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 10 transcript(s)...
Querying Taster for transcript #1: ENST00000553728
Querying Taster for transcript #2: ENST00000341749
Querying Taster for transcript #3: ENST00000557038
Querying Taster for transcript #4: ENST00000396165
Querying Taster for transcript #5: ENST00000280083
Querying Taster for transcript #6: ENST00000556148
Querying Taster for transcript #7: ENST00000348007
Querying Taster for transcript #8: ENST00000553352
Querying Taster for transcript #9: ENST00000341502
Querying Taster for transcript #10: ENST00000396158
MT speed 3.57 s - this script 4.171289 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
MIA2	polymorphism_automatic	2.71952583996704e-06	simple_aae		affected		G726R	single base exchange	rs1060878		show file
MIA2	polymorphism_automatic	2.71952583996704e-06	simple_aae		affected		G658R	single base exchange	rs1060878		show file
MIA2	polymorphism_automatic	2.71952583996704e-06	simple_aae		affected		G709R	single base exchange	rs1060878		show file
MIA2	polymorphism_automatic	2.71952583996704e-06	simple_aae		affected		G738R	single base exchange	rs1060878		show file
MIA2	polymorphism_automatic	2.71952583996704e-06	simple_aae		affected		G663R	single base exchange	rs1060878		show file
MIA2	polymorphism_automatic	2.71952583996704e-06	simple_aae		affected		G709R	single base exchange	rs1060878		show file
MIA2	polymorphism_automatic	2.71952583996704e-06	simple_aae		affected		G743R	single base exchange	rs1060878		show file
MIA2	polymorphism_automatic	5.72370082196905e-06	simple_aae		affected		G695R	single base exchange	rs1060878		show file
MIA2	polymorphism_automatic	5.1057933138976e-05	simple_aae		affected		G738R	single base exchange	rs1060878		show file

some transcripts had annotation problems and are not shown

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999728047416 (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)

chr14:39818145G>AN/A show variant in all transcripts IGV

HGNC symbol

MIA2

Ensembl transcript ID

ENST00000341749

Genbank transcript ID

NM_203354

UniProt peptide

O15320

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2176G>A
cDNA.2279G>A
g.83658G>A

AA changes

G726R Score: 125 explain score(s)

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

726

frameshift

known variant

Reference ID: rs1060878

database	homozygous (A/A)	heterozygous	allele carriers
1000G	259	1038	1297
ExAC	7734	17299	25033

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.362	0.999
	0.326	0.999
(flanking)	3.54	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	83658	wt: 0.6961 / mu: 0.7634 (marginal change - not scored)	wt: CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA mu: CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA	ccag\|GGGA
Acc increased	83655	wt: 0.24 / mu: 0.37	wt: CTTCTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCA mu: CTTCTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCA	ccac\|CAGG
Donor increased	83654	wt: 0.22 / mu: 0.85	wt: TTTCCACCAGGGGAT mu: TTTCCACCAAGGGAT	TCCA\|ccag
Donor increased	83658	wt: 0.65 / mu: 0.95	wt: CACCAGGGGATTTCC mu: CACCAAGGGATTTCC	CCAG\|ggga
Acc gained	83660	0.60	mu: CGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCACC	aagg\|GATT
Donor gained	83653	0.94	mu: TTTTCCACCAAGGGA	TTCC\|acca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

726

mutated

not conserved

726

Ptroglodytes

not conserved

ENSPTRG00000006297

738

Mmulatta

not conserved

ENSMMUG00000021121

739

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000021000

740

Ggallus

not conserved

ENSGALG00000010189

1259

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000023516

623

Dmelanogaster

no alignment

FBgn0031842

n/a

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
502	804	COMPBIAS	Pro-rich.	lost
776	776	CONFLICT	S -> F (in Ref. 2; AAN77610).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2379 / 2379

