MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000380880
Querying Taster for transcript #2: ENST00000380881
Querying Taster for transcript #3: ENST00000422223
MT speed 0 s - this script 4.055527 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FREM1	polymorphism_automatic	0.517139597198225	simple_aae		affected		V439L	single base exchange	rs2779500		show file
FREM1	polymorphism_automatic	0.517139597198225	simple_aae		affected		V440L	single base exchange	rs2779500		show file
FREM1	polymorphism_automatic	0.517139597198225	simple_aae		affected		V439L	single base exchange	rs2779500		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.482860402801775 (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)

chr9:14846036C>GN/A show variant in all transcripts IGV

HGNC symbol

FREM1

Ensembl transcript ID

ENST00000380880

Genbank transcript ID

N/A

UniProt peptide

Q5H8C1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1315G>C
cDNA.2099G>C
g.64958G>C

AA changes

V439L Score: 32 explain score(s)

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

439

frameshift

known variant

Reference ID: rs2779500

database	homozygous (G/G)	heterozygous	allele carriers
1000G	663	1182	1845
ExAC	17923	-3079	14844

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.41	1
	0.899	1
(flanking)	2.717	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
Donor increased	64963	wt: 0.54 / mu: 0.75	wt: GTTGTCGACAATGAC mu: CTTGTCGACAATGAC	TGTC\|gaca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

439

mutated

all conserved

439

Ptroglodytes

all identical

ENSPTRG00000020782

437

Mmulatta

all identical

ENSMMUG00000008128

437

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000059049

445

Ggallus

all identical

ENSGALG00000005426

386

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

all conserved

C48E7.6

165

FSHTD

Xtropicalis

all conserved

ENSXETG00000003300

444

protein features

start (aa)	end (aa)	feature	details
395	502	REPEAT	CSPG 2.	lost
503	621	REPEAT	CSPG 3.	might get lost (downstream of altered splice site)
560	560	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
622	622	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
622	758	REPEAT	CSPG 4.	might get lost (downstream of altered splice site)
759	869	REPEAT	CSPG 5.	might get lost (downstream of altered splice site)
870	1005	REPEAT	CSPG 6.	might get lost (downstream of altered splice site)
1006	1129	REPEAT	CSPG 7.	might get lost (downstream of altered splice site)
1014	1014	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1130	1256	REPEAT	CSPG 8.	might get lost (downstream of altered splice site)
1257	1375	REPEAT	CSPG 9.	might get lost (downstream of altered splice site)
1376	1487	REPEAT	CSPG 10.	might get lost (downstream of altered splice site)
1488	1608	REPEAT	CSPG 11.	might get lost (downstream of altered splice site)
1566	1566	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1609	1729	REPEAT	CSPG 12.	might get lost (downstream of altered splice site)
1731	1830	DOMAIN	Calx-beta.	might get lost (downstream of altered splice site)
1735	1735	CONFLICT	I -> N (in Ref. 5; AAH31064).	might get lost (downstream of altered splice site)
1861	1861	CONFLICT	S -> A (in Ref. 3; CAE46048).	might get lost (downstream of altered splice site)
1907	1909	MOTIF	Cell attachment site (Potential).	might get lost (downstream of altered splice site)
2060	2174	DOMAIN	C-type lectin.	might get lost (downstream of altered splice site)
2151	2151	DISULFID	By similarity.	might get lost (downstream of altered splice site)
2165	2165	DISULFID	By similarity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

