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: ENST00000319555
MT speed 0 s - this script 2.820963 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ZFPM1	polymorphism_automatic	7.97395482976526e-12	simple_aae		affected		R22G	single base exchange	rs3751673		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999992026 (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)

chr16:88552370A>GN/A show variant in all transcripts IGV

HGNC symbol

ZFPM1

Ensembl transcript ID

ENST00000319555

Genbank transcript ID

NM_153813

UniProt peptide

Q8IX07

alteration type

single base exchange

alteration region

CDS

DNA changes

c.64A>G
cDNA.386A>G
g.32646A>G

AA changes

R22G Score: 125 explain score(s)

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

frameshift

known variant

Reference ID: rs3751673

database	homozygous (G/G)	heterozygous	allele carriers
1000G	753	1167	1920
ExAC	12849	7069	19918

regulatory features

H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.097	0.124
	-0.439	0.075
(flanking)	0.269	0.157

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	32645	wt: 0.24 / mu: 0.96	wt: GAGGCCAGAGAGGAG mu: GAGGCCGGAGAGGAG	GGCC\|agag
Donor gained	32637	0.31	mu: GAGACATGGAGGCCG	GACA\|tgga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000049577

Ggallus

no alignment

ENSGALG00000006099

n/a

Trubripes

no alignment

ENSTRUG00000001306

n/a

Drerio

not conserved

ENSDARG00000041572

Dmelanogaster

no alignment

FBgn0003963

n/a

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000023988

protein features

start (aa)	end (aa)	feature	details
22	22	CONFLICT	R -> G (in Ref. 1; AAN45858).	lost
241	264	ZN_FING	C2HC-type 1.	might get lost (downstream of altered splice site)
290	314	ZN_FING	C2H2-type 1.	might get lost (downstream of altered splice site)
320	342	ZN_FING	C2H2-type 2.	might get lost (downstream of altered splice site)
330	341	REGION	Interaction with TACC3 (By similarity).	might get lost (downstream of altered splice site)
348	371	ZN_FING	C2H2-type 3.	might get lost (downstream of altered splice site)
444	447	CONFLICT	EPLA -> AP (in Ref. 1; AAN45858).	might get lost (downstream of altered splice site)
491	491	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
494	494	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
577	699	ZN_FING	C2HC-type 2.	might get lost (downstream of altered splice site)
638	638	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
653	653	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
666	666	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
668	668	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
683	705	ZN_FING	C2HC-type 3.	might get lost (downstream of altered splice site)
698	698	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
699	699	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
786	786	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
794	800	REGION	Interaction with CTBP2 (By similarity).	might get lost (downstream of altered splice site)
817	839	ZN_FING	C2HC-type 4.	might get lost (downstream of altered splice site)
854	877	ZN_FING	C2H2-type 4.	might get lost (downstream of altered splice site)
901	901	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
909	909	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
935	935	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
974	1000	ZN_FING	C2HC-type 5.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3021 / 3021

