mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.626081901308732 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
heterozygous in TGP or ExAC
known disease mutation at this position (HGMD CM950481)
known disease mutation: rs16243 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:49210264G>AN/A show variant in all transcripts IGV

HGNC symbol

FSHR

Ensembl transcript ID

ENST00000346173

Genbank transcript ID

N/A

UniProt peptide

P23945

alteration type

single base exchange

alteration region

CDS

DNA changes

c.566C>T
cDNA.676C>T
g.171413C>T

AA changes

A189V Score: 64 explain score(s)

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

189

frameshift

known variant

Reference ID: rs121909658

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	75	75

known disease mutation: rs16243 (pathogenic for Ovarian dysgenesis 1) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950481)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950481)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950481)

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.243	1
	4.075	1
(flanking)	4.075	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	171418	wt: 0.2409 / mu: 0.2608 (marginal change - not scored)	wt: CATTCAATGGAACCC mu: TATTCAATGGAACCC	TTCA\|atgg
Donor gained	171409	0.32	mu: ACAACTGTGTATTCA	AACT\|gtgt
Donor gained	171406	0.60	mu: TACACAACTGTGTAT	CACA\|actg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

189

mutated

not conserved

189

Ptroglodytes

not conserved

ENSPTRG00000011914

189

QEIHNCAFNGTQLDELNLSDNNNLE

SGPVILDISRTRIHSLPSYGLEN

Mmulatta

not conserved

ENSMMUG00000017196

189

QEIHNCAFNGTQLDELNLSDNNNLE

SGPVILDISRTRIHSLPSYGLEN

Fcatus

all identical

ENSFCAG00000001215

189

QLDELNLSDNINLEELPNDVFQGASGPVILDISRTRIHSLPSYGLEN

Mmusculus

not conserved

ENSMUSG00000032937

190

GIQEIHNCAFNGTQLDELNLSDN

SGPVVLDISRTKVYSLPNHGLEN

Ggallus

not conserved

ENSGALG00000009100

245

Trubripes

no homologue

Drerio

all identical

ENSDARG00000071494

195

Dmelanogaster

all conserved

FBgn0016650

392

Celegans

not conserved

C50H2.1

323

Xtropicalis

not conserved

ENSXETG00000025827

STG

protein features

start (aa)	end (aa)	feature	details
18	366	TOPO_DOM	Extracellular (Potential).	lost
170	192	REPEAT	LRR 6.	lost
187	192	TURN		lost
191	191	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
193	199	STRAND		might get lost (downstream of altered splice site)
193	216	REPEAT	LRR 7.	might get lost (downstream of altered splice site)
197	198	CONFLICT	EL -> AV (in Ref. 1; AAA52477).	might get lost (downstream of altered splice site)
199	199	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
211	216	TURN		might get lost (downstream of altered splice site)
217	240	REPEAT	LRR 8.	might get lost (downstream of altered splice site)
221	224	STRAND		might get lost (downstream of altered splice site)
235	237	STRAND		might get lost (downstream of altered splice site)
241	259	REPEAT	LRR 9.	might get lost (downstream of altered splice site)
243	245	STRAND		might get lost (downstream of altered splice site)
258	260	TURN		might get lost (downstream of altered splice site)
266	268	STRAND		might get lost (downstream of altered splice site)
272	280	HELIX		might get lost (downstream of altered splice site)
293	293	CARBOHYD	N-linked (GlcNAc...) (By similarity).	might get lost (downstream of altered splice site)
295	295	CONFLICT	S -> P (in Ref. 8; CAA48179).	might get lost (downstream of altered splice site)
318	318	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
345	348	STRAND		might get lost (downstream of altered splice site)
367	387	TRANSMEM	Helical; Name=1; (Potential).	might get lost (downstream of altered splice site)
388	398	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
399	421	TRANSMEM	Helical; Name=2; (Potential).	might get lost (downstream of altered splice site)
422	443	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
442	442	DISULFID	By similarity.	might get lost (downstream of altered splice site)
444	465	TRANSMEM	Helical; Name=3; (Potential).	might get lost (downstream of altered splice site)
466	485	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
486	508	TRANSMEM	Helical; Name=4; (Potential).	might get lost (downstream of altered splice site)
509	528	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
517	517	DISULFID	By similarity.	might get lost (downstream of altered splice site)
529	550	TRANSMEM	Helical; Name=5; (Potential).	might get lost (downstream of altered splice site)
551	573	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
574	597	TRANSMEM	Helical; Name=6; (Potential).	might get lost (downstream of altered splice site)
598	608	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
609	630	TRANSMEM	Helical; Name=7; (Potential).	might get lost (downstream of altered splice site)
631	695	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