6540 / 6540

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

2180 / 2180

position of stopcodon in wt / mu cDNA

7324 / 7324

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

785 / 785

chromosome

strand

-1

last intron/exon boundary

7125

theoretical NMD boundary in CDS

6290

length of CDS

6540

coding sequence (CDS) position

1315

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

2099

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

64958

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

14846036

original gDNA sequence snippet

TCACTTGGGAACAGTTTCAGGTTGTCGACAATGACGACATT

altered gDNA sequence snippet

TCACTTGGGAACAGTTTCAGCTTGTCGACAATGACGACATT

original cDNA sequence snippet

TCACTTGGGAACAGTTTCAGGTTGTCGACAATGACGACATT

altered cDNA sequence snippet

TCACTTGGGAACAGTTTCAGCTTGTCGACAATGACGACATT

wildtype AA sequence

MNSLSWGAAN AVLLLLLLAW ASPTFISINR GVRVMKGHSA FLSGDDLKFA IPKEKDACKV
EVVMNEPITQ RVGKLTPQVF DCHFLPNEVK YVHNGCPILD EDTVKLRLYR FTERDTFIET
FILWVYLLEP DCNIIHMSNN VLEVPEFNGL SQAIDKNLLR FDYDRMASLE CTVSLDTART
RLPAHGQMVL GEPRPEEPRG DQPHSFFPES QLRAKLKCPG GSCTPGLKKI GSLKVSCEEF
LLMGLRYQHL DPPSPNIDYI SIQLDLTDTR SKIVYKSESA WLPVYIRAGI PNQIPKAAFM
AVFILEVDQF ILTSLTTSVL DCEEDETPKP LLVFNITKAP LQGYVTHLLD HTRPISSFTW
KDLSDMQIAY QPPNSSHSER RHDEVELEVY DFFFERSAPM TVHISIRTAD TNAPRVSWNT
GLSLLEGQSR AITWEQFQVV DNDDIGAVRL VTVGGLQHGW LTLRGGKGFL FTVADLQAGV
VRYHHDDSDS TKDFVVFRIF DGHHSIRHKF PINVLPKDDS PPFLITNVVI ELEEGQTILI
QGSMLRASDV DASDDYIFFN ITKPPQAGEI MKKPGPGLIG YPVHGFLQRD LFNGIIYYRH
FGGEIFEDSF QFVLWDSHEP PNLSVPQVAT IHITPVDDQL PKEAPGVSRH LVVKETEVAY
ITKKQLHFID SESYDRELVY TITTPPFFSF SHRHLDAGKL FMVDSIPKVV KNPTALELRS
FTQHAVNYMK VAYMPPMQDI GPHCRDVQFT FSVSNQHGGT LHGICFNITI LPVDNQVPEA
FTNPLKVTEG GQSIISTEHI LISDADTKLD NIDLSLRELP LHGRVELNGF PLNSGGTFSW
GDLHTLKVRY QHDGTEVLQD DLLLEVTDGT NSAEFVLHVE VFPVNDEPPV LKADLMPVMN
CSEGGEVVIT SEYIFATDVD SDNLKLMFVI AREPQHGVVR RAGVTVDQFS QRDVISEAVT
YKHTGGEIGL MPCFDTITLV VSDGEAGPFV NGCCYNGPNP SVPLHASFPV YDLNITVYPV
DNQPPSIAIG PVFVVDEGCS TALTVNHLSA TDPDTAADDL EFVLVSPPQF GYLENILPSV
GFEKSNIGIS IDSFQWKDMN AFHINYVQSR HLRIEPTADQ FTVYVTDGKH HSLEIPFSII
INPTNDEAPD FVVQNITVCE GQMKELDSSI ISAVDLDIPQ DALLFSITQK PRHGLLIDRG
FSKDFSENKQ PANPHQKHAP VHSFSMELLK TGMRLTYMHD DSESLADDFT IQLSDGKHKI
LKTISVEVIP VNDEKPMLSK KAEIAMNMGE TRIISSAILS AIDEDSPREK IYYVFERLPQ
NGQLQLKIGR DWVPLSPGMK CTQEEVDLNL LRYTHTGAMD SQNQDSFTFY LWDGNNRSPA
LDCQITIKDM EKGDIVILTK PLVVSKGDRG FLTTTTLLAV DGTDKPEELL YVITSPPRYG
QIEYVHYPGV PITNFSQMDV VGQTVCYVHK SKVTVSSDRF RFIISNGLRT EHGVFEITLE
TVDRALPVVT RNKGLRLAQG AVGLLSPDLL QLTDPDTPAE NLTFLLVQLP QHGQLYLWGT
GLLQHNFTQQ DVDSKNVAYR HSGGDSQTDC FTFMATDGTN QGFIVNGRVW EEPVLFTIQV
DQLDKTAPRI TLLHSPSQVG LLKNGCYGIY ITSRVLKASD PDTEDDQIIF KILQGPKHGH
LENTTTGEFI HEKFSQKDLN SKTILYIINP SLEVNSDTVE FQIMDPTGNS ATPQILELKW
SHIEWSQTEY EVCENVGLLP LEIIRRGYSM DSAFVGIKVN QVSAAVGKDF TVIPSKLIQF
DPGMSTKMWN IAITYDGLEE DDEVFEVILN SPVNAVLGTK TKAAVKILDS KGGQCHPSYS
SNQSKHSTWE KGIWHLLPPG SSSSTTSGSF HLERRPLPSS MQLAVIRGDT LRGFDSTDLS
QRKLRTRGNG KTVRPSSVYR NGTDIIYNYH GIVSLKLEDD SFPTHKRKAK VSIISQPQKT
IKVAELPQAD KVESTTDSHF PRQDQLPSFP KNCTLELKGL FHFEEGIQKL YQCNGIAWKA
WSPQTKDVED KSCPAGWHQH SGYCHILITE QKGTWNAAAQ ACREQYLGNL VTVFSRQHMR
WLWDIGGRKS FWIGLNDQVH AGHWEWIGGE PVAFTNGRRG PSQRSKLGKS CVLVQRQGKW
QTKDCRRAKP HNYVCSRKL*

