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: ENST00000280481
MT speed 0.72 s - this script 2.808359 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FREM2	disease_causing	0.999999999913392	simple_aae		affected		E1972K	single base exchange	rs121434356		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999913392 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM051481)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:39358840G>AN/A show variant in all transcripts IGV

HGNC symbol

FREM2

Ensembl transcript ID

ENST00000280481

Genbank transcript ID

NM_207361

UniProt peptide

Q5SZK8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.5914G>A
cDNA.6130G>A
g.97575G>A

AA changes

E1972K Score: 56 explain score(s)

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

1972

frameshift

known variant

Reference ID: rs121434356

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

known disease mutation at this position, please check HGMD for details (HGMD ID CM051481)

known disease mutation at this position, please check HGMD for details (HGMD ID CM051481)
known disease mutation at this position, please check HGMD for details (HGMD ID CM051481)

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.225	0.952
	6.317	1
(flanking)	5.216	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	97576	wt: 0.7924 / mu: 0.7948 (marginal change - not scored)	wt: AATTGATGACTCTTTGTACGAGGAGGAGGAAACCTTCCATG mu: AATTGATGACTCTTTGTACAAGGAGGAGGAAACCTTCCATG	acga\|GGAG
Acc increased	97572	wt: 0.29 / mu: 0.40	wt: TCATAATTGATGACTCTTTGTACGAGGAGGAGGAAACCTTC mu: TCATAATTGATGACTCTTTGTACAAGGAGGAGGAAACCTTC	ttgt\|ACGA
Donor increased	97571	wt: 0.30 / mu: 0.73	wt: TCTTTGTACGAGGAG mu: TCTTTGTACAAGGAG	TTTG\|tacg
Donor marginally increased	97577	wt: 0.9852 / mu: 0.9943 (marginal change - not scored)	wt: TACGAGGAGGAGGAA mu: TACAAGGAGGAGGAA	CGAG\|gagg
Donor gained	97575	0.67	mu: TGTACAAGGAGGAGG	TACA\|agga

distance from splice site

106

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1972

mutated

all conserved

1972

Ptroglodytes

all identical

ENSPTRG00000005800

1972

Mmulatta

all identical

ENSMMUG00000002702

1973

Fcatus

all identical

ENSFCAG00000007720

1747

Mmusculus

all identical

ENSMUSG00000037016

1961

Ggallus

all identical

ENSGALG00000017041

1982

Trubripes

all identical

ENSTRUG00000008677

1873

Drerio

all identical

ENSDARG00000074369

1920

Dmelanogaster

no homologue

Celegans

no alignment

C48E7.6

n/a

Xtropicalis

all identical

ENSXETG00000015989

1904

protein features

start (aa)	end (aa)	feature	details
47	3113	TOPO_DOM	Extracellular (Potential).	lost
1871	1982	DOMAIN	Calx-beta 2.	lost
1997	2103	DOMAIN	Calx-beta 3.	might get lost (downstream of altered splice site)
2030	2030	CONFLICT	V -> A (in Ref. 2; CAD98088).	might get lost (downstream of altered splice site)
2112	2112	CONFLICT	E -> K (in Ref. 3; BAC87040).	might get lost (downstream of altered splice site)
2116	2116	CONFLICT	A -> T (in Ref. 3; BAC87040).	might get lost (downstream of altered splice site)
2118	2220	DOMAIN	Calx-beta 4.	might get lost (downstream of altered splice site)
2238	2342	DOMAIN	Calx-beta 5.	might get lost (downstream of altered splice site)
2359	2359	CONFLICT	Y -> H (in Ref. 2; CAD98088).	might get lost (downstream of altered splice site)
2508	2508	CONFLICT	L -> P (in Ref. 3; BAC87040).	might get lost (downstream of altered splice site)
2638	2638	CONFLICT	E -> K (in Ref. 3; BAC87040).	might get lost (downstream of altered splice site)
2682	2682	CONFLICT	F -> I (in Ref. 2; CAD98088).	might get lost (downstream of altered splice site)
2777	2777	CONFLICT	T -> S (in Ref. 2; CAI46253).	might get lost (downstream of altered splice site)
2786	2786	CONFLICT	E -> G (in Ref. 2; CAD98036).	might get lost (downstream of altered splice site)
2968	2968	CONFLICT	V -> I (in Ref. 2; CAD98088/CAE45813).	might get lost (downstream of altered splice site)
3081	3081	CONFLICT	D -> G (in Ref. 2; CAD98088).	might get lost (downstream of altered splice site)
3114	3134	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
3135	3169	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

