mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.0573014083941378 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM0910799)
known disease mutation: rs8376 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr8:97157179G>TN/A show variant in all transcripts IGV

HGNC symbol

GDF6

Ensembl transcript ID

ENST00000287020

Genbank transcript ID

NM_001001557

UniProt peptide

Q6KF10

alteration type

single base exchange

alteration region

CDS

DNA changes

c.980C>A
cDNA.1080C>A
g.15842C>A

AA changes

P327H Score: 77 explain score(s)

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

327

frameshift

known variant

Reference ID: rs121909356

database	homozygous (T/T)	heterozygous	allele carriers
1000G	0	1	1
ExAC	0	24	24

known disease mutation: rs8376 (pathogenic for Microphthalmia, isolated 4) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM0910799)

known disease mutation at this position, please check HGMD for details (HGMD ID CM0910799)
known disease mutation at this position, please check HGMD for details (HGMD ID CM0910799)

regulatory features

CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.804	0.845
	1.468	0.941
(flanking)	0.701	0.961

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	15845	wt: 0.27 / mu: 0.41	wt: TGCCAGGCCTTGGCTGCCCTCGCCCGGCCGCCGGCGGCGGC mu: TGCCAGGCCTTGGCTGCACTCGCCCGGCCGCCGGCGGCGGC	cctc\|GCCC

distance from splice site

574

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

327

mutated

not conserved

327

Ptroglodytes

all identical

ENSPTRG00000020439

305

Mmulatta

all identical

ENSMMUG00000011267

327

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000051279

330

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000004399

310

Drerio

not conserved

ENSDARG00000053479

289

Dmelanogaster

not conserved

FBgn0000490

490

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
23	330	PROPEP	Potential. /FTId=PRO_0000342206.	lost
331	335	COMPBIAS	Poly-Arg.	might get lost (downstream of altered splice site)
354	354	DISULFID	By similarity.	might get lost (downstream of altered splice site)
383	383	DISULFID	By similarity.	might get lost (downstream of altered splice site)
387	387	DISULFID	By similarity.	might get lost (downstream of altered splice site)
419	419	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
419	419	DISULFID	Interchain (By similarity).	might get lost (downstream of altered splice site)
420	420	DISULFID	By similarity.	might get lost (downstream of altered splice site)
452	452	DISULFID	By similarity.	might get lost (downstream of altered splice site)
454	454	DISULFID	By similarity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1368 / 1368

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

456 / 456

position of stopcodon in wt / mu cDNA

1468 / 1468

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

101 / 101

chromosome

strand

-1

last intron/exon boundary

507

theoretical NMD boundary in CDS

356

length of CDS

1368

coding sequence (CDS) position

980

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

1080

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

15842

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

97157179

original gDNA sequence snippet

GGATGCCAGGCCTTGGCTGCCCTCGCCCGGCCGCCGGCGGC

altered gDNA sequence snippet

GGATGCCAGGCCTTGGCTGCACTCGCCCGGCCGCCGGCGGC

original cDNA sequence snippet

GGATGCCAGGCCTTGGCTGCCCTCGCCCGGCCGCCGGCGGC

altered cDNA sequence snippet

GGATGCCAGGCCTTGGCTGCACTCGCCCGGCCGCCGGCGGC

wildtype AA sequence

MDTPRVLLSA VFLISFLWDL PGFQQASISS SSSSAELGST KGMRSRKEGK MQRAPRDSDA
GREGQEPQPR PQDEPRAQQP RAQEPPGRGP RVVPHEYMLS IYRTYSIAEK LGINASFFQS
SKSANTITSF VDRGLDDLSH TPLRRQKYLF DVSMLSDKEE LVGAELRLFR QAPSAPWGPP
AGPLHVQLFP CLSPLLLDAR TLDPQGAPPA GWEVFDVWQG LRHQPWKQLC LELRAAWGEL
DAGEAEARAR GPQQPPPPDL RSLGFGRRVR PPQERALLVV FTRSQRKNLF AEMREQLGSA
EAAGPGAGAE GSWPPPSGAP DARPWLPSPG RRRRRTAFAS RHGKRHGKKS RLRCSKKPLH
VNFKELGWDD WIIAPLEYEA YHCEGVCDFP LRSHLEPTNH AIIQTLMNSM DPGSTPPSCC
VPTKLTPISI LYIDAGNNVV YKQYEDMVVE SCGCR*

mutated AA sequence

MDTPRVLLSA VFLISFLWDL PGFQQASISS SSSSAELGST KGMRSRKEGK MQRAPRDSDA
GREGQEPQPR PQDEPRAQQP RAQEPPGRGP RVVPHEYMLS IYRTYSIAEK LGINASFFQS
SKSANTITSF VDRGLDDLSH TPLRRQKYLF DVSMLSDKEE LVGAELRLFR QAPSAPWGPP
AGPLHVQLFP CLSPLLLDAR TLDPQGAPPA GWEVFDVWQG LRHQPWKQLC LELRAAWGEL
DAGEAEARAR GPQQPPPPDL RSLGFGRRVR PPQERALLVV FTRSQRKNLF AEMREQLGSA
EAAGPGAGAE GSWPPPSGAP DARPWLHSPG RRRRRTAFAS RHGKRHGKKS RLRCSKKPLH
VNFKELGWDD WIIAPLEYEA YHCEGVCDFP LRSHLEPTNH AIIQTLMNSM DPGSTPPSCC
VPTKLTPISI LYIDAGNNVV YKQYEDMVVE SCGCR*

speed

1.05 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