mutated AA sequence

MNSLSWGAAN AVLLLLLLAW ASPTFISINR GVRVMKGHSA FLSGDDLKFA IPKEKDACKV
EVVMNEPITQ RVGKLTPQVF DCHFLPNEVK YVHNGCPILD EDTVKLRLYR FTERDTFIET
FILWVYLLEP DCNIIHMSNN VLEVPEFNGL SQAIDKNLLR FDYDRMASLE CTVSLDTART
RLPAHGQMVL GEPRPEEPRG DQPHSFFPES QLRAKLKCPG GSCTPGLKKI GSLKVSCEEF
LLMGLRYQHL DPPSPNIDYI SIQLDLTDTR SKIVYKSESA WLPVYIRAGI PNQIPKAAFM
AVFILEVDQF ILTSLTTSVL DCEEDETPKP LLVFNITKAP LQGYVTHLLD HTRPISSFTW
KDLSDMQIAY QPPNSSHSER RHDEVELEVY DFFFERSAPM TVHISIRTAD TNAPRVSWNT
GLSLLEGQSR AITWEQFQLV DNDDIGAVRL VTVGGLQHGW LTLRGGKGFL FTVADLQAGV
VRYHHDDSDS TKDFVVFRIF DGHHSIRHKF PINVLPKDDS PPFLITNVVI ELEEGQTILI
QGSMLRASDV DASDDYIFFN ITKPPQAGEI MKKPGPGLIG YPVHGFLQRD LFNGIIYYRH
FGGEIFEDSF QFVLWDSHEP PNLSVPQVAT IHITPVDDQL PKEAPGVSRH LVVKETEVAY
ITKKQLHFID SESYDRELVY TITTPPFFSF SHRHLDAGKL FMVDSIPKVV KNPTALELRS
FTQHAVNYMK VAYMPPMQDI GPHCRDVQFT FSVSNQHGGT LHGICFNITI LPVDNQVPEA
FTNPLKVTEG GQSIISTEHI LISDADTKLD NIDLSLRELP LHGRVELNGF PLNSGGTFSW
GDLHTLKVRY QHDGTEVLQD DLLLEVTDGT NSAEFVLHVE VFPVNDEPPV LKADLMPVMN
CSEGGEVVIT SEYIFATDVD SDNLKLMFVI AREPQHGVVR RAGVTVDQFS QRDVISEAVT
YKHTGGEIGL MPCFDTITLV VSDGEAGPFV NGCCYNGPNP SVPLHASFPV YDLNITVYPV
DNQPPSIAIG PVFVVDEGCS TALTVNHLSA TDPDTAADDL EFVLVSPPQF GYLENILPSV
GFEKSNIGIS IDSFQWKDMN AFHINYVQSR HLRIEPTADQ FTVYVTDGKH HSLEIPFSII
INPTNDEAPD FVVQNITVCE GQMKELDSSI ISAVDLDIPQ DALLFSITQK PRHGLLIDRG
FSKDFSENKQ PANPHQKHAP VHSFSMELLK TGMRLTYMHD DSESLADDFT IQLSDGKHKI
LKTISVEVIP VNDEKPMLSK KAEIAMNMGE TRIISSAILS AIDEDSPREK IYYVFERLPQ
NGQLQLKIGR DWVPLSPGMK CTQEEVDLNL LRYTHTGAMD SQNQDSFTFY LWDGNNRSPA
LDCQITIKDM EKGDIVILTK PLVVSKGDRG FLTTTTLLAV DGTDKPEELL YVITSPPRYG
QIEYVHYPGV PITNFSQMDV VGQTVCYVHK SKVTVSSDRF RFIISNGLRT EHGVFEITLE
TVDRALPVVT RNKGLRLAQG AVGLLSPDLL QLTDPDTPAE NLTFLLVQLP QHGQLYLWGT
GLLQHNFTQQ DVDSKNVAYR HSGGDSQTDC FTFMATDGTN QGFIVNGRVW EEPVLFTIQV
DQLDKTAPRI TLLHSPSQVG LLKNGCYGIY ITSRVLKASD PDTEDDQIIF KILQGPKHGH
LENTTTGEFI HEKFSQKDLN SKTILYIINP SLEVNSDTVE FQIMDPTGNS ATPQILELKW
SHIEWSQTEY EVCENVGLLP LEIIRRGYSM DSAFVGIKVN QVSAAVGKDF TVIPSKLIQF
DPGMSTKMWN IAITYDGLEE DDEVFEVILN SPVNAVLGTK TKAAVKILDS KGGQCHPSYS
SNQSKHSTWE KGIWHLLPPG SSSSTTSGSF HLERRPLPSS MQLAVIRGDT LRGFDSTDLS
QRKLRTRGNG KTVRPSSVYR NGTDIIYNYH GIVSLKLEDD SFPTHKRKAK VSIISQPQKT
IKVAELPQAD KVESTTDSHF PRQDQLPSFP KNCTLELKGL FHFEEGIQKL YQCNGIAWKA
WSPQTKDVED KSCPAGWHQH SGYCHILITE QKGTWNAAAQ ACREQYLGNL VTVFSRQHMR
WLWDIGGRKS FWIGLNDQVH AGHWEWIGGE PVAFTNGRRG PSQRSKLGKS CVLVQRQGKW
QTKDCRRAKP HNYVCSRKL*