9510 / 9510

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

3170 / 3170

position of stopcodon in wt / mu cDNA

9726 / 9726

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

217 / 217

chromosome

strand

last intron/exon boundary

9223

theoretical NMD boundary in CDS

8956

length of CDS

9510

coding sequence (CDS) position

5914

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

6130

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

97575

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

39358840

original gDNA sequence snippet

TAATTGATGACTCTTTGTACGAGGAGGAGGAAACCTTCCAT

altered gDNA sequence snippet

TAATTGATGACTCTTTGTACAAGGAGGAGGAAACCTTCCAT

original cDNA sequence snippet

TAATTGATGACTCTTTGTACGAGGAGGAGGAAACCTTCCAT

altered cDNA sequence snippet

TAATTGATGACTCTTTGTACAAGGAGGAGGAAACCTTCCAT

wildtype AA sequence

MHSAGTPGLS SRRTGNSTSF QPGPPPPPRL LLLLLLLLSL VSRVPAQPAA FGRALLSPGL
AGAAGVPAEE AIVLANRGLR VPFGREVWLD PLHDLVLQVQ PGDRCAVSVL DNDALAQRPG
RLSPKRFPCD FGPGEVRYSH LGARSPSRDR VRLQLRYDAP GGAVVLPLVL EVEVVFTQLE
VVTRNLPLVV EELLGTSNAL DARSLEFAFQ PETEECRVGI LSGLGALPRY GELLHYPQVP
GGAREGGAPE TLLMDCKAFQ ELGVRYRHTA ASRSPNRDWI PMVVELRSRG APVGSPALKR
EHFQVLVRIR GGAENTAPKP SFVAMMMMEV DQFVLTALTP DMLAAEDAES PSDLLIFNLT
SPFQPGQGYL VSTDDRSLPL SSFTQRDLRL LKIAYQPPSE DSDQERLFEL ELEVVDLEGA
ASDPFAFMVV VKPMNTMAPV VTRNTGLILY EGQSRPLTGP AGSGPQNLVI SDEDDLEAVR
LEVVAGLRHG HLVILGASSG SSAPKSFTVA ELAAGQVVYQ HDDRDGSLSD NLVLRMVDGG
GRHQVQFLFP ITLVPVDDQP PVLNANTGLT LAEGETVPIL PLSLSATDMD SDDSLLLFVL
ESPFLTTGHL LLRQTHPPHE KQELLRGLWR KEGAFYERTV TEWQQQDITE GRLFYRHSGP
HSPGPVTDQF TFRVQDNHDP PNQSGLQRFV IRIHPVDRLP PELGSGCPLR MVVQESQLTP
LRKKWLRYTD LDTDDRELRY TVTQSPTDTD ENHLPAPLGT LVLTDNPSVV VTHFTQAQIN
HHKIAYRPPG QELGVATRVA QFQFQVEDRA GNVAPGTFTL YLHPVDNQPP EILNTGFTIQ
EKGHHILSET ELHVNDVDTD VAHISFTLTQ APKHGHMRVS GQILHVGGLF HLEDIKQGRV
SYAHNGDKSL TDSCSLEVSD RHHVVPITLR VNVRPVDDEV PILSHPTGTL ESYLDVLENG
ATEITANVIK GTNEETDDLM LTFLLEDPPL YGEILVNGIP AEQFTQRDIL EGSVVYTHTS
GEIGLLPKAD SFNLSLSDMS QEWRIGGNTI QGVTIWVTIL PVDSQAPEIF VGEQLIVMEG
DKSVITSVHI SAEDVDSLND DILCTIVIQP TSGYVENISP APGSEKSRAG IAISAFNLKD
LRQGHINYVQ SVHKGVEPVE DRFVFRCSDG INFSERQFFP IVIIPTNDEQ PEMFMREFMV