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

793 / 793

position of stopcodon in wt / mu cDNA

2482 / 2482

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

104 / 104

chromosome

strand

last intron/exon boundary

2316

theoretical NMD boundary in CDS

2162

length of CDS

2379

coding sequence (CDS) position

2176

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

2279

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

83658

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

39818145

original gDNA sequence snippet

CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA

altered gDNA sequence snippet

CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA

original cDNA sequence snippet

CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA

altered cDNA sequence snippet

CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA

wildtype AA sequence

MELKSPEEEV VAALPEGMRP DSNLYGFPWE LVICAAVVGF FAVLFFLWRS FRSVRSRLYV
GREKKLALML SGLIEEKSKL LEKFSLVQKE YEGYEVESSL KDASFEKEAT EAQSLEATCE
KLNRSNSELE DEILCLEKEL KEEKSKHSEQ DELMADISKR IQSLEDESKS LKSQVAEAKM
TFKIFQMNEE RLKIAIKDAL NENSQLQESQ KQLLQEAEVW KEQVSELNKQ KVTFEDSKVH
AEQVLNDKES HIKTLTERLL KMKDWAAMLG EDITDDDNLE LEMNSESENG AYLDNPPKGA
LKKLIHAAKL NASLKTLEGE RNQIYIQLSE VDKTKEELTE HIKNLQTEQA SLQSENTHFE
NENQKLQQKL KVMTELYQEN EMKLHRKLTV EENYRLEKEE KLSKVDEKIS HATEELETYR
KRAKDLEEEL ERTIHSYQGQ IISHEKKAHD NWLAARNAER NLNDLRKENA HNRQKLTETE
LKFELLEKDP YALDVPNTAF GREHSPYGPS PLGWPSSETR AFLSPPTLLE GPLRLSPLLP
GGGGRGSRGP GNPLDHQITN ERGESSCDRL TDPHRAPSDT GSLSPPWDQD RRMMFPPPGQ
SYPDSALPPQ RQDRFCSNSG RLSGPAELRS FNMPSLDKMD GSMPSEMESS RNDTKDDLGN
LNVPDSSLPA ENEATGPGFV PPPLAPIRGP LFPVDARGPF LRRGPPFPPP PPGAMFGASR
DYFPPGDFPG PPPAPFAMRN VYPPRGFPPY LPPRPGFFPP PPHSEGRSEF PSGLIPPSNE
PATEHPEPQQ ET*

mutated AA sequence

MELKSPEEEV VAALPEGMRP DSNLYGFPWE LVICAAVVGF FAVLFFLWRS FRSVRSRLYV
GREKKLALML SGLIEEKSKL LEKFSLVQKE YEGYEVESSL KDASFEKEAT EAQSLEATCE
KLNRSNSELE DEILCLEKEL KEEKSKHSEQ DELMADISKR IQSLEDESKS LKSQVAEAKM
TFKIFQMNEE RLKIAIKDAL NENSQLQESQ KQLLQEAEVW KEQVSELNKQ KVTFEDSKVH
AEQVLNDKES HIKTLTERLL KMKDWAAMLG EDITDDDNLE LEMNSESENG AYLDNPPKGA
LKKLIHAAKL NASLKTLEGE RNQIYIQLSE VDKTKEELTE HIKNLQTEQA SLQSENTHFE
NENQKLQQKL KVMTELYQEN EMKLHRKLTV EENYRLEKEE KLSKVDEKIS HATEELETYR
KRAKDLEEEL ERTIHSYQGQ IISHEKKAHD NWLAARNAER NLNDLRKENA HNRQKLTETE
LKFELLEKDP YALDVPNTAF GREHSPYGPS PLGWPSSETR AFLSPPTLLE GPLRLSPLLP
GGGGRGSRGP GNPLDHQITN ERGESSCDRL TDPHRAPSDT GSLSPPWDQD RRMMFPPPGQ
SYPDSALPPQ RQDRFCSNSG RLSGPAELRS FNMPSLDKMD GSMPSEMESS RNDTKDDLGN
LNVPDSSLPA ENEATGPGFV PPPLAPIRGP LFPVDARGPF LRRGPPFPPP PPGAMFGASR
DYFPPRDFPG PPPAPFAMRN VYPPRGFPPY LPPRPGFFPP PPHSEGRSEF PSGLIPPSNE
PATEHPEPQQ ET*

speed

0.38 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: 0.99999728047416 (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)

chr14:39818145G>AN/A show variant in all transcripts IGV

HGNC symbol

MIA2

Ensembl transcript ID

ENST00000557038

Genbank transcript ID

N/A

UniProt peptide

O15320

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1972G>A
cDNA.2240G>A
g.83658G>A

