mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 5.1696817582027e-10 (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)
protein features (might be) affected
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

ENST00000520605

Genbank transcript ID

N/A

UniProt peptide

P11686

alteration type

single base exchange

alteration region

intron

DNA changes

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

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

distance from splice site

262

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
59	197	PROPEP	/FTId=PRO_0000033479.	might get lost (downstream of altered splice site)
91	96	STRAND		might get lost (downstream of altered splice site)
94	197	DOMAIN	BRICHOS.	might get lost (downstream of altered splice site)
97	99	TURN		might get lost (downstream of altered splice site)
100	105	STRAND		might get lost (downstream of altered splice site)
106	109	TURN		might get lost (downstream of altered splice site)
110	116	STRAND		might get lost (downstream of altered splice site)
121	125	STRAND		might get lost (downstream of altered splice site)
134	143	HELIX		might get lost (downstream of altered splice site)
183	189	HELIX		might get lost (downstream of altered splice site)
194	197	STRAND		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

30 / 30

chromosome

strand

last intron/exon boundary

306

theoretical NMD boundary in CDS

226

length of CDS

468

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)

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

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MDVGSKEVLM ESPPVLEMSI GAPEAQQRLA LSEHLVTTAT FSIGSTGLVV YDYQQLLIAY
KPAPGTCCYI MKIAPESIPS LEALTRKVHN FQGQWKPQRE RKRPGQRVFC SFCRRARSCF
CPHRRDKPWR NGSLGRGWEW AEVAPRGPGT PATTE*

mutated AA sequence

N/A

speed

0.54 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