MEGMSLVIDT PILNAADADV PLDDLTFTIT QFPTHGHIMN QLINGTVLVE SFTLDQIIES
SSIIYEHDDS ETQEDSFVIK LTDGKHSVEK TVLIIVIPVD DETPRMTINN GLEIEIGDTK
IINNKILMAT DLDSEDKSLV YIIRYGPGHG LLQRRKPTGA FENITLGMNF TQDEVDRNLI
QYVHLGQEGI RDLIKFDVTD GINPLIDRYF YVSIGSIDIV FPDVISKGVS LKEGGKVTLT
TDLLSTSDLN SPDENLVFTI TRAPMRGHLE CTDQPGVSIT SFTQLQLAGN KIYYIHTADD
EVKMDSFEFQ VTDGRNPVFR TFRISISDVD NKKPVVTIHK LVVSESENKL ITPFELTVED
RDTPDKLLKF TITQVPIHGH LLFNNTRPVM VFTKQDLNEN LISYKHDGTE SSEDSFSFTV
TDGTHTDFYV FPDTVFETRR PQVMKIQVLA VDNSVPQIAV NKGASTLRTL ATGHLGFMIT
SKILKVEDRD SLHISLRFIV TEAPQHGYLL NLDKGNHSIT QFTQADIDDM KICYVLREGA
NATSDMFYFA VEDGGGNKLT YQNFRLNWAW ISFEKEYYLV NEDSKFLDVV LKRRGYLGET
SFISIGTRDR TAEKDKDFKG KAQKQVQFNP GQTRATWRVR ILSDGEHEQS ETFQVVLSEP
VLAALEFPTV ATVEIVDPGD EPTVFIPQSK YSVEEDVGEL FIPIRRSGDV SQELMVVCYT
QQGTATGTVP TSVLSYSDYI SRPEDHTSVV RFDKDEREKL CRIVIIDDSL YEEEETFHVL
LSMPMGGRIG SEFPGAQVTI VPDKDDEPIF YFGDVEYSVD ESAGYVEVQV WRTGTDLSKS
SSVTVRSRKT DPPSADAGTD YVGISRNLDF APGVNMQPVR VVILDDLGQP ALEGIEKFEL
VLRMPMNAAL GEPSKATVSI NDSVSDLPKM QFKERIYTGS ESDGQIVTMI HRTGDVQYRS
SVRCYTRQGS AQVMMDFEER PNTDTSIITF LPGETEKPCI LELMDDVLYE EVEELRLVLG
TPQSNSPFGA AVGEQNETLI RIRDDADKTV IKFGETKFSV TEPKEPGESV VIRIPVIRQG
DTSKVSIVRV HTKDGSATSG EDYHPVSEEI EFKEGETQHV VEIEVTFDGV REMREAFTVH
LKPDENMIAE MQLTKAIVYI EEMSSMADVT FPSVPQIVSL LMYDDTSKAK ESAEPMSGYP
VICITACNPK YSDYDKTGSI CASENINDTL TRYRWLISAP AGPDGVTSPM REVDFDTFFT
SSKMVTLDSI YFQPGSRVQC AARAVNTNGD EGLELMSPIV TISREEGLCQ PRVPGVVGAE
PFSAKLRYTG PEDADYTNLI KLTVTMPHID GMLPVISTRE LSNFELTLSP DGTRVGNHKC
SNLLDYTEVK THYGFLTDAT KNPEIIGETY PYQYSLSIRG STTLRFYRNL NLEACLWEFV
SYYDMSELLA DCGGTIGTDG QVLNLVQSYV TLRVPLYVSY VFHSPVGVGG WQHFDLKSEL
RLTFVYDTAI LWNDGIGSPP EAELQGSLYP TSMRIGDEGR LAVHFKTEAQ FHGLFVLSHP
ASFTSSVIMS ADHPGLTFSL RLIRSEPTYN QPVQQWSFVS DFAVRDYSGT YTVKLVPCTA
PSHQEYRLPV TCNPREPVTF DLDIRFQQVS DPVAAEFSLN TQMYLLSKKS LWLSDGSMGF
GQESDVAFAE GDIIYGRVMV DPVQNLGDSF YCSIEKVFLC TGADGYVPKY SPMNAEYGCL
ADSPSLLYRF KIVDKAQPET QATSFGNVLF NAKLAVDDPE AILLVNQPGS DGFKVDSTPL
FQVALGREWY IHTIYTVRSK DNANRGIGKR SVEYHSLVSQ GKPQSTTKSR KKREIRSTPS
LAWEIGAENS RGTNIQHIAL DRTKRQIPHG RAPPDGILPW ELNSPSSAVS LVTVVGGTTV
GLLTICLTVI AVLMCRGKES FRGKDAPKGS SSSEPMVPPQ SHHNDSSEV*