AA changes

G658R Score: 125 explain score(s)

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

658

frameshift

known variant

Reference ID: rs1060878

database	homozygous (A/A)	heterozygous	allele carriers
1000G	259	1038	1297
ExAC	7734	17299	25033

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.362	0.999
	0.326	0.999
(flanking)	3.54	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	83658	wt: 0.6961 / mu: 0.7634 (marginal change - not scored)	wt: CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA mu: CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA	ccag\|GGGA
Acc increased	83655	wt: 0.24 / mu: 0.37	wt: CTTCTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCA mu: CTTCTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCA	ccac\|CAGG
Donor increased	83654	wt: 0.22 / mu: 0.85	wt: TTTCCACCAGGGGAT mu: TTTCCACCAAGGGAT	TCCA\|ccag
Donor increased	83658	wt: 0.65 / mu: 0.95	wt: CACCAGGGGATTTCC mu: CACCAAGGGATTTCC	CCAG\|ggga
Acc gained	83660	0.60	mu: CGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCACC	aagg\|GATT
Donor gained	83653	0.94	mu: TTTTCCACCAAGGGA	TTCC\|acca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

658

mutated

not conserved

658

Ptroglodytes

not conserved

ENSPTRG00000006297

738

Mmulatta

not conserved

ENSMMUG00000021121

739

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000021000

740

Ggallus

not conserved

ENSGALG00000010189

1259

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000023516

636

Dmelanogaster

no alignment

FBgn0031842

n/a

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
502	804	COMPBIAS	Pro-rich.	lost
678	678	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
776	776	CONFLICT	S -> F (in Ref. 2; AAN77610).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2175 / 2175

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

725 / 725

position of stopcodon in wt / mu cDNA

2443 / 2443

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

269 / 269

chromosome

strand

last intron/exon boundary

2277

theoretical NMD boundary in CDS

1958

length of CDS

2175

coding sequence (CDS) position

1972

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

2240

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

83658

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

39818145

original gDNA sequence snippet

CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA

altered gDNA sequence snippet

CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA

original cDNA sequence snippet

CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA

altered cDNA sequence snippet

CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA

wildtype AA sequence

MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE ATEAQSLEAT CEKLNRSNSE
LEDEILCLEK ELKEEKSKHS EQDELMADIS KRIQSLEDES KSLKSQVAEA KMTFKIFQMN
EERLKIAIKD ALNENSQLQE SQKQLLQEAE VWKEQVSELN KQKVTFEDSK VHAEQVLNDK
ESHIKTLTER LLKMKDWAAM LGEDITDDDN LELEMNSESE NGAYLDNPPK GALKKLIHAA
KLNASLKTLE GERNQIYIQL SEVDKTKEEL TEHIKNLQTE QASLQSENTH FENENQKLQQ
KLKVMTELYQ ENEMKLHRKL TVEENYRLEK EEKLSKVDEK ISHATEELET YRKRAKDLEE
ELERTIHSYQ GQIISHEKKA HDNWLAARNA ERNLNDLRKE NAHNRQKLTE TELKFELLEK
DPYALDVPNT AFGREHSPYG PSPLGWPSSE TRAFLSPPTL LEGPLRLSPL LPGGGGRGSR
GPGNPLDHQI TNERGESSCD RLTDPHRAPS DTGSLSPPWD QDRRMMFPPP GQSYPDSALP
PQRQDRFCSN SGRLSGPAEL RSFNMPSLDK MDGSMPSEME SSRNDTKDDL GNLNVPDSSL
PAENEATGPG FVPPPLAPIR GPLFPVDARG PFLRRGPPFP PPPPGAMFGA SRDYFPPGDF
PGPPPAPFAM RNVYPPRGFP PYLPPRPGFF PPPPHSEGRS EFPSGLIPPS NEPATEHPEP
QQET*

