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: ENST00000298532
MT speed 0 s - this script 2.324936 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SNAPC4	polymorphism_automatic	2.72152699398731e-06	simple_aae				H799Q	single base exchange	rs3812571		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999997278473006 (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 CM1010096)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:139275294G>CN/A show variant in all transcripts IGV

HGNC symbol

SNAPC4

Ensembl transcript ID

ENST00000298532

Genbank transcript ID

NM_003086

UniProt peptide

Q5SXM2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2397C>G
cDNA.2766C>G
g.17956C>G

AA changes

H799Q Score: 24 explain score(s)

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

799

frameshift

known variant

Reference ID: rs3812571

database	homozygous (C/C)	heterozygous	allele carriers
1000G	446	1142	1588
ExAC	11007	10753	21760

known disease mutation at this position, please check HGMD for details (HGMD ID CM1010096)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.563	0.997
	0.869	0.999
(flanking)	1.186	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	17947	wt: 0.5574 / mu: 0.5802 (marginal change - not scored)	wt: GTTGCCTCCTGTGTCCCGCAGCTGTTCCACATCGATACTGC mu: GTTGCCTCCTGTGTCCCGCAGCTGTTCCAGATCGATACTGC	gcag\|CTGT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

799

mutated

not conserved

799

Ptroglodytes

not conserved

ENSPTRG00000021554

758

Mmulatta

not conserved

ENSMMUG00000003086

799

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000036281

781

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no alignment

FBgn0037540

n/a

Celegans

no alignment

F32H2.1

n/a

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4410 / 4410

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

1470 / 1470

position of stopcodon in wt / mu cDNA

4779 / 4779

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

370 / 370

chromosome

strand

-1

last intron/exon boundary

4787

theoretical NMD boundary in CDS

4367

length of CDS

4410

coding sequence (CDS) position

2397

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

2766

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

17956

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

139275294

original gDNA sequence snippet

TGTGTCCCGCAGCTGTTCCACATCGATACTGCCGGCTGCTT

altered gDNA sequence snippet

TGTGTCCCGCAGCTGTTCCAGATCGATACTGCCGGCTGCTT

original cDNA sequence snippet

CTGTTTACCCAGCTGTTCCACATCGATACTGCCGGCTGCTT

altered cDNA sequence snippet

CTGTTTACCCAGCTGTTCCAGATCGATACTGCCGGCTGCTT

wildtype AA sequence

MDVDAEREKI TQEIKELERI LDPGSSGSHV EISESSLESD SEADSLPSED LDPADPPISE
EERWGEASND EDDPKDKTLP EDPETCLQLN MVYQEVIQEK LAEANLLLAQ NREQQEELMR
DLAGSKGTKV KDGKSLPPST YMGHFMKPYF KDKVTGVGPP ANEDTREKAA QGIKAFEELL
VTKWKNWEKA LLRKSVVSDR LQRLLQPKLL KLEYLHQKQS KVSSELERQA LEKQGREAEK
EIQDINQLPE EALLGNRLDS HDWEKISNIN FEGSRSAEEI RKFWQNSEHP SINKQEWSRE
EEERLQAIAA AHGHLEWQKI AEELGTSRSA FQCLQKFQQH NKALKRKEWT EEEDRMLTQL
VQEMRVGSHI PYRRIVYYME GRDSMQLIYR WTKSLDPGLK KGYWAPEEDA KLLQAVAKYG
EQDWFKIREE VPGRSDAQCR DRYLRRLHFS LKKGRWNLKE EEQLIELIEK YGVGHWAKIA
SELPHRSGSQ CLSKWKIMMG KKQGLRRRRR RARHSVRWSS TSSSGSSSGS SGGSSSSSSS
SSEEDEPEQA QAGEGDRALL SPQYMVPDMD LWVPARQSTS QPWRGGAGAW LGGPAASLSP
PKGSSASQGG SKEASTTAAA PGEETSPVQV PARAHGPVPR SAQASHSADT RPAGAEKQAL
EGGRRLLTVP VETVLRVLRA NTAARSCTQK EQLRQPPLPT SSPGVSSGDS VARSHVQWLR
HRATQSGQRR WRHALHRRLL NRRLLLAVTP WVGDVVVPCT QASQRPAVVQ TQADGLREQL
QQARLASTPV FTLFTQLFHI DTAGCLEVVR ERKALPPRLP QAGARDPPVH LLQASSSAQS
TPGHLFPNVP AQEASKSASH KGSRRLASSR VERTLPQASL LASTGPRPKP KTVSELLQEK
RLQEARAREA TRGPVVLPSQ LLVSSSVILQ PPLPHTPHGR PAPGPTVLNV PLSGPGAPAA
AKPGTSGSWQ EAGTSAKDKR LSTMQALPLA PVFSEAEGTA PAASQAPALG PGQISVSCPE
SGLGQSQAPA ASRKQGLPEA PPFLPAAPSP TPLPVQPLSL THIGGPHVAT SVPLPVTWVL
TAQGLLPVPV PAVVSLPRPA GTPGPAGLLA TLLPPLTETR AAQGPRAPAL SSSWQPPANM
NREPEPSCRT DTPAPPTHAL SQSPAEADGS VAFVPGEAQV AREIPEPRTS SHADPPEAEP
PWSGRLPAFG GVIPATEPRG TPGSPSGTQE PRGPLGLEKL PLRQPGPEKG ALDLEKPPLP
QPGPEKGALD LGLLSQEGEA ATQQWLGGQR GVRVPLLGSR LPYQPPALCS LRALSGLLLH
KKALEHKATS LVVGGEAERP AGALQASLGL VRGQLQDNPA YLLLRARFLA AFTLPALLAT
LAPQGVRTTL SVPSRVGSES EDEDLLSELE LADRDGQPGC TTATCPIQGA PDSGKCSASS
CLDTSNDPDD LDVLRTRHAR HTRKRRRLV*