mutated AA sequence

MHSAGTPGLS SRRTGNSTSF QPGPPPPPRL LLLLLLLLSL VSRVPAQPAA FGRALLSPGL
AGAAGVPAEE AIVLANRGLR VPFGREVWLD PLHDLVLQVQ PGDRCAVSVL DNDALAQRPG
RLSPKRFPCD FGPGEVRYSH LGARSPSRDR VRLQLRYDAP GGAVVLPLVL EVEVVFTQLE
VVTRNLPLVV EELLGTSNAL DARSLEFAFQ PETEECRVGI LSGLGALPRY GELLHYPQVP
GGAREGGAPE TLLMDCKAFQ ELGVRYRHTA ASRSPNRDWI PMVVELRSRG APVGSPALKR
EHFQVLVRIR GGAENTAPKP SFVAMMMMEV DQFVLTALTP DMLAAEDAES PSDLLIFNLT
SPFQPGQGYL VSTDDRSLPL SSFTQRDLRL LKIAYQPPSE DSDQERLFEL ELEVVDLEGA
ASDPFAFMVV VKPMNTMAPV VTRNTGLILY EGQSRPLTGP AGSGPQNLVI SDEDDLEAVR
LEVVAGLRHG HLVILGASSG SSAPKSFTVA ELAAGQVVYQ HDDRDGSLSD NLVLRMVDGG
GRHQVQFLFP ITLVPVDDQP PVLNANTGLT LAEGETVPIL PLSLSATDMD SDDSLLLFVL
ESPFLTTGHL LLRQTHPPHE KQELLRGLWR KEGAFYERTV TEWQQQDITE GRLFYRHSGP
HSPGPVTDQF TFRVQDNHDP PNQSGLQRFV IRIHPVDRLP PELGSGCPLR MVVQESQLTP
LRKKWLRYTD LDTDDRELRY TVTQSPTDTD ENHLPAPLGT LVLTDNPSVV VTHFTQAQIN
HHKIAYRPPG QELGVATRVA QFQFQVEDRA GNVAPGTFTL YLHPVDNQPP EILNTGFTIQ
EKGHHILSET ELHVNDVDTD VAHISFTLTQ APKHGHMRVS GQILHVGGLF HLEDIKQGRV
SYAHNGDKSL TDSCSLEVSD RHHVVPITLR VNVRPVDDEV PILSHPTGTL ESYLDVLENG
ATEITANVIK GTNEETDDLM LTFLLEDPPL YGEILVNGIP AEQFTQRDIL EGSVVYTHTS
GEIGLLPKAD SFNLSLSDMS QEWRIGGNTI QGVTIWVTIL PVDSQAPEIF VGEQLIVMEG
DKSVITSVHI SAEDVDSLND DILCTIVIQP TSGYVENISP APGSEKSRAG IAISAFNLKD
LRQGHINYVQ SVHKGVEPVE DRFVFRCSDG INFSERQFFP IVIIPTNDEQ PEMFMREFMV
MEGMSLVIDT PILNAADADV PLDDLTFTIT QFPTHGHIMN QLINGTVLVE SFTLDQIIES
SSIIYEHDDS ETQEDSFVIK LTDGKHSVEK TVLIIVIPVD DETPRMTINN GLEIEIGDTK
IINNKILMAT DLDSEDKSLV YIIRYGPGHG LLQRRKPTGA FENITLGMNF TQDEVDRNLI
QYVHLGQEGI RDLIKFDVTD GINPLIDRYF YVSIGSIDIV FPDVISKGVS LKEGGKVTLT
TDLLSTSDLN SPDENLVFTI TRAPMRGHLE CTDQPGVSIT SFTQLQLAGN KIYYIHTADD
EVKMDSFEFQ VTDGRNPVFR TFRISISDVD NKKPVVTIHK LVVSESENKL ITPFELTVED
RDTPDKLLKF TITQVPIHGH LLFNNTRPVM VFTKQDLNEN LISYKHDGTE SSEDSFSFTV
