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: ENST00000356865
MT speed 0 s - this script 3.030589 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ATP10A	polymorphism_automatic	3.41288545470109e-05	simple_aae		affected		A1179T	single base exchange	rs2076744		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999965871145453 (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)

chr15:25926179C>TN/A show variant in all transcripts IGV

HGNC symbol

ATP10A

Ensembl transcript ID

ENST00000356865

Genbank transcript ID

NM_024490

UniProt peptide

O60312

alteration type

single base exchange

alteration region

CDS

DNA changes

c.3535G>A
cDNA.3647G>A
g.184139G>A

AA changes

A1179T Score: 58 explain score(s)

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

1179

frameshift

known variant

Reference ID: rs2076744

database	homozygous (T/T)	heterozygous	allele carriers
1000G	248	917	1165
ExAC	3106	18251	21357

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.796	0.979
	0.157	0.147
(flanking)	-0.884	0.07

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	184143	wt: 0.70 / mu: 0.86	wt: CGCCTTCCAGAGCCT mu: CACCTTCCAGAGCCT	CCTT\|ccag
Donor increased	184130	wt: 0.30 / mu: 0.35	wt: ACATGGCCGACGCCG mu: ACATGGCCGACGCCA	ATGG\|ccga
Donor gained	184135	0.62	mu: GCCGACGCCACCTTC	CGAC\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1179

mutated

not conserved

1179

Ptroglodytes

all identical

ENSPTRG00000030356

1179

Mmulatta

not conserved

ENSMMUG00000017641

1183

Fcatus

no alignment

ENSFCAG00000007606

n/a

Mmusculus

all identical

ENSMUSG00000025324

1193

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000061039

1178

Dmelanogaster

not conserved

FBgn0032120

1345

Celegans

not conserved

W09D10.2

1229

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
1171	1192	TRANSMEM	Helical; (Potential).	lost
1193	1199	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
1200	1222	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1223	1228	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1229	1249	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1250	1267	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
1268	1292	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1293	1499	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

4500 / 4500

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

1500 / 1500

position of stopcodon in wt / mu cDNA

4612 / 4612

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

113 / 113

chromosome

strand

-1

last intron/exon boundary

3979

theoretical NMD boundary in CDS

3816

length of CDS

4500

coding sequence (CDS) position

3535

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

3647

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

184139

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

25926179

original gDNA sequence snippet

GGTTTAACATGGCCGACGCCGCCTTCCAGAGCCTGGTTTGC

altered gDNA sequence snippet

GGTTTAACATGGCCGACGCCACCTTCCAGAGCCTGGTTTGC

original cDNA sequence snippet

GGTTTAACATGGCCGACGCCGCCTTCCAGAGCCTGGTTTGC

altered cDNA sequence snippet

GGTTTAACATGGCCGACGCCACCTTCCAGAGCCTGGTTTGC

wildtype AA sequence

MEREPAGTEE PGPPGRRRRR EGRTRTVRSN LLPPPGAEDP AAGAAKGERR RRRGCAQHLA
DNRLKTTKYT LLSFLPKNLF EQFHRPANVY FVFIALLNFV PAVNAFQPGL ALAPVLFILA
ITAFRDLWED YSRHRSDHKI NHLGCLVFSR EEKKYVNRFW KEIHVGDFVR LRCNEIFPAD
ILLLSSSDPD GLCHIETANL DGETNLKRRQ VVRGFSELVS EFNPLTFTSV IECEKPNNDL
SRFRGCIIHD NGKKAGLYKE NLLLRGCTLR NTDAVVGIVI YAGHETKALL NNSGPRYKRS
KLERQMNCDV LWCVLLLVCM SLFSAVGHGL WIWRYQEKKS LFYVPKSDGS SLSPVTAAVY
SFLTMIIVLQ VLIPISLYVS IEIVKACQVY FINQDMQLYD EETDSQLQCR ALNITEDLGQ
IQYIFSDKTG TLTENKMVFR RCTVSGVEYS HDANAQRLAR YQEADSEEEE VVPRGGSVSQ
RGSIGSHQSV RVVHRTQSTK SHRRTGSRAE AKRASMLSKH TAFSSPMEKD ITPDPKLLEK
VSECDKSLAV ARHQEHLLAH LSPELSDVFD FFIALTICNT VVVTSPDQPR TKVRVRFELK
SPVKTIEDFL RRFTPSCLTS GCSSIGSLAA NKSSHKLGSS FPSTPSSDGM LLRLEERLGQ
PTSAIASNGY SSQADNWASE LAQEQESERE LRYEAESPDE AALVYAARAY NCVLVERLHD
QVSVELPHLG RLTFELLHTL GFDSVRKRMS VVIRHPLTDE INVYTKGADS VVMDLLQPCS
SVDARGRHQK KIRSKTQNYL NVYAAEGLRT LCIAKRVLSK EEYACWLQSH LEAESSLENS
EELLFQSAIR LETNLHLLGA TGIEDRLQDG VPETISKLRQ AGLQIWVLTG DKQETAVNIA
YACKLLDHDE EVITLNATSQ EACAALLDQC LCYVQSRGLQ RAPEKTKGKV SMRFSSLCPP
STSTASGRRP SLVIDGRSLA YALEKNLEDK FLFLAKQCRS VLCCRSTPLQ KSMVVKLVRS
KLKAMTLAIG DGANDVSMIQ VADVGVGISG QEGMQAVMAS DFAVPKFRYL ERLLILHGHW
CYSRLANMVL YFFYKNTMFV GLLFWFQFFC GFSASTMIDQ WYLIFFNLLF SSLPPLVTGV
LDRDVPANVL LTNPQLYKSG QNMEEYRPRT FWFNMADAAF QSLVCFSIPY LAYYDSNVDL
FTWGTPIVTI ALLTFLLHLG IETKTWTWLN WITCGFSVLL FFTVALIYNA SCATCYPPSN
PYWTMQALLG DPVFYLTCLM TPVAALLPRL FFRSLQGRVF PTQLQLARQL TRKSPRRCSA
PKETFAQGRL PKDSGTEHSS GRTVKTSVPL SQPSWHTQQP VCSLEASGEP STVDMSMPVR
EHTLLEGLSA PAPMSSAPGE AVLRSPGGCP EESKVRAAST GRVTPLSSLF SLPTFSLLNW
ISSWSLVSRL GSVLQFSRTE QLADGQAGRG LPVQPHSGRS GLQGPDHRLL IGASSRRSQ*