speed

0.53 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

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.482860402801775 (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)

chr9:14846036C>GN/A show variant in all transcripts IGV

HGNC symbol

FREM1

Ensembl transcript ID

ENST00000380881

Genbank transcript ID

N/A

UniProt peptide

Q5H8C1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1318G>C
cDNA.2134G>C
g.64958G>C

AA changes

V440L Score: 32 explain score(s)

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

440

frameshift

known variant

Reference ID: rs2779500

database	homozygous (G/G)	heterozygous	allele carriers
1000G	663	1182	1845
ExAC	17923	-3079	14844

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.41	1
	0.899	1
(flanking)	2.717	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
Donor increased	64963	wt: 0.54 / mu: 0.75	wt: GTTGTCGACAATGAC mu: CTTGTCGACAATGAC	TGTC\|gaca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

440

mutated

all conserved

440

Ptroglodytes

all identical

ENSPTRG00000020782

437

Mmulatta

all identical

ENSMMUG00000008128

437

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000059049

445

Ggallus

all identical

ENSGALG00000005426

386

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

all conserved

C48E7.6

165

FSHTD

Xtropicalis

all conserved

ENSXETG00000003300

444

protein features

start (aa)	end (aa)	feature	details
395	502	REPEAT	CSPG 2.	lost
503	621	REPEAT	CSPG 3.	might get lost (downstream of altered splice site)
560	560	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
622	622	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
622	758	REPEAT	CSPG 4.	might get lost (downstream of altered splice site)
759	869	REPEAT	CSPG 5.	might get lost (downstream of altered splice site)
870	1005	REPEAT	CSPG 6.	might get lost (downstream of altered splice site)
1006	1129	REPEAT	CSPG 7.	might get lost (downstream of altered splice site)
1014	1014	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1130	1256	REPEAT	CSPG 8.	might get lost (downstream of altered splice site)
1257	1375	REPEAT	CSPG 9.	might get lost (downstream of altered splice site)
1376	1487	REPEAT	CSPG 10.	might get lost (downstream of altered splice site)
1488	1608	REPEAT	CSPG 11.	might get lost (downstream of altered splice site)
1566	1566	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1609	1729	REPEAT	CSPG 12.	might get lost (downstream of altered splice site)
1731	1830	DOMAIN	Calx-beta.	might get lost (downstream of altered splice site)
1735	1735	CONFLICT	I -> N (in Ref. 5; AAH31064).	might get lost (downstream of altered splice site)
1861	1861	CONFLICT	S -> A (in Ref. 3; CAE46048).	might get lost (downstream of altered splice site)
1907	1909	MOTIF	Cell attachment site (Potential).	might get lost (downstream of altered splice site)
2060	2174	DOMAIN	C-type lectin.	might get lost (downstream of altered splice site)
2151	2151	DISULFID	By similarity.	might get lost (downstream of altered splice site)
2165	2165	DISULFID	By similarity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