TDGTHTDFYV FPDTVFETRR PQVMKIQVLA VDNSVPQIAV NKGASTLRTL ATGHLGFMIT
SKILKVEDRD SLHISLRFIV TEAPQHGYLL NLDKGNHSIT QFTQADIDDM KICYVLREGA
NATSDMFYFA VEDGGGNKLT YQNFRLNWAW ISFEKEYYLV NEDSKFLDVV LKRRGYLGET
SFISIGTRDR TAEKDKDFKG KAQKQVQFNP GQTRATWRVR ILSDGEHEQS ETFQVVLSEP
VLAALEFPTV ATVEIVDPGD EPTVFIPQSK YSVEEDVGEL FIPIRRSGDV SQELMVVCYT
QQGTATGTVP TSVLSYSDYI SRPEDHTSVV RFDKDEREKL CRIVIIDDSL YKEEETFHVL
LSMPMGGRIG SEFPGAQVTI VPDKDDEPIF YFGDVEYSVD ESAGYVEVQV WRTGTDLSKS
SSVTVRSRKT DPPSADAGTD YVGISRNLDF APGVNMQPVR VVILDDLGQP ALEGIEKFEL
VLRMPMNAAL GEPSKATVSI NDSVSDLPKM QFKERIYTGS ESDGQIVTMI HRTGDVQYRS
SVRCYTRQGS AQVMMDFEER PNTDTSIITF LPGETEKPCI LELMDDVLYE EVEELRLVLG
TPQSNSPFGA AVGEQNETLI RIRDDADKTV IKFGETKFSV TEPKEPGESV VIRIPVIRQG
DTSKVSIVRV HTKDGSATSG EDYHPVSEEI EFKEGETQHV VEIEVTFDGV REMREAFTVH
LKPDENMIAE MQLTKAIVYI EEMSSMADVT FPSVPQIVSL LMYDDTSKAK ESAEPMSGYP
VICITACNPK YSDYDKTGSI CASENINDTL TRYRWLISAP AGPDGVTSPM REVDFDTFFT
SSKMVTLDSI YFQPGSRVQC AARAVNTNGD EGLELMSPIV TISREEGLCQ PRVPGVVGAE
PFSAKLRYTG PEDADYTNLI KLTVTMPHID GMLPVISTRE LSNFELTLSP DGTRVGNHKC
SNLLDYTEVK THYGFLTDAT KNPEIIGETY PYQYSLSIRG STTLRFYRNL NLEACLWEFV
SYYDMSELLA DCGGTIGTDG QVLNLVQSYV TLRVPLYVSY VFHSPVGVGG WQHFDLKSEL
RLTFVYDTAI LWNDGIGSPP EAELQGSLYP TSMRIGDEGR LAVHFKTEAQ FHGLFVLSHP
ASFTSSVIMS ADHPGLTFSL RLIRSEPTYN QPVQQWSFVS DFAVRDYSGT YTVKLVPCTA
PSHQEYRLPV TCNPREPVTF DLDIRFQQVS DPVAAEFSLN TQMYLLSKKS LWLSDGSMGF
GQESDVAFAE GDIIYGRVMV DPVQNLGDSF YCSIEKVFLC TGADGYVPKY SPMNAEYGCL
ADSPSLLYRF KIVDKAQPET QATSFGNVLF NAKLAVDDPE AILLVNQPGS DGFKVDSTPL
FQVALGREWY IHTIYTVRSK DNANRGIGKR SVEYHSLVSQ GKPQSTTKSR KKREIRSTPS
LAWEIGAENS RGTNIQHIAL DRTKRQIPHG RAPPDGILPW ELNSPSSAVS LVTVVGGTTV
GLLTICLTVI AVLMCRGKES FRGKDAPKGS SSSEPMVPPQ SHHNDSSEV*

speed

0.72 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

disease causing

Problems