1902 / 1902

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

634 / 634

position of stopcodon in wt / mu cDNA

2012 / 2012

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

111 / 111

chromosome

strand

-1

last intron/exon boundary

779

theoretical NMD boundary in CDS

618

length of CDS

1902

coding sequence (CDS) position

566

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

676

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

171413

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

49210264

original gDNA sequence snippet

TCAAGAAATACACAACTGTGCATTCAATGGAACCCAACTAG

altered gDNA sequence snippet

TCAAGAAATACACAACTGTGTATTCAATGGAACCCAACTAG

original cDNA sequence snippet

TCAAGAAATACACAACTGTGCATTCAATGGAACCCAACTAG

altered cDNA sequence snippet

TCAAGAAATACACAACTGTGTATTCAATGGAACCCAACTAG

wildtype AA sequence

MALLLVSLLA FLSLGSGCHH RICHCSNRVF LCQESKVTEI PSDLPRNAIE LRFVLTKLRV
IQKGAFSGFG DLEKIEISQN DVLEVIEADV FSNLPKLHEI RIEKANNLLY INPEAFQNLP
NLQYLLISNT GIKHLPDVHK IHSLQKVLLD IQDNINIHTI ERNSFVGLSF ESVILWLNKN
GIQEIHNCAF NGTQLDELNL SDNNNLEELP NDVFHGASGP VILSELHPIC NKSILRQEVD
YMTQARGQRS SLAEDNESSY SRGFDMTYTE FDYDLCNEVV DVTCSPKPDA FNPCEDIMGY
NILRVLIWFI SILAITGNII VLVILTTSQY KLTVPRFLMC NLAFADLCIG IYLLLIASVD
IHTKSQYHNY AIDWQTGAGC DAAGFFTVFA SELSVYTLTA ITLERWHTIT HAMQLDCKVQ
LRHAASVMVM GWIFAFAAAL FPIFGISSYM KVSICLPMDI DSPLSQLYVM SLLVLNVLAF
VVICGCYIHI YLTVRNPNIV SSSSDTRIAK RMAMLIFTDF LCMAPISFFA ISASLKVPLI
TVSKAKILLV LFHPINSCAN PFLYAIFTKN FRRDFFILLS KCGCYEMQAQ IYRTETSSTV
HNTHPRNGHC SSAPRVTSGS TYILVPLSHL AQN*

mutated AA sequence

MALLLVSLLA FLSLGSGCHH RICHCSNRVF LCQESKVTEI PSDLPRNAIE LRFVLTKLRV
IQKGAFSGFG DLEKIEISQN DVLEVIEADV FSNLPKLHEI RIEKANNLLY INPEAFQNLP
NLQYLLISNT GIKHLPDVHK IHSLQKVLLD IQDNINIHTI ERNSFVGLSF ESVILWLNKN
GIQEIHNCVF NGTQLDELNL SDNNNLEELP NDVFHGASGP VILSELHPIC NKSILRQEVD
YMTQARGQRS SLAEDNESSY SRGFDMTYTE FDYDLCNEVV DVTCSPKPDA FNPCEDIMGY
NILRVLIWFI SILAITGNII VLVILTTSQY KLTVPRFLMC NLAFADLCIG IYLLLIASVD
IHTKSQYHNY AIDWQTGAGC DAAGFFTVFA SELSVYTLTA ITLERWHTIT HAMQLDCKVQ
LRHAASVMVM GWIFAFAAAL FPIFGISSYM KVSICLPMDI DSPLSQLYVM SLLVLNVLAF
VVICGCYIHI YLTVRNPNIV SSSSDTRIAK RMAMLIFTDF LCMAPISFFA ISASLKVPLI
TVSKAKILLV LFHPINSCAN PFLYAIFTKN FRRDFFILLS KCGCYEMQAQ IYRTETSSTV
HNTHPRNGHC SSAPRVTSGS TYILVPLSHL AQN*

speed

0.51 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