6543 / 6543

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

2181 / 2181

position of stopcodon in wt / mu cDNA

7359 / 7359

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

817 / 817

chromosome

strand

-1

last intron/exon boundary

7160

theoretical NMD boundary in CDS

6293

length of CDS

6543

coding sequence (CDS) position

1318

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

2134

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

64958

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

14846036

original gDNA sequence snippet

TCACTTGGGAACAGTTTCAGGTTGTCGACAATGACGACATT

altered gDNA sequence snippet

TCACTTGGGAACAGTTTCAGCTTGTCGACAATGACGACATT

original cDNA sequence snippet

TCACTTGGGAACAGTTTCAGGTTGTCGACAATGACGACATT

altered cDNA sequence snippet

TCACTTGGGAACAGTTTCAGCTTGTCGACAATGACGACATT

wildtype AA sequence

MNSLSWGAAN AVLLLLLLAW ASPTFISINR GVRVMKGHSA FLSGDDLKFA IPKEKDACKV
EVVMNEPITQ RVGKLTPQVF DCHFLPNEVK YVHNGCPILD EDTVKLRLYR FTERDTFIET
FILWVYLLEP DCNIIHMSNN VLEVPEFNGL SQAIDKNLLR FDYDRMASLE CTVSLDTART
RLPAHGQMVL GEPRPEEPRG DQPHSFFPES QLRAKLKCPG GSCTPGLKKI GSLKVSCEEF
LLMGLRYQHL DPPSPNIDYI SIQLDLTDTR SKIVYKKSES AWLPVYIRAG IPNQIPKAAF
MAVFILEVDQ FILTSLTTSV LDCEEDETPK PLLVFNITKA PLQGYVTHLL DHTRPISSFT
WKDLSDMQIA YQPPNSSHSE RRHDEVELEV YDFFFERSAP MTVHISIRTA DTNAPRVSWN
TGLSLLEGQS RAITWEQFQV VDNDDIGAVR LVTVGGLQHG WLTLRGGKGF LFTVADLQAG
VVRYHHDDSD STKDFVVFRI FDGHHSIRHK FPINVLPKDD SPPFLITNVV IELEEGQTIL
IQGSMLRASD VDASDDYIFF NITKPPQAGE IMKKPGPGLI GYPVHGFLQR DLFNGIIYYR
HFGGEIFEDS FQFVLWDSHE PPNLSVPQVA TIHITPVDDQ LPKEAPGVSR HLVVKETEVA
YITKKQLHFI DSESYDRELV YTITTPPFFS FSHRHLDAGK LFMVDSIPKV VKNPTALELR
SFTQHAVNYM KVAYMPPMQD IGPHCRDVQF TFSVSNQHGG TLHGICFNIT ILPVDNQVPE
AFTNPLKVTE GGQSIISTEH ILISDADTKL DNIDLSLREL PLHGRVELNG FPLNSGGTFS
WGDLHTLKVR YQHDGTEVLQ DDLLLEVTDG TNSAEFVLHV EVFPVNDEPP VLKADLMPVM
NCSEGGEVVI TSEYIFATDV DSDNLKLMFV IAREPQHGVV RRAGVTVDQF SQRDVISEAV
TYKHTGGEIG LMPCFDTITL VVSDGEAGPF VNGCCYNGPN PSVPLHASFP VYDLNITVYP
VDNQPPSIAI GPVFVVDEGC STALTVNHLS ATDPDTAADD LEFVLVSPPQ FGYLENILPS
VGFEKSNIGI SIDSFQWKDM NAFHINYVQS RHLRIEPTAD QFTVYVTDGK HHSLEIPFSI
IINPTNDEAP DFVVQNITVC EGQMKELDSS IISAVDLDIP QDALLFSITQ KPRHGLLIDR
GFSKDFSENK QPANPHQKHA PVHSFSMELL KTGMRLTYMH DDSESLADDF TIQLSDGKHK
ILKTISVEVI PVNDEKPMLS KKAEIAMNMG ETRIISSAIL SAIDEDSPRE KIYYVFERLP
QNGQLQLKIG RDWVPLSPGM KCTQEEVDLN LLRYTHTGAM DSQNQDSFTF YLWDGNNRSP
ALDCQITIKD MEKGDIVILT KPLVVSKGDR GFLTTTTLLA VDGTDKPEEL LYVITSPPRY
GQIEYVHYPG VPITNFSQMD VVGQTVCYVH KSKVTVSSDR FRFIISNGLR TEHGVFEITL
ETVDRALPVV TRNKGLRLAQ GAVGLLSPDL LQLTDPDTPA ENLTFLLVQL PQHGQLYLWG
TGLLQHNFTQ QDVDSKNVAY RHSGGDSQTD CFTFMATDGT NQGFIVNGRV WEEPVLFTIQ
VDQLDKTAPR ITLLHSPSQV GLLKNGCYGI YITSRVLKAS DPDTEDDQII FKILQGPKHG
HLENTTTGEF IHEKFSQKDL NSKTILYIIN PSLEVNSDTV EFQIMDPTGN SATPQILELK
WSHIEWSQTE YEVCENVGLL PLEIIRRGYS MDSAFVGIKV NQVSAAVGKD FTVIPSKLIQ
FDPGMSTKMW NIAITYDGLE EDDEVFEVIL NSPVNAVLGT KTKAAVKILD SKGGQCHPSY
SSNQSKHSTW EKGIWHLLPP GSSSSTTSGS FHLERRPLPS SMQLAVIRGD TLRGFDSTDL
SQRKLRTRGN GKTVRPSSVY RNGTDIIYNY HGIVSLKLED DSFPTHKRKA KVSIISQPQK
TIKVAELPQA DKVESTTDSH FPRQDQLPSF PKNCTLELKG LFHFEEGIQK LYQCNGIAWK
AWSPQTKDVE DKSCPAGWHQ HSGYCHILIT EQKGTWNAAA QACREQYLGN LVTVFSRQHM
RWLWDIGGRK SFWIGLNDQV HAGHWEWIGG EPVAFTNGRR GPSQRSKLGK SCVLVQRQGK
WQTKDCRRAK PHNYVCSRKL *