mutated AA sequence

MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE ATEAQSLEAT CEKLNRSNSE
LEDEILCLEK ELKEEKSKHS EQDELMADIS KRIQSLEDES KSLKSQVAEA KMTFKIFQMN
EERLKIAIKD ALNENSQLQE SQKQLLQEAE VWKEQVSELN KQKVTFEDSK VHAEQVLNDK
ESHIKTLTER LLKMKDWAAM LGEDITDDDN LELEMNSESE NGAYLDNPPK GALKKLIHAA
KLNASLKTLE GERNQIYIQL SEVDKTKEEL TEHIKNLQTE QASLQSENTH FENENQKLQQ
KLKVMTELYQ ENEMKLHRKL TVEENYRLEK EEKLSKVDEK ISHATEELET YRKRAKDLEE
ELERTIHSYQ GQIISHEKKA HDNWLAARNA ERNLNDLRKE NAHNRQKLTE TELKFELLEK
DPYALDVPNT AFGREHSPYG PSPLGWPSSE TRAFLSPPTL LEGPLRLSPL LPGGGGRGSR
GPGNPLDHQI TNERGESSCD RLTDPHRAPS DTGSLSPPWD QDRRMMFPPP GQSYPDSALP
PQRQDRFCSN SGRLSGPAEL RSFNMPSLDK MDGSMPSEME SSRNDTKDDL GNLNVPDSSL
PAENEATGPG FVPPPLAPIR GPLFPVDARG PFLRRGPPFP PPPPGAMFGA SRDYFPPRDF
PGPPPAPFAM RNVYPPRGFP PYLPPRPGFF PPPPHSEGRS EFPSGLIPPS NEPATEHPEP
QQET*

speed

0.36 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999728047416 (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)

chr14:39818145G>AN/A show variant in all transcripts IGV

HGNC symbol

MIA2

Ensembl transcript ID

ENST00000396165

Genbank transcript ID

N/A

UniProt peptide

O15320

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2125G>A
cDNA.2709G>A
g.83658G>A

AA changes

G709R Score: 125 explain score(s)

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

709

frameshift

known variant

Reference ID: rs1060878

database	homozygous (A/A)	heterozygous	allele carriers
1000G	259	1038	1297
ExAC	7734	17299	25033

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.362	0.999
	0.326	0.999
(flanking)	3.54	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	83658	wt: 0.6961 / mu: 0.7634 (marginal change - not scored)	wt: CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA mu: CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA	ccag\|GGGA
Acc increased	83655	wt: 0.24 / mu: 0.37	wt: CTTCTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCA mu: CTTCTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCA	ccac\|CAGG
Donor increased	83654	wt: 0.22 / mu: 0.85	wt: TTTCCACCAGGGGAT mu: TTTCCACCAAGGGAT	TCCA\|ccag
Donor increased	83658	wt: 0.65 / mu: 0.95	wt: CACCAGGGGATTTCC mu: CACCAAGGGATTTCC	CCAG\|ggga
Acc gained	83660	0.60	mu: CGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCACC	aagg\|GATT
Donor gained	83653	0.94	mu: TTTTCCACCAAGGGA	TTCC\|acca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

709

mutated

not conserved

709

Ptroglodytes

not conserved

ENSPTRG00000006297

738

Mmulatta

not conserved

ENSMMUG00000021121

739

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000021000

740

Ggallus

not conserved

ENSGALG00000010189

1258

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000023516

623

Dmelanogaster

no alignment

FBgn0031842

n/a

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
502	804	COMPBIAS	Pro-rich.	lost
776	776	CONFLICT	S -> F (in Ref. 2; AAN77610).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2328 / 2328

