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

strand

last intron/exon boundary

1213

theoretical NMD boundary in CDS

904

length of CDS

1080

coding sequence (CDS) position

473

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

731

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

35384

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

31013667

original gDNA sequence snippet

CAACTTCAGCTGGCTGTTGGCAGAAGCCGTCTACCTGAACT

altered gDNA sequence snippet

CAACTTCAGCTGGCTGTTGGAAGAAGCCGTCTACCTGAACT

original cDNA sequence snippet

CAACTTCAGCTGGCTGTTGGCAGAAGCCGTCTACCTGAACT

altered cDNA sequence snippet

CAACTTCAGCTGGCTGTTGGAAGAAGCCGTCTACCTGAACT

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 TNFSWLLEEA VYLNCLLAST SPSSRRAFWW
LVLAGWGLPV LFTGTWVSCK LAFEDIACWD LDDTSPYWWI IKGPIVLSVG VNFGLFLNII
RILVRKLEPA QGSLHTQSQY WRLSKSTLFL IPLFGIHYII FNFLPDNAGL GIRLPLELGL
GSFQGFIVAI LYCFLNQEVR TEISRKWHGH DPELLPAWRT RAKWTTPSRS AAKVLTSMC*

speed

1.27 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