mutated AA sequence

MNSLSWGAAN AVLLLLLLAW ASPTFISINR GVRVMKGHSA FLSGDDLKFA IPKEKDACKV
EVVMNEPITQ RVGKLTPQVF DCHFLPNEVK YVHNGCPILD EDTVKLRLYR FTERDTFIET
FILWVYLLEP DCNIIHMSNN VLEVPEFNGL SQAIDKNLLR FDYDRMASLE CTVSLDTART
RLPAHGQMVL GEPRPEEPRG DQPHSFFPES QLRAKLKCPG GSCTPGLKKI GSLKVSCEEF
LLMGLRYQHL DPPSPNIDYI SIQLDLTDTR SKIVYKKSES AWLPVYIRAG IPNQIPKAAF
MAVFILEVDQ FILTSLTTSV LDCEEDETPK PLLVFNITKA PLQGYVTHLL DHTRPISSFT
WKDLSDMQIA YQPPNSSHSE RRHDEVELEV YDFFFERSAP MTVHISIRTA DTNAPRVSWN
TGLSLLEGQS RAITWEQFQL VDNDDIGAVR LVTVGGLQHG WLTLRGGKGF LFTVADLQAG
VVRYHHDDSD STKDFVVFRI FDGHHSIRHK FPINVLPKDD SPPFLITNVV IELEEGQTIL
IQGSMLRASD VDASDDYIFF NITKPPQAGE IMKKPGPGLI GYPVHGFLQR DLFNGIIYYR
HFGGEIFEDS FQFVLWDSHE PPNLSVPQVA TIHITPVDDQ LPKEAPGVSR HLVVKETEVA
YITKKQLHFI DSESYDRELV YTITTPPFFS FSHRHLDAGK LFMVDSIPKV VKNPTALELR
SFTQHAVNYM KVAYMPPMQD IGPHCRDVQF TFSVSNQHGG TLHGICFNIT ILPVDNQVPE
AFTNPLKVTE GGQSIISTEH ILISDADTKL DNIDLSLREL PLHGRVELNG FPLNSGGTFS
WGDLHTLKVR YQHDGTEVLQ DDLLLEVTDG TNSAEFVLHV EVFPVNDEPP VLKADLMPVM
NCSEGGEVVI TSEYIFATDV DSDNLKLMFV IAREPQHGVV RRAGVTVDQF SQRDVISEAV
TYKHTGGEIG LMPCFDTITL VVSDGEAGPF VNGCCYNGPN PSVPLHASFP VYDLNITVYP
VDNQPPSIAI GPVFVVDEGC STALTVNHLS ATDPDTAADD LEFVLVSPPQ FGYLENILPS
VGFEKSNIGI SIDSFQWKDM NAFHINYVQS RHLRIEPTAD QFTVYVTDGK HHSLEIPFSI
IINPTNDEAP DFVVQNITVC EGQMKELDSS IISAVDLDIP QDALLFSITQ KPRHGLLIDR
GFSKDFSENK QPANPHQKHA PVHSFSMELL KTGMRLTYMH DDSESLADDF TIQLSDGKHK
ILKTISVEVI PVNDEKPMLS KKAEIAMNMG ETRIISSAIL SAIDEDSPRE KIYYVFERLP
QNGQLQLKIG RDWVPLSPGM KCTQEEVDLN LLRYTHTGAM DSQNQDSFTF YLWDGNNRSP
ALDCQITIKD MEKGDIVILT KPLVVSKGDR GFLTTTTLLA VDGTDKPEEL LYVITSPPRY
GQIEYVHYPG VPITNFSQMD VVGQTVCYVH KSKVTVSSDR FRFIISNGLR TEHGVFEITL
ETVDRALPVV TRNKGLRLAQ GAVGLLSPDL LQLTDPDTPA ENLTFLLVQL PQHGQLYLWG
TGLLQHNFTQ QDVDSKNVAY RHSGGDSQTD CFTFMATDGT NQGFIVNGRV WEEPVLFTIQ
VDQLDKTAPR ITLLHSPSQV GLLKNGCYGI YITSRVLKAS DPDTEDDQII FKILQGPKHG
HLENTTTGEF IHEKFSQKDL NSKTILYIIN PSLEVNSDTV EFQIMDPTGN SATPQILELK
WSHIEWSQTE YEVCENVGLL PLEIIRRGYS MDSAFVGIKV NQVSAAVGKD FTVIPSKLIQ
FDPGMSTKMW NIAITYDGLE EDDEVFEVIL NSPVNAVLGT KTKAAVKILD SKGGQCHPSY
SSNQSKHSTW EKGIWHLLPP GSSSSTTSGS FHLERRPLPS SMQLAVIRGD TLRGFDSTDL
SQRKLRTRGN GKTVRPSSVY RNGTDIIYNY HGIVSLKLED DSFPTHKRKA KVSIISQPQK
TIKVAELPQA DKVESTTDSH FPRQDQLPSF PKNCTLELKG LFHFEEGIQK LYQCNGIAWK
AWSPQTKDVE DKSCPAGWHQ HSGYCHILIT EQKGTWNAAA QACREQYLGN LVTVFSRQHM
RWLWDIGGRK SFWIGLNDQV HAGHWEWIGG EPVAFTNGRR GPSQRSKLGK SCVLVQRQGK
WQTKDCRRAK PHNYVCSRKL *