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

1007 / 1007

position of stopcodon in wt / mu cDNA

3343 / 3343

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

323 / 323

chromosome

strand

last intron/exon boundary

1512

theoretical NMD boundary in CDS

1139

length of CDS

3021

coding sequence (CDS) position

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

386

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

32646

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

88552370

original gDNA sequence snippet

CCCTCGGAGACATGGAGGCCAGAGAGGAGGTGCAGTTGGTG

altered gDNA sequence snippet

CCCTCGGAGACATGGAGGCCGGAGAGGAGGTGCAGTTGGTG

original cDNA sequence snippet

CCCTCGGAGACATGGAGGCCAGAGAGGAGGTGCAGTTGGTG

altered cDNA sequence snippet

CCCTCGGAGACATGGAGGCCGGAGAGGAGGTGCAGTTGGTG

wildtype AA sequence

MSRRKQSNPR QIKRSLGDME AREEVQLVGA SHMEQKATAP EAPSPPSADV NSPPPLPPPT
SPGGPKELEG QEPEPRPTEE EPGSPWSGPD ELEPVVQDGQ RRIRARLSLA TGLSWGPFHG
SVQTRASSPR QAEPSPALTL LLVDEACWLR TLPQALTEAE ANTEIHRKDD ALWCRVTKPV
PAGGLLSVLL TAEPHSTPGH PVKKEPAEPT CPAPAHDLQL LPQQAGMASI LATAVINKDV
FPCKDCGIWY RSERNLQAHL LYYCASRQGT GSPAAAATDE KPKETYPNER VCPFPQCRKS
CPSASSLEIH MRSHSGERPF VCLICLSAFT TKANCERHLK VHTDTLSGVC HSCGFISTTR
DILYSHLVTN HMVCQPGSKG EIYSPGAGHP ATKLPPDSLG SFQQQHTALQ GPLASADLGL
APTPSPGLDR KALAEATNGE ARAEPLAQNG GSSEPPAAPR SIKVEAVEEP EAAPILGPGE
PGPQAPSRTP SPRSPAPARV KAELSSPTPG SSPVPGELGL AGALFLPQYV FGPDAAPPAS
EILAKMSELV HSRLQQGAGA GAGGAQTGLF PGAPKGATCF ECEITFSNVN NYYVHKRLYC
SGRRAPEDAP AARRPKAPPG PARAPPGQPA EPDAPRSSPG PGAREEGAGG AATPEDGAGG
RGSEGSQSPG SSVDDAEDDP SRTLCEACNI RFSRHETYTV HKRYYCASRH DPPPRRPAAP
PGPPGPAAPP APSPAAPVRT RRRRKLYELH AAGAPPPPPP GHAPAPESPR PGSGSGSGPG
LAPARSPGPA ADGPIDLSKK PRRPLPGAPA PALADYHECT ACRVSFHSLE AYLAHKKYSC
PAAPPPGALG LPAAACPYCP PNGPVRGDLL EHFRLAHGLL LGAPLAGPGV EARTPADRGP
SPAPAPAASP QPGSRGPRDG LGPEPQEPPP GPPPSPAAAP EAVPPPPAPP SYSDKGVQTP
SKGTPAPLPN GNHRYCRLCN IKFSSLSTFI AHKKYYCSSH AAEHVK*

mutated AA sequence

MSRRKQSNPR QIKRSLGDME AGEEVQLVGA SHMEQKATAP EAPSPPSADV NSPPPLPPPT
SPGGPKELEG QEPEPRPTEE EPGSPWSGPD ELEPVVQDGQ RRIRARLSLA TGLSWGPFHG
SVQTRASSPR QAEPSPALTL LLVDEACWLR TLPQALTEAE ANTEIHRKDD ALWCRVTKPV
PAGGLLSVLL TAEPHSTPGH PVKKEPAEPT CPAPAHDLQL LPQQAGMASI LATAVINKDV
FPCKDCGIWY RSERNLQAHL LYYCASRQGT GSPAAAATDE KPKETYPNER VCPFPQCRKS
CPSASSLEIH MRSHSGERPF VCLICLSAFT TKANCERHLK VHTDTLSGVC HSCGFISTTR
DILYSHLVTN HMVCQPGSKG EIYSPGAGHP ATKLPPDSLG SFQQQHTALQ GPLASADLGL
APTPSPGLDR KALAEATNGE ARAEPLAQNG GSSEPPAAPR SIKVEAVEEP EAAPILGPGE
PGPQAPSRTP SPRSPAPARV KAELSSPTPG SSPVPGELGL AGALFLPQYV FGPDAAPPAS
EILAKMSELV HSRLQQGAGA GAGGAQTGLF PGAPKGATCF ECEITFSNVN NYYVHKRLYC
SGRRAPEDAP AARRPKAPPG PARAPPGQPA EPDAPRSSPG PGAREEGAGG AATPEDGAGG
RGSEGSQSPG SSVDDAEDDP SRTLCEACNI RFSRHETYTV HKRYYCASRH DPPPRRPAAP
PGPPGPAAPP APSPAAPVRT RRRRKLYELH AAGAPPPPPP GHAPAPESPR PGSGSGSGPG
LAPARSPGPA ADGPIDLSKK PRRPLPGAPA PALADYHECT ACRVSFHSLE AYLAHKKYSC
PAAPPPGALG LPAAACPYCP PNGPVRGDLL EHFRLAHGLL LGAPLAGPGV EARTPADRGP
SPAPAPAASP QPGSRGPRDG LGPEPQEPPP GPPPSPAAAP EAVPPPPAPP SYSDKGVQTP
SKGTPAPLPN GNHRYCRLCN IKFSSLSTFI AHKKYYCSSH AAEHVK*

speed

0.76 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