MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000415846
MT speed 0 s - this script 2.402154 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SLFN14	polymorphism_automatic	0.000520981747115012	simple_aae		affected		Q93R	single base exchange	rs10512472		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999479018252885 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM168223)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:33884804T>CN/A show variant in all transcripts IGV

HGNC symbol

SLFN14

Ensembl transcript ID

ENST00000415846

Genbank transcript ID

NM_001129820

UniProt peptide

P0C7P3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.278A>G
cDNA.314A>G
g.314A>G

AA changes

Q93R Score: 43 explain score(s)

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

frameshift

known variant

Reference ID: rs10512472

database	homozygous (C/C)	heterozygous	allele carriers
1000G	152	874	1026
ExAC	458	3143	3601

known disease mutation at this position, please check HGMD for details (HGMD ID CM168223)

regulatory features

H3K27me1, Histone, Histone 3 Lysine 27 mono-methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.69	1
	2.219	1
(flanking)	1.313	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
Acc marginally increased	315	wt: 0.8400 / mu: 0.8512 (marginal change - not scored)	wt: CTCCTTCCTTCAGGTTCACAGAAATACCTTGACTACATGCA mu: CTCCTTCCTTCAGGTTCACGGAAATACCTTGACTACATGCA	acag\|AAAT
Acc marginally increased	307	wt: 0.9453 / mu: 0.9576 (marginal change - not scored)	wt: TTCAAAAGCTCCTTCCTTCAGGTTCACAGAAATACCTTGAC mu: TTCAAAAGCTCCTTCCTTCAGGTTCACGGAAATACCTTGAC	tcag\|GTTC
Acc marginally increased	306	wt: 0.7615 / mu: 0.8210 (marginal change - not scored)	wt: TTTCAAAAGCTCCTTCCTTCAGGTTCACAGAAATACCTTGA mu: TTTCAAAAGCTCCTTCCTTCAGGTTCACGGAAATACCTTGA	ttca\|GGTT
Acc increased	305	wt: 0.30 / mu: 0.38	wt: TTTTCAAAAGCTCCTTCCTTCAGGTTCACAGAAATACCTTG mu: TTTTCAAAAGCTCCTTCCTTCAGGTTCACGGAAATACCTTG	cttc\|AGGT
Donor marginally increased	316	wt: 0.2451 / mu: 0.2593 (marginal change - not scored)	wt: CACAGAAATACCTTG mu: CACGGAAATACCTTG	CAGA\|aata
Donor gained	313	0.99	mu: GTTCACGGAAATACC	TCAC\|ggaa

distance from splice site

314

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000039969

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
356	356	CONFLICT	P -> S (in Ref. 2; AAI40848/AAI57878/ AAI57880).	might get lost (downstream of altered splice site)
593	600	NP_BIND	ATP (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2739 / 2739