speed

0.56 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.482860402801775 (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)

chr9:14846036C>GN/A show variant in all transcripts IGV

HGNC symbol

FREM1

Ensembl transcript ID

ENST00000422223

Genbank transcript ID

NM_144966

UniProt peptide

Q5H8C1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1315G>C
cDNA.2131G>C
g.64958G>C

AA changes

V439L Score: 32 explain score(s)

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

439

frameshift

known variant

Reference ID: rs2779500

database	homozygous (G/G)	heterozygous	allele carriers
1000G	663	1182	1845
ExAC	17923	-3079	14844

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.41	1
	0.899	1
(flanking)	2.717	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
Donor increased	64963	wt: 0.54 / mu: 0.75	wt: GTTGTCGACAATGAC mu: CTTGTCGACAATGAC	TGTC\|gaca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

439

mutated

all conserved

439

Ptroglodytes

all identical

ENSPTRG00000020782

437

Mmulatta

all identical

ENSMMUG00000008128

437

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000059049

445

Ggallus

all identical

ENSGALG00000005426

386

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

all conserved

C48E7.6

165

FSHTD

Xtropicalis

all conserved

ENSXETG00000003300

444

protein features

start (aa)	end (aa)	feature	details
395	502	REPEAT	CSPG 2.	lost
503	621	REPEAT	CSPG 3.	might get lost (downstream of altered splice site)
560	560	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
622	622	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
622	758	REPEAT	CSPG 4.	might get lost (downstream of altered splice site)
759	869	REPEAT	CSPG 5.	might get lost (downstream of altered splice site)
870	1005	REPEAT	CSPG 6.	might get lost (downstream of altered splice site)
1006	1129	REPEAT	CSPG 7.	might get lost (downstream of altered splice site)
1014	1014	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1130	1256	REPEAT	CSPG 8.	might get lost (downstream of altered splice site)
1257	1375	REPEAT	CSPG 9.	might get lost (downstream of altered splice site)
1376	1487	REPEAT	CSPG 10.	might get lost (downstream of altered splice site)
1488	1608	REPEAT	CSPG 11.	might get lost (downstream of altered splice site)
1566	1566	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1609	1729	REPEAT	CSPG 12.	might get lost (downstream of altered splice site)
1731	1830	DOMAIN	Calx-beta.	might get lost (downstream of altered splice site)
1735	1735	CONFLICT	I -> N (in Ref. 5; AAH31064).	might get lost (downstream of altered splice site)
1861	1861	CONFLICT	S -> A (in Ref. 3; CAE46048).	might get lost (downstream of altered splice site)
1907	1909	MOTIF	Cell attachment site (Potential).	might get lost (downstream of altered splice site)
2060	2174	DOMAIN	C-type lectin.	might get lost (downstream of altered splice site)
2151	2151	DISULFID	By similarity.	might get lost (downstream of altered splice site)
2165	2165	DISULFID	By similarity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