mutated AA sequence

MEREPAGTEE PGPPGRRRRR EGRTRTVRSN LLPPPGAEDP AAGAAKGERR RRRGCAQHLA
DNRLKTTKYT LLSFLPKNLF EQFHRPANVY FVFIALLNFV PAVNAFQPGL ALAPVLFILA
ITAFRDLWED YSRHRSDHKI NHLGCLVFSR EEKKYVNRFW KEIHVGDFVR LRCNEIFPAD
ILLLSSSDPD GLCHIETANL DGETNLKRRQ VVRGFSELVS EFNPLTFTSV IECEKPNNDL
SRFRGCIIHD NGKKAGLYKE NLLLRGCTLR NTDAVVGIVI YAGHETKALL NNSGPRYKRS
KLERQMNCDV LWCVLLLVCM SLFSAVGHGL WIWRYQEKKS LFYVPKSDGS SLSPVTAAVY
SFLTMIIVLQ VLIPISLYVS IEIVKACQVY FINQDMQLYD EETDSQLQCR ALNITEDLGQ
IQYIFSDKTG TLTENKMVFR RCTVSGVEYS HDANAQRLAR YQEADSEEEE VVPRGGSVSQ
RGSIGSHQSV RVVHRTQSTK SHRRTGSRAE AKRASMLSKH TAFSSPMEKD ITPDPKLLEK
VSECDKSLAV ARHQEHLLAH LSPELSDVFD FFIALTICNT VVVTSPDQPR TKVRVRFELK
SPVKTIEDFL RRFTPSCLTS GCSSIGSLAA NKSSHKLGSS FPSTPSSDGM LLRLEERLGQ
PTSAIASNGY SSQADNWASE LAQEQESERE LRYEAESPDE AALVYAARAY NCVLVERLHD
QVSVELPHLG RLTFELLHTL GFDSVRKRMS VVIRHPLTDE INVYTKGADS VVMDLLQPCS
SVDARGRHQK KIRSKTQNYL NVYAAEGLRT LCIAKRVLSK EEYACWLQSH LEAESSLENS
EELLFQSAIR LETNLHLLGA TGIEDRLQDG VPETISKLRQ AGLQIWVLTG DKQETAVNIA
YACKLLDHDE EVITLNATSQ EACAALLDQC LCYVQSRGLQ RAPEKTKGKV SMRFSSLCPP
STSTASGRRP SLVIDGRSLA YALEKNLEDK FLFLAKQCRS VLCCRSTPLQ KSMVVKLVRS
KLKAMTLAIG DGANDVSMIQ VADVGVGISG QEGMQAVMAS DFAVPKFRYL ERLLILHGHW
CYSRLANMVL YFFYKNTMFV GLLFWFQFFC GFSASTMIDQ WYLIFFNLLF SSLPPLVTGV
LDRDVPANVL LTNPQLYKSG QNMEEYRPRT FWFNMADATF QSLVCFSIPY LAYYDSNVDL
FTWGTPIVTI ALLTFLLHLG IETKTWTWLN WITCGFSVLL FFTVALIYNA SCATCYPPSN
PYWTMQALLG DPVFYLTCLM TPVAALLPRL FFRSLQGRVF PTQLQLARQL TRKSPRRCSA
PKETFAQGRL PKDSGTEHSS GRTVKTSVPL SQPSWHTQQP VCSLEASGEP STVDMSMPVR
EHTLLEGLSA PAPMSSAPGE AVLRSPGGCP EESKVRAAST GRVTPLSSLF SLPTFSLLNW
ISSWSLVSRL GSVLQFSRTE QLADGQAGRG LPVQPHSGRS GLQGPDHRLL IGASSRRSQ*

speed

0.97 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
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MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

Problems