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

913 / 913

position of stopcodon in wt / mu cDNA

2775 / 2775

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

37 / 37

chromosome

strand

-1

last intron/exon boundary

1941

theoretical NMD boundary in CDS

1854

length of CDS

2739

coding sequence (CDS) position

278

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

314

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

314

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

33884804

original gDNA sequence snippet

GCTCCTTCCTTCAGGTTCACAGAAATACCTTGACTACATGC

altered gDNA sequence snippet

GCTCCTTCCTTCAGGTTCACGGAAATACCTTGACTACATGC

original cDNA sequence snippet

GCTCCTTCCTTCAGGTTCACAGAAATACCTTGACTACATGC

altered cDNA sequence snippet

GCTCCTTCCTTCAGGTTCACGGAAATACCTTGACTACATGC

wildtype AA sequence

MESLKTDTEM PYPEVIVDVG RVIFGEENRK KMTNSCLKRS ENSRIIRAIC ALLNSGGGVI
KAEIDDKTYS YQCHGLGQDL ETSFQKLLPS GSQKYLDYMQ QGHNLLIFVK SWSPDVFSLP
LRICSLRSNL YRRDVTSAIN LSASSALELL REKGFRAQRG RPRVKKLHPQ QVLNRCIQEE
EDMRILASEF FKKDKLMYKE KLNFTESTHV EFKRFTTKKV IPRIKEMLPH YVSAFANTQG
GYVLIGVDDK SKEVVGCKWE KVNPDLLKKE IENCIEKLPT FHFCCEKPKV NFTTKILNVY
QKDVLDGYVC VIQVEPFCCV VFAEAPDSWI MKDNSVTRLT AEQWVVMMLD TQSAPPSLVT
DYNSCLISSA SSARKSPGYP IKVHKFKEAL QRHLFPVTQE EVQFKPESLC KKLFSDHKEL
EGLMKTLIHP CSQGIVIFSR SWAGDVGFRK EQNVLCDALL IAVNSPVVLY TILIDPNWPG
GLEYARNTAH QLKQKLQTVG GYTGKVCIIP RLIHLSSTQS RPGEIPLRYP RSYRLADEEE
MEDLLQALVV VSLSSRSLLS DQMGCEFFNL LIMEQSQLLS ESLQKTRELF IYCFPGVRKT
ALAIKIMEKI KDLFHCKPKE ILYVCESDSL KDFVTQQTTC QAVTRKTFMQ GEFLKIKHIV
MDETENFCSK YGNWYMKAKN ITHPKAKGTG SENLHHGILW LFLDPFQIHH ADVNGLPPPS
AQFPRKTITS GIHCALEIAK VMKEEMKRIK ENPPSNMSPD TLALFSETAY EEATCAQALP
GVCETKTNLT TEQIANYVAR KCHSLFQCGY LPKDIAILCR RGEDRGRYRL ALLKAMELIE
THRPSEVVFS PATGVWGSHI VLDSIQQFSG LERTVVFGLS PECDQSEEFH KLCFASRAIK
HLYLLYEKRA AY*

mutated AA sequence

MESLKTDTEM PYPEVIVDVG RVIFGEENRK KMTNSCLKRS ENSRIIRAIC ALLNSGGGVI
KAEIDDKTYS YQCHGLGQDL ETSFQKLLPS GSRKYLDYMQ QGHNLLIFVK SWSPDVFSLP
LRICSLRSNL YRRDVTSAIN LSASSALELL REKGFRAQRG RPRVKKLHPQ QVLNRCIQEE
EDMRILASEF FKKDKLMYKE KLNFTESTHV EFKRFTTKKV IPRIKEMLPH YVSAFANTQG
GYVLIGVDDK SKEVVGCKWE KVNPDLLKKE IENCIEKLPT FHFCCEKPKV NFTTKILNVY
QKDVLDGYVC VIQVEPFCCV VFAEAPDSWI MKDNSVTRLT AEQWVVMMLD TQSAPPSLVT
DYNSCLISSA SSARKSPGYP IKVHKFKEAL QRHLFPVTQE EVQFKPESLC KKLFSDHKEL
EGLMKTLIHP CSQGIVIFSR SWAGDVGFRK EQNVLCDALL IAVNSPVVLY TILIDPNWPG
GLEYARNTAH QLKQKLQTVG GYTGKVCIIP RLIHLSSTQS RPGEIPLRYP RSYRLADEEE
MEDLLQALVV VSLSSRSLLS DQMGCEFFNL LIMEQSQLLS ESLQKTRELF IYCFPGVRKT
ALAIKIMEKI KDLFHCKPKE ILYVCESDSL KDFVTQQTTC QAVTRKTFMQ GEFLKIKHIV
MDETENFCSK YGNWYMKAKN ITHPKAKGTG SENLHHGILW LFLDPFQIHH ADVNGLPPPS
AQFPRKTITS GIHCALEIAK VMKEEMKRIK ENPPSNMSPD TLALFSETAY EEATCAQALP
GVCETKTNLT TEQIANYVAR KCHSLFQCGY LPKDIAILCR RGEDRGRYRL ALLKAMELIE
THRPSEVVFS PATGVWGSHI VLDSIQQFSG LERTVVFGLS PECDQSEEFH KLCFASRAIK
HLYLLYEKRA AY*

speed

0.33 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
back to results table

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

Problems