6540 / 6540

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

2180 / 2180

position of stopcodon in wt / mu cDNA

7356 / 7356

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

817 / 817

chromosome

strand

-1

last intron/exon boundary

7157

theoretical NMD boundary in CDS

6290

length of CDS

6540

coding sequence (CDS) position

1315

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

2131

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

64958

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

14846036

original gDNA sequence snippet

TCACTTGGGAACAGTTTCAGGTTGTCGACAATGACGACATT

altered gDNA sequence snippet

TCACTTGGGAACAGTTTCAGCTTGTCGACAATGACGACATT

original cDNA sequence snippet

TCACTTGGGAACAGTTTCAGGTTGTCGACAATGACGACATT

altered cDNA sequence snippet

TCACTTGGGAACAGTTTCAGCTTGTCGACAATGACGACATT

wildtype AA sequence

mutated AA sequence

MNSLSWGAAN AVLLLLLLAW ASPTFISINR GVRVMKGHSA FLSGDDLKFA IPKEKDACKV
EVVMNEPITQ RVGKLTPQVF DCHFLPNEVK YVHNGCPILD EDTVKLRLYR FTERDTFIET
FILWVYLLEP DCNIIHMSNN VLEVPEFNGL SQAIDKNLLR FDYDRMASLE CTVSLDTART
RLPAHGQMVL GEPRPEEPRG DQPHSFFPES QLRAKLKCPG GSCTPGLKKI GSLKVSCEEF
LLMGLRYQHL DPPSPNIDYI SIQLDLTDTR SKIVYKSESA WLPVYIRAGI PNQIPKAAFM
AVFILEVDQF ILTSLTTSVL DCEEDETPKP LLVFNITKAP LQGYVTHLLD HTRPISSFTW
KDLSDMQIAY QPPNSSHSER RHDEVELEVY DFFFERSAPM TVHISIRTAD TNAPRVSWNT
GLSLLEGQSR AITWEQFQLV DNDDIGAVRL VTVGGLQHGW LTLRGGKGFL FTVADLQAGV
VRYHHDDSDS TKDFVVFRIF DGHHSIRHKF PINVLPKDDS PPFLITNVVI ELEEGQTILI
QGSMLRASDV DASDDYIFFN ITKPPQAGEI MKKPGPGLIG YPVHGFLQRD LFNGIIYYRH
FGGEIFEDSF QFVLWDSHEP PNLSVPQVAT IHITPVDDQL PKEAPGVSRH LVVKETEVAY
ITKKQLHFID SESYDRELVY TITTPPFFSF SHRHLDAGKL FMVDSIPKVV KNPTALELRS
FTQHAVNYMK VAYMPPMQDI GPHCRDVQFT FSVSNQHGGT LHGICFNITI LPVDNQVPEA
FTNPLKVTEG GQSIISTEHI LISDADTKLD NIDLSLRELP LHGRVELNGF PLNSGGTFSW
GDLHTLKVRY QHDGTEVLQD DLLLEVTDGT NSAEFVLHVE VFPVNDEPPV LKADLMPVMN
CSEGGEVVIT SEYIFATDVD SDNLKLMFVI AREPQHGVVR RAGVTVDQFS QRDVISEAVT
YKHTGGEIGL MPCFDTITLV VSDGEAGPFV NGCCYNGPNP SVPLHASFPV YDLNITVYPV
DNQPPSIAIG PVFVVDEGCS TALTVNHLSA TDPDTAADDL EFVLVSPPQF GYLENILPSV
GFEKSNIGIS IDSFQWKDMN AFHINYVQSR HLRIEPTADQ FTVYVTDGKH HSLEIPFSII
INPTNDEAPD FVVQNITVCE GQMKELDSSI ISAVDLDIPQ DALLFSITQK PRHGLLIDRG
FSKDFSENKQ PANPHQKHAP VHSFSMELLK TGMRLTYMHD DSESLADDFT IQLSDGKHKI
LKTISVEVIP VNDEKPMLSK KAEIAMNMGE TRIISSAILS AIDEDSPREK IYYVFERLPQ
NGQLQLKIGR DWVPLSPGMK CTQEEVDLNL LRYTHTGAMD SQNQDSFTFY LWDGNNRSPA
LDCQITIKDM EKGDIVILTK PLVVSKGDRG FLTTTTLLAV DGTDKPEELL YVITSPPRYG
QIEYVHYPGV PITNFSQMDV VGQTVCYVHK SKVTVSSDRF RFIISNGLRT EHGVFEITLE
TVDRALPVVT RNKGLRLAQG AVGLLSPDLL QLTDPDTPAE NLTFLLVQLP QHGQLYLWGT
GLLQHNFTQQ DVDSKNVAYR HSGGDSQTDC FTFMATDGTN QGFIVNGRVW EEPVLFTIQV
DQLDKTAPRI TLLHSPSQVG LLKNGCYGIY ITSRVLKASD PDTEDDQIIF KILQGPKHGH
LENTTTGEFI HEKFSQKDLN SKTILYIINP SLEVNSDTVE FQIMDPTGNS ATPQILELKW
SHIEWSQTEY EVCENVGLLP LEIIRRGYSM DSAFVGIKVN QVSAAVGKDF TVIPSKLIQF
DPGMSTKMWN IAITYDGLEE DDEVFEVILN SPVNAVLGTK TKAAVKILDS KGGQCHPSYS
SNQSKHSTWE KGIWHLLPPG SSSSTTSGSF HLERRPLPSS MQLAVIRGDT LRGFDSTDLS
QRKLRTRGNG KTVRPSSVYR NGTDIIYNYH GIVSLKLEDD SFPTHKRKAK VSIISQPQKT
IKVAELPQAD KVESTTDSHF PRQDQLPSFP KNCTLELKGL FHFEEGIQKL YQCNGIAWKA
WSPQTKDVED KSCPAGWHQH SGYCHILITE QKGTWNAAAQ ACREQYLGNL VTVFSRQHMR
WLWDIGGRKS FWIGLNDQVH AGHWEWIGGE PVAFTNGRRG PSQRSKLGKS CVLVQRQGKW
QTKDCRRAKP HNYVCSRKL*

speed

1.34 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems