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 CM080377)
known disease mutation: rs16254 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:49217768G>TN/A show variant in all transcripts IGV

HGNC symbol

FSHR

Ensembl transcript ID

ENST00000541117

Genbank transcript ID

N/A

UniProt peptide

P23945

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.144C>A
g.163909C>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121909665
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs16254 (pathogenic for Ovarian hyperstimulation syndrome) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM080377)

known disease mutation at this position, please check HGMD for details (HGMD ID CM080377)
known disease mutation at this position, please check HGMD for details (HGMD ID CM080377)

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.054	0.998
	3.775	1
(flanking)	3.151	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

splice site change before start ATG (at aa -135) |

effect	gDNA position	score	detection sequence	exon-intron border
Acc marginally increased	163904	wt: 0.6695 / mu: 0.6843 (marginal change - not scored)	wt: ATTTTGTTTCTCTCTAGGTTAATATCCAACACAGGTATTAA mu: ATTTTGTTTCTCTCTAGGTTAATATACAACACAGGTATTAA	gtta\|ATAT
Acc marginally increased	163899	wt: 0.9952 / mu: 0.9955 (marginal change - not scored)	wt: CTCTCATTTTGTTTCTCTCTAGGTTAATATCCAACACAGGT mu: CTCTCATTTTGTTTCTCTCTAGGTTAATATACAACACAGGT	tcta\|GGTT
Donor marginally increased	163912	wt: 0.9629 / mu: 0.9662 (marginal change - not scored)	wt: ATCCAACACAGGTAT mu: ATACAACACAGGTAT	CCAA\|caca
Acc gained	163908	0.44	mu: TGTTTCTCTCTAGGTTAATATACAACACAGGTATTAAGCAC	atat\|ACAA

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	17	SIGNAL	Potential.	might get lost (downstream of altered splice site)
13	13	CONFLICT	S -> R (in Ref. 8; CAA48179).	might get lost (downstream of altered splice site)
18	18	DISULFID		might get lost (downstream of altered splice site)
18	46	DOMAIN	LRRNT.	might get lost (downstream of altered splice site)
18	366	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
21	26	STRAND		might get lost (downstream of altered splice site)
23	23	DISULFID		might get lost (downstream of altered splice site)
25	25	DISULFID		might get lost (downstream of altered splice site)
29	34	STRAND		might get lost (downstream of altered splice site)
32	32	DISULFID		might get lost (downstream of altered splice site)
49	55	STRAND		might get lost (downstream of altered splice site)
49	72	REPEAT	LRR 1.	might get lost (downstream of altered splice site)
59	61	STRAND		might get lost (downstream of altered splice site)
63	68	TURN		might get lost (downstream of altered splice site)
73	97	REPEAT	LRR 2.	might get lost (downstream of altered splice site)
74	78	STRAND		might get lost (downstream of altered splice site)
88	93	STRAND		might get lost (downstream of altered splice site)
98	118	REPEAT	LRR 3.	might get lost (downstream of altered splice site)
99	105	STRAND		might get lost (downstream of altered splice site)
112	112	CONFLICT	N -> T (in Ref. 1; AAA52477).	might get lost (downstream of altered splice site)
115	117	STRAND		might get lost (downstream of altered splice site)
119	143	REPEAT	LRR 4.	might get lost (downstream of altered splice site)
124	130	STRAND		might get lost (downstream of altered splice site)
143	145	STRAND		might get lost (downstream of altered splice site)
144	169	REPEAT	LRR 5.	might get lost (downstream of altered splice site)
147	153	STRAND		might get lost (downstream of altered splice site)
168	171	STRAND		might get lost (downstream of altered splice site)
170	192	REPEAT	LRR 6.	might get lost (downstream of altered splice site)
173	176	STRAND		might get lost (downstream of altered splice site)
187	192	TURN		might get lost (downstream of altered splice site)
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

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

554 / 554

chromosome

strand

-1

last intron/exon boundary

616

theoretical NMD boundary in CDS

length of CDS

1296

coding sequence (CDS) position

N/A

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

144

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

163909

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

49217768

original gDNA sequence snippet

GTTTCTCTCTAGGTTAATATCCAACACAGGTATTAAGCACC

altered gDNA sequence snippet

GTTTCTCTCTAGGTTAATATACAACACAGGTATTAAGCACC

original cDNA sequence snippet

GACTCTGAAAAGGTTAATATCCAACACAGGTATTAAGCACC

altered cDNA sequence snippet

GACTCTGAAAAGGTTAATATACAACACAGGTATTAAGCACC

wildtype AA sequence

MEASLTYPSH CCAFANWRRQ ISELHPICNK SILRQEVDYM TQARGQRSSL AEDNESSYSR
GFDMTYTEFD YDLCNEVVDV TCSPKPDAFN PCEDIMGYNI LRVLIWFISI LAITGNIIVL
VILTTSQYKL TVPRFLMCNL AFADLCIGIY LLLIASVDIH TKSQYHNYAI DWQTGAGCDA
AGFFTVFASE LSVYTLTAIT LERWHTITHA MQLDCKVQLR HAASVMVMGW IFAFAAALFP
IFGISSYMKV SICLPMDIDS PLSQLYVMSL LVLNVLAFVV ICGCYIHIYL TVRNPNIVSS
SSDTRIAKRM AMLIFTDFLC MAPISFFAIS ASLKVPLITV SKAKILLVLF HPINSCANPF
LYAIFTKNFR RDFFILLSKC GCYEMQAQIY RTETSSTVHN THPRNGHCSS APRVTSGSTY
ILVPLSHLAQ N*

mutated AA sequence

N/A

speed

0.31 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