mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 0.999309585713288 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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)

chr4:83582211C>GN/A show variant in all transcripts IGV

HGNC symbol

SCD5

Ensembl transcript ID

ENST00000319540

Genbank transcript ID

NM_001037582

UniProt peptide

Q86SK9

alteration type

single base exchange

alteration region

intron

DNA changes

g.137800G>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs3733227

database	homozygous (G/G)	heterozygous	allele carriers
1000G	933	1181	2114
ExAC	26134	-19501	6633

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.986	0.077
	1.135	0.071
(flanking)	0.305	0.033

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	137803	wt: 0.9884 / mu: 0.9927 (marginal change - not scored)	wt: AAGAAGGAAGAGCTC mu: AACAAGGAAGAGCTC	GAAG\|gaag
Donor increased	137802	wt: 0.80 / mu: 0.92	wt: AAAGAAGGAAGAGCT mu: AAACAAGGAAGAGCT	AGAA\|ggaa
Donor marginally increased	137801	wt: 0.9808 / mu: 0.9871 (marginal change - not scored)	wt: GAAAGAAGGAAGAGC mu: GAAACAAGGAAGAGC	AAGA\|agga
Donor marginally increased	137795	wt: 0.8937 / mu: 0.9382 (marginal change - not scored)	wt: CATCCAGAAAGAAGG mu: CATCCAGAAACAAGG	TCCA\|gaaa
Donor increased	137798	wt: 0.24 / mu: 0.47	wt: CCAGAAAGAAGGAAG mu: CCAGAAACAAGGAAG	AGAA\|agaa

distance from splice site

19649

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
194	214	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
216	238	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
272	276	MOTIF	Histidine box-3 (By similarity).	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

321 / 321

chromosome

strand

-1

last intron/exon boundary

1123

theoretical NMD boundary in CDS

752

length of CDS

993

coding sequence (CDS) position

N/A

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

N/A

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

137800

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

83582211

original gDNA sequence snippet

GTACACAGCACATCCAGAAAGAAGGAAGAGCTCTCAATCAA

altered gDNA sequence snippet

GTACACAGCACATCCAGAAACAAGGAAGAGCTCTCAATCAA

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MPGPATDAGK IPFCDAKEEI RAGLESSEGG GGPERPGARG QRQNIVWRNV VLMSLLHLGA
VYSLVLIPKA KPLTLLWAYF CFLLAALGVT AGAHRLWSHR SYRAKLPLRI FLAVANSMAF
QNDIFEWSRD HRAHHKYSET DADPHNARRG FFFSHIGWLF VRKHRDVIEK GRKLDVTDLL
ADPVVRIQRK YYKISVVLMC FVVPTLVPWY IWGESLWNSY FLASILRYTI SLNISWLVNS
AAHMYGNRPY DKHISPRQNP LVALGAIGEG FHNYHHTFPF DYSASEFGLN FNPTTWFIDF
MCWLGLATDR KRATKPMIEA RKARTGDSSA *

mutated AA sequence

N/A

speed

0.61 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