mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999979307386 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:148407893C>AN/A show variant in all transcripts IGV

HGNC symbol

SH3TC2

Ensembl transcript ID

ENST00000538184

Genbank transcript ID

N/A

UniProt peptide

Q8TF17

alteration type

single base exchange

alteration region

CDS

DNA changes

c.43G>T
cDNA.932G>T
g.34834G>T

AA changes

A15S Score: 99 explain score(s)

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

frameshift

known variant

Reference ID: rs6875902

database	homozygous (A/A)	heterozygous	allele carriers
1000G	126	731	857
ExAC	2739	18911	21650

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.113	0.272
	0.125	0.205
(flanking)	-0.085	0.213

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	34843	wt: 0.48 / mu: 0.80	wt: CTGAGAACTTCGCCCCCATATTGGCTTTTCTGGATCATGAG mu: CTGAGAACTTCTCCCCCATATTGGCTTTTCTGGATCATGAG	atat\|TGGC
Acc increased	34845	wt: 0.62 / mu: 0.86	wt: GAGAACTTCGCCCCCATATTGGCTTTTCTGGATCATGAGGG mu: GAGAACTTCTCCCCCATATTGGCTTTTCTGGATCATGAGGG	attg\|GCTT
Acc gained	34841	0.57	mu: GGCTGAGAACTTCTCCCCCATATTGGCTTTTCTGGATCATG	ccat\|ATTG

distance from splice site

225

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000017392

468

Mmulatta

not conserved

ENSMMUG00000019820

468

Fcatus

all identical

ENSFCAG00000007955

469

Mmusculus

all identical

ENSMUSG00000045629

468

Ggallus

no alignment

ENSGALG00000002806

n/a

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000089917

470

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
104	104	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
268	331	DOMAIN	SH3.	might get lost (downstream of altered splice site)
334	334	CONFLICT	M -> R (in Ref. 6; BAB85571).	might get lost (downstream of altered splice site)
528	561	REPEAT	TPR 1.	might get lost (downstream of altered splice site)
757	790	REPEAT	TPR 2.	might get lost (downstream of altered splice site)
836	869	REPEAT	TPR 3.	might get lost (downstream of altered splice site)
1001	1037	REPEAT	TPR 4.	might get lost (downstream of altered splice site)
1084	1118	REPEAT	TPR 5.	might get lost (downstream of altered splice site)
1119	1152	REPEAT	TPR 6.	might get lost (downstream of altered splice site)
1158	1158	CONFLICT	V -> I (in Ref. 6; BAB85571).	might get lost (downstream of altered splice site)
1166	1199	REPEAT	TPR 7.	might get lost (downstream of altered splice site)
1210	1244	REPEAT	TPR 8.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2181 / 2181

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

727 / 727

position of stopcodon in wt / mu cDNA

3070 / 3070

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

890 / 890

chromosome

strand

-1

last intron/exon boundary

3198

theoretical NMD boundary in CDS

2258

length of CDS

2181

coding sequence (CDS) position

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

932

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

34834

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

148407893

original gDNA sequence snippet

AGGAGGAGGCTGAGAACTTCGCCCCCATATTGGCTTTTCTG

altered gDNA sequence snippet

AGGAGGAGGCTGAGAACTTCTCCCCCATATTGGCTTTTCTG

original cDNA sequence snippet

AGGAGGAGGCTGAGAACTTCGCCCCCATATTGGCTTTTCTG

altered cDNA sequence snippet

AGGAGGAGGCTGAGAACTTCTCCCCCATATTGGCTTTTCTG

wildtype AA sequence

MDLSTGQEEE AENFAPILAF LDHEGYADHF KSLYDFSFSF LTSSFYSFSE EDEFVAYLEA
SRKWAKKSHM TWAHARLCFL LGRLSIRKVK LSQARVYFEE AIHILNGAFE DLSLVATLYI
NLAAIYLKQR LRHKGSALLE KAGALLACLP DRESSAKHEL DVVAYVLRQG IVVGSSPLEA
RACFLAIRLL LSLGRHEEVL PFAERLQLLS GHPPASEAVA SVLSFLYDKK YLPHLAVASV
QQHGIQSAQG MSLPIWQVHL VLQNTTKLLG FPSPGWGEVS ALACPMLRQA LAACEELADR
STQRALCLIL SKVYLEHRSP DGAIHYLSQA LVLGQLLGEQ ESFESSLCLA WAYLLASQAK
KALDVLEPLL CSLKETESLT QRGVIYNLLG LALQGEGRVN RAAKSYLRAL NRAQEVGDVH
NQAVAMANLG HLSLKSWAQH PARNYLLQAV RLYCELQASK ETDMELVQVF LWLAQVLVSG
HQLTHGLLCY EMALLFGLRH RHLKSQLQAT KSLCHFYSSV SPNPEACITY HEHWLALAQQ
LRDREMEGRL LESLGQLYRN LNTARSLRRS LTCIKESLRI FIDLGETDKA AEAWLGAGRL
HYLMQEDELV ELCLQAAIQT ALKSEEPLLA LKLYEEAGDV FFNGTRHRHH AVEYYRAGAV
PLARRLKAVR TELRIFNKLT ELQISLEGYE KALEFATLAA RLSTVTEARA GGLSPPGYSV
LLPAHV*

mutated AA sequence

MDLSTGQEEE AENFSPILAF LDHEGYADHF KSLYDFSFSF LTSSFYSFSE EDEFVAYLEA
SRKWAKKSHM TWAHARLCFL LGRLSIRKVK LSQARVYFEE AIHILNGAFE DLSLVATLYI
NLAAIYLKQR LRHKGSALLE KAGALLACLP DRESSAKHEL DVVAYVLRQG IVVGSSPLEA
RACFLAIRLL LSLGRHEEVL PFAERLQLLS GHPPASEAVA SVLSFLYDKK YLPHLAVASV
QQHGIQSAQG MSLPIWQVHL VLQNTTKLLG FPSPGWGEVS ALACPMLRQA LAACEELADR
STQRALCLIL SKVYLEHRSP DGAIHYLSQA LVLGQLLGEQ ESFESSLCLA WAYLLASQAK
KALDVLEPLL CSLKETESLT QRGVIYNLLG LALQGEGRVN RAAKSYLRAL NRAQEVGDVH
NQAVAMANLG HLSLKSWAQH PARNYLLQAV RLYCELQASK ETDMELVQVF LWLAQVLVSG
HQLTHGLLCY EMALLFGLRH RHLKSQLQAT KSLCHFYSSV SPNPEACITY HEHWLALAQQ
LRDREMEGRL LESLGQLYRN LNTARSLRRS LTCIKESLRI FIDLGETDKA AEAWLGAGRL
HYLMQEDELV ELCLQAAIQT ALKSEEPLLA LKLYEEAGDV FFNGTRHRHH AVEYYRAGAV
PLARRLKAVR TELRIFNKLT ELQISLEGYE KALEFATLAA RLSTVTEARA GGLSPPGYSV
LLPAHV*

speed

1.31 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