mutated AA sequence

MDVDAEREKI TQEIKELERI LDPGSSGSHV EISESSLESD SEADSLPSED LDPADPPISE
EERWGEASND EDDPKDKTLP EDPETCLQLN MVYQEVIQEK LAEANLLLAQ NREQQEELMR
DLAGSKGTKV KDGKSLPPST YMGHFMKPYF KDKVTGVGPP ANEDTREKAA QGIKAFEELL
VTKWKNWEKA LLRKSVVSDR LQRLLQPKLL KLEYLHQKQS KVSSELERQA LEKQGREAEK
EIQDINQLPE EALLGNRLDS HDWEKISNIN FEGSRSAEEI RKFWQNSEHP SINKQEWSRE
EEERLQAIAA AHGHLEWQKI AEELGTSRSA FQCLQKFQQH NKALKRKEWT EEEDRMLTQL
VQEMRVGSHI PYRRIVYYME GRDSMQLIYR WTKSLDPGLK KGYWAPEEDA KLLQAVAKYG
EQDWFKIREE VPGRSDAQCR DRYLRRLHFS LKKGRWNLKE EEQLIELIEK YGVGHWAKIA
SELPHRSGSQ CLSKWKIMMG KKQGLRRRRR RARHSVRWSS TSSSGSSSGS SGGSSSSSSS
SSEEDEPEQA QAGEGDRALL SPQYMVPDMD LWVPARQSTS QPWRGGAGAW LGGPAASLSP
PKGSSASQGG SKEASTTAAA PGEETSPVQV PARAHGPVPR SAQASHSADT RPAGAEKQAL
EGGRRLLTVP VETVLRVLRA NTAARSCTQK EQLRQPPLPT SSPGVSSGDS VARSHVQWLR
HRATQSGQRR WRHALHRRLL NRRLLLAVTP WVGDVVVPCT QASQRPAVVQ TQADGLREQL
QQARLASTPV FTLFTQLFQI DTAGCLEVVR ERKALPPRLP QAGARDPPVH LLQASSSAQS
TPGHLFPNVP AQEASKSASH KGSRRLASSR VERTLPQASL LASTGPRPKP KTVSELLQEK
RLQEARAREA TRGPVVLPSQ LLVSSSVILQ PPLPHTPHGR PAPGPTVLNV PLSGPGAPAA
AKPGTSGSWQ EAGTSAKDKR LSTMQALPLA PVFSEAEGTA PAASQAPALG PGQISVSCPE
SGLGQSQAPA ASRKQGLPEA PPFLPAAPSP TPLPVQPLSL THIGGPHVAT SVPLPVTWVL
TAQGLLPVPV PAVVSLPRPA GTPGPAGLLA TLLPPLTETR AAQGPRAPAL SSSWQPPANM
NREPEPSCRT DTPAPPTHAL SQSPAEADGS VAFVPGEAQV AREIPEPRTS SHADPPEAEP
PWSGRLPAFG GVIPATEPRG TPGSPSGTQE PRGPLGLEKL PLRQPGPEKG ALDLEKPPLP
QPGPEKGALD LGLLSQEGEA ATQQWLGGQR GVRVPLLGSR LPYQPPALCS LRALSGLLLH
KKALEHKATS LVVGGEAERP AGALQASLGL VRGQLQDNPA YLLLRARFLA AFTLPALLAT
LAPQGVRTTL SVPSRVGSES EDEDLLSELE LADRDGQPGC TTATCPIQGA PDSGKCSASS
CLDTSNDPDD LDVLRTRHAR HTRKRRRLV*

speed

0.26 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
back to results table

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

Problems