mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999945197 (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)

chr19:54664209G>CN/A show variant in all transcripts IGV

HGNC symbol

TMC4

Ensembl transcript ID

ENST00000416963

Genbank transcript ID

N/A

UniProt peptide

Q7Z404

alteration type

single base exchange

alteration region

CDS

DNA changes

c.811C>G
cDNA.811C>G
g.12736C>G

AA changes

Q271E Score: 29 explain score(s)

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

271

frameshift

known variant

Reference ID: rs36657

database	homozygous (C/C)	heterozygous	allele carriers
1000G	723	1119	1842
ExAC	15602	1563	17165

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2AZ, Histone, Histone 2A variant Z
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.344	0.942
	-0.39	0.084
(flanking)	-0.321	0.073

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 increased	12735	wt: 0.74 / mu: 0.99	wt: CAGAGACAGACGGTG mu: CAGAGAGAGACGGTG	GAGA\|caga
Donor lost	12741	0.23	wt: CAGACGGTGAGCCAG	GACG\|gtga
Donor gained	12732	0.60	mu: CGTCAGAGAGAGACG	TCAG\|agag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

271

mutated

all conserved

271

Ptroglodytes

all conserved

ENSPTRG00000011446

689

Mmulatta

all conserved

ENSMMUG00000009704

417

Fcatus

all conserved

ENSFCAG00000003603

411

Mmusculus

all conserved

ENSMUSG00000019734

671

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000015812

570

Drerio

not conserved

ENSDARG00000031757

670

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
250	270	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
271	348	TOPO_DOM	Extracellular (Potential).	lost
321	321	CONFLICT	K -> Q (in Ref. 1; AAP78781).	might get lost (downstream of altered splice site)
349	369	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
370	394	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
395	415	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
397	397	CONFLICT	S -> P (in Ref. 2; AAP69870).	might get lost (downstream of altered splice site)
416	425	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
426	446	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
447	483	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
484	504	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
505	542	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
543	565	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
566	592	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
569	569	CONFLICT	L -> V (in Ref. 1; AAP78781).	might get lost (downstream of altered splice site)
593	613	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
614	654	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
642	642	CONFLICT	T -> A (in Ref. 2; AAP69870).	might get lost (downstream of altered splice site)
655	677	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
678	712	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

885 / 885

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

295 / 295

position of stopcodon in wt / mu cDNA

885 / 885

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

1 / 1

chromosome

strand

-1

last intron/exon boundary

817

theoretical NMD boundary in CDS

766

length of CDS

885

coding sequence (CDS) position

811

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

811

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

12736

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

54664209

original gDNA sequence snippet

CTGAGCTCAAACGTCAGAGACAGACGGTGAGCCAGGCGGGT

altered gDNA sequence snippet

CTGAGCTCAAACGTCAGAGAGAGACGGTGAGCCAGGCGGGT

original cDNA sequence snippet

CTGAGCTCAAACGTCAGAGACAGACGGAGGCGCAGAATAAA

altered cDNA sequence snippet

CTGAGCTCAAACGTCAGAGAGAGACGGAGGCGCAGAATAAA

wildtype AA sequence

MKGGGGQRDV GADRTVFLRL ASLVVLLFSL WNQITCGGDS EAEDCKTCGY NYKQLPCWET
VLGQEMYKLL LFDLLTVLAV ALLIQFPRKL LCGLCPGALG RLAGTQEFQV PDEVLGLIYA
QTVVWVGSFF CPLLPLLNTV KFLLLFYLKK LTLFSTCSPA ARTFRASAAN FFFPLVLLLG
LAISSVPLLY SIFLIPPSKL CGPFRGQSSI WAQIPESISS LPETTQNFLF FLGTQAFAVP
LLLISSILMA YTVALANSYG RLISELKRQR QTEAQNKVFL ARRAVALTST KPAL*

mutated AA sequence

speed

0.79 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