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

776 / 776

position of stopcodon in wt / mu cDNA

2912 / 2912

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

585 / 585

chromosome

strand

last intron/exon boundary

2746

theoretical NMD boundary in CDS

2111

length of CDS

2328

coding sequence (CDS) position

2125

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

2709

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

83658

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

39818145

original gDNA sequence snippet

CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA

altered gDNA sequence snippet

CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA

original cDNA sequence snippet

CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA

altered cDNA sequence snippet

CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA

wildtype AA sequence

MRPDSNLYGF PWELVICAAV VGFFAVLFFL WRSFRSVRSR LYVGREKKLA LMLSGLIEEK
SKLLEKFSLV QKEYEGYEVE SSLKDASFEK EATEAQSLEA TCEKLNRSNS ELEDEILCLE
KELKEEKSKH SEQDELMADI SKRIQSLEDE SKSLKSQVAE AKMTFKIFQM NEERLKIAIK
DALNENSQLQ ESQKQLLQEA EVWKEQVSEL NKQKVTFEDS KVHAEQVLND KESHIKTLTE
RLLKMKDWAA MLGEDITDDD NLELEMNSES ENGAYLDNPP KGALKKLIHA AKLNASLKTL
EGERNQIYIQ LSEVDKTKEE LTEHIKNLQT EQASLQSENT HFENENQKLQ QKLKVMTELY
QENEMKLHRK LTVEENYRLE KEEKLSKVDE KISHATEELE TYRKRAKDLE EELERTIHSY
QGQIISHEKK AHDNWLAARN AERNLNDLRK ENAHNRQKLT ETELKFELLE KDPYALDVPN
TAFGREHSPY GPSPLGWPSS ETRAFLSPPT LLEGPLRLSP LLPGGGGRGS RGPGNPLDHQ
ITNERGESSC DRLTDPHRAP SDTGSLSPPW DQDRRMMFPP PGQSYPDSAL PPQRQDRFCS
NSGRLSGPAE LRSFNMPSLD KMDGSMPSEM ESSRNDTKDD LGNLNVPDSS LPAENEATGP
GFVPPPLAPI RGPLFPVDAR GPFLRRGPPF PPPPPGAMFG ASRDYFPPGD FPGPPPAPFA
MRNVYPPRGF PPYLPPRPGF FPPPPHSEGR SEFPSGLIPP SNEPATEHPE PQQET*

mutated AA sequence

MRPDSNLYGF PWELVICAAV VGFFAVLFFL WRSFRSVRSR LYVGREKKLA LMLSGLIEEK
SKLLEKFSLV QKEYEGYEVE SSLKDASFEK EATEAQSLEA TCEKLNRSNS ELEDEILCLE
KELKEEKSKH SEQDELMADI SKRIQSLEDE SKSLKSQVAE AKMTFKIFQM NEERLKIAIK
DALNENSQLQ ESQKQLLQEA EVWKEQVSEL NKQKVTFEDS KVHAEQVLND KESHIKTLTE
RLLKMKDWAA MLGEDITDDD NLELEMNSES ENGAYLDNPP KGALKKLIHA AKLNASLKTL
EGERNQIYIQ LSEVDKTKEE LTEHIKNLQT EQASLQSENT HFENENQKLQ QKLKVMTELY
QENEMKLHRK LTVEENYRLE KEEKLSKVDE KISHATEELE TYRKRAKDLE EELERTIHSY
QGQIISHEKK AHDNWLAARN AERNLNDLRK ENAHNRQKLT ETELKFELLE KDPYALDVPN
TAFGREHSPY GPSPLGWPSS ETRAFLSPPT LLEGPLRLSP LLPGGGGRGS RGPGNPLDHQ
ITNERGESSC DRLTDPHRAP SDTGSLSPPW DQDRRMMFPP PGQSYPDSAL PPQRQDRFCS
NSGRLSGPAE LRSFNMPSLD KMDGSMPSEM ESSRNDTKDD LGNLNVPDSS LPAENEATGP
GFVPPPLAPI RGPLFPVDAR GPFLRRGPPF PPPPPGAMFG ASRDYFPPRD FPGPPPAPFA
MRNVYPPRGF PPYLPPRPGF FPPPPHSEGR SEFPSGLIPP SNEPATEHPE PQQET*

speed

0.22 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999728047416 (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)

chr14:39818145G>AN/A show variant in all transcripts IGV

HGNC symbol

MIA2

Ensembl transcript ID

ENST00000280083

Genbank transcript ID

NM_005930

UniProt peptide

O15320

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2212G>A
cDNA.2526G>A
g.83658G>A

AA changes

G738R Score: 125 explain score(s)

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

738

frameshift

known variant

Reference ID: rs1060878

database	homozygous (A/A)	heterozygous	allele carriers
1000G	259	1038	1297
ExAC	7734	17299	25033

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.362	0.999
	0.326	0.999
(flanking)	3.54	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	83658	wt: 0.6961 / mu: 0.7634 (marginal change - not scored)	wt: CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA mu: CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA	ccag\|GGGA
Acc increased	83655	wt: 0.24 / mu: 0.37	wt: CTTCTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCA mu: CTTCTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCA	ccac\|CAGG
Donor increased	83654	wt: 0.22 / mu: 0.85	wt: TTTCCACCAGGGGAT mu: TTTCCACCAAGGGAT	TCCA\|ccag
Donor increased	83658	wt: 0.65 / mu: 0.95	wt: CACCAGGGGATTTCC mu: CACCAAGGGATTTCC	CCAG\|ggga
Acc gained	83660	0.60	mu: CGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCACC	aagg\|GATT
Donor gained	83653	0.94	mu: TTTTCCACCAAGGGA	TTCC\|acca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

738

mutated

not conserved

738

Ptroglodytes

not conserved

ENSPTRG00000006297

738

Mmulatta

not conserved

ENSMMUG00000021121

739

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000021000

740

Ggallus

not conserved

ENSGALG00000010189

1259

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000023516

623

Dmelanogaster

no alignment

FBgn0031842

n/a

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
502	804	COMPBIAS	Pro-rich.	lost
776	776	CONFLICT	S -> F (in Ref. 2; AAN77610).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2415 / 2415

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

805 / 805

position of stopcodon in wt / mu cDNA

2729 / 2729

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

315 / 315

chromosome

strand

last intron/exon boundary

2563

theoretical NMD boundary in CDS

2198

length of CDS

2415

coding sequence (CDS) position

2212

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

2526

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

83658

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

39818145

original gDNA sequence snippet

CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA

altered gDNA sequence snippet

CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA

original cDNA sequence snippet

CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA

altered cDNA sequence snippet

CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA

wildtype AA sequence

MEEPGVTPQP YLGLLLEELR RVVAALPEGM RPDSNLYGFP WELVICAAVV GFFAVLFFLW
RSFRSVRSRL YVGREKKLAL MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE
ATEAQSLEAT CEKLNRSNSE LEDEILCLEK ELKEEKSKHS EQDELMADIS KRIQSLEDES
KSLKSQVAEA KMTFKIFQMN EERLKIAIKD ALNENSQLQE SQKQLLQEAE VWKEQVSELN
KQKVTFEDSK VHAEQVLNDK ESHIKTLTER LLKMKDWAAM LGEDITDDDN LELEMNSESE
NGAYLDNPPK GALKKLIHAA KLNASLKTLE GERNQIYIQL SEVDKTKEEL TEHIKNLQTE
QASLQSENTH FENENQKLQQ KLKVMTELYQ ENEMKLHRKL TVEENYRLEK EEKLSKVDEK
ISHATEELET YRKRAKDLEE ELERTIHSYQ GQIISHEKKA HDNWLAARNA ERNLNDLRKE
NAHNRQKLTE TELKFELLEK DPYALDVPNT AFGREHSPYG PSPLGWPSSE TRAFLSPPTL
LEGPLRLSPL LPGGGGRGSR GPGNPLDHQI TNERGESSCD RLTDPHRAPS DTGSLSPPWD
QDRRMMFPPP GQSYPDSALP PQRQDRFCSN SGRLSGPAEL RSFNMPSLDK MDGSMPSEME
SSRNDTKDDL GNLNVPDSSL PAENEATGPG FVPPPLAPIR GPLFPVDARG PFLRRGPPFP
PPPPGAMFGA SRDYFPPGDF PGPPPAPFAM RNVYPPRGFP PYLPPRPGFF PPPPHSEGRS
EFPSGLIPPS NEPATEHPEP QQET*

mutated AA sequence

MEEPGVTPQP YLGLLLEELR RVVAALPEGM RPDSNLYGFP WELVICAAVV GFFAVLFFLW
RSFRSVRSRL YVGREKKLAL MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE
ATEAQSLEAT CEKLNRSNSE LEDEILCLEK ELKEEKSKHS EQDELMADIS KRIQSLEDES
KSLKSQVAEA KMTFKIFQMN EERLKIAIKD ALNENSQLQE SQKQLLQEAE VWKEQVSELN
KQKVTFEDSK VHAEQVLNDK ESHIKTLTER LLKMKDWAAM LGEDITDDDN LELEMNSESE
NGAYLDNPPK GALKKLIHAA KLNASLKTLE GERNQIYIQL SEVDKTKEEL TEHIKNLQTE
QASLQSENTH FENENQKLQQ KLKVMTELYQ ENEMKLHRKL TVEENYRLEK EEKLSKVDEK
ISHATEELET YRKRAKDLEE ELERTIHSYQ GQIISHEKKA HDNWLAARNA ERNLNDLRKE
NAHNRQKLTE TELKFELLEK DPYALDVPNT AFGREHSPYG PSPLGWPSSE TRAFLSPPTL
LEGPLRLSPL LPGGGGRGSR GPGNPLDHQI TNERGESSCD RLTDPHRAPS DTGSLSPPWD
QDRRMMFPPP GQSYPDSALP PQRQDRFCSN SGRLSGPAEL RSFNMPSLDK MDGSMPSEME
SSRNDTKDDL GNLNVPDSSL PAENEATGPG FVPPPLAPIR GPLFPVDARG PFLRRGPPFP
PPPPGAMFGA SRDYFPPRDF PGPPPAPFAM RNVYPPRGFP PYLPPRPGFF PPPPHSEGRS
EFPSGLIPPS NEPATEHPEP QQET*

speed

0.17 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999728047416 (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)

chr14:39818145G>AN/A show variant in all transcripts IGV

HGNC symbol

MIA2

Ensembl transcript ID

ENST00000556148

Genbank transcript ID

N/A

UniProt peptide

O15320

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1987G>A
cDNA.2166G>A
g.83658G>A

AA changes

G663R Score: 125 explain score(s)

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

663

frameshift

known variant

Reference ID: rs1060878

database	homozygous (A/A)	heterozygous	allele carriers
1000G	259	1038	1297
ExAC	7734	17299	25033

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.362	0.999
	0.326	0.999
(flanking)	3.54	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	83658	wt: 0.6961 / mu: 0.7634 (marginal change - not scored)	wt: CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA mu: CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA	ccag\|GGGA
Acc increased	83655	wt: 0.24 / mu: 0.37	wt: CTTCTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCA mu: CTTCTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCA	ccac\|CAGG
Donor increased	83654	wt: 0.22 / mu: 0.85	wt: TTTCCACCAGGGGAT mu: TTTCCACCAAGGGAT	TCCA\|ccag
Donor increased	83658	wt: 0.65 / mu: 0.95	wt: CACCAGGGGATTTCC mu: CACCAAGGGATTTCC	CCAG\|ggga
Acc gained	83660	0.60	mu: CGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCACC	aagg\|GATT
Donor gained	83653	0.94	mu: TTTTCCACCAAGGGA	TTCC\|acca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

663

mutated

not conserved

663

Ptroglodytes

not conserved

ENSPTRG00000006297

738

Mmulatta

not conserved

ENSMMUG00000021121

739

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000021000

740

Ggallus

not conserved

ENSGALG00000010189

1259

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000023516

623

Dmelanogaster

no alignment

FBgn0031842

n/a

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
502	804	COMPBIAS	Pro-rich.	lost
678	678	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
776	776	CONFLICT	S -> F (in Ref. 2; AAN77610).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2190 / 2190

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

730 / 730

position of stopcodon in wt / mu cDNA

2369 / 2369

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

180 / 180

chromosome

strand

last intron/exon boundary

2203

theoretical NMD boundary in CDS

1973

length of CDS

2190

coding sequence (CDS) position

1987

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

2166

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

83658

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

39818145

original gDNA sequence snippet

CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA

altered gDNA sequence snippet

CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA

original cDNA sequence snippet

CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA

altered cDNA sequence snippet

CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA

wildtype AA sequence

MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE ATEAQSLEVE NQMATCEKLN
RSNSELEDEI LCLEKELKEE KSKHSEQDEL MADISKRIQS LEDESKSLKS QVAEAKMTFK
IFQMNEERLK IAIKDALNEN SQLQESQKQL LQEAEVWKEQ VSELNKQKVT FEDSKVHAEQ
VLNDKESHIK TLTERLLKMK DWAAMLGEDI TDDDNLELEM NSESENGAYL DNPPKGALKK
LIHAAKLNAS LKTLEGERNQ IYIQLSEVDK TKEELTEHIK NLQTEQASLQ SENTHFENEN
QKLQQKLKVM TELYQENEMK LHRKLTVEEN YRLEKEEKLS KVDEKISHAT EELETYRKRA
KDLEEELERT IHSYQGQIIS HEKKAHