mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 8.12255490164704e-13 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM040800)
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr8:22021517G>AN/A show variant in all transcripts IGV

HGNC symbol

SFTPC

Ensembl transcript ID

ENST00000522109

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

3'UTR

DNA changes

cDNA.917G>A
g.7092G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs1124

database	homozygous (A/A)	heterozygous	allele carriers
1000G	163	856	1019
ExAC	5638	21491	27129

known disease mutation at this position, please check HGMD for details (HGMD ID CM040800)

regulatory features

Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.73	0.975
	0.581	0.988
(flanking)	1.825	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing
splice site change occurs after stopcodon (at aa 295) splice site change occurs after stopcodon (at aa 296) splice site change occurs after stopcodon (at aa 298)

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	7095	sequence motif lost	-	wt: CACC\|ctgt mu: CACC.ctgt
Donor gained	7087	0.97	mu: ATGGCCGTGAACACC	GGCC\|gtga
Donor gained	7084	0.31	mu: GGCATGGCCGTGAAC	CATG\|gccg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

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

signal is predicted to be ok

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

25 / 25

chromosome

strand

last intron/exon boundary

349

theoretical NMD boundary in CDS

274

length of CDS

453

coding sequence (CDS) position

N/A

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

917

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

7092

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

22021517

original gDNA sequence snippet

CTTCCTGGGCATGGCCGTGAGCACCCTGTGTGGCGAGGTGC

altered gDNA sequence snippet

CTTCCTGGGCATGGCCGTGAACACCCTGTGTGGCGAGGTGC

original cDNA sequence snippet

CTTCCTGGGCATGGCCGTGAGCACC

altered cDNA sequence snippet

CTTCCTGGGCATGGCCGTGAACACC

wildtype AA sequence

MDVGSKEVLM ESPPDYSAAP RGRFGIPCCP VHLKRLLIVV VVVVLIVVVI VGALLMGLHM
SQKHTEMVLE MSIGAPEAQQ RLALSEHLVT TATFSIGSTG LVVYDYQQLL IAYKPAPGTC
CYIMKIAPES IPSLEALTRK VHNFQVCVCG *

mutated AA sequence

N/A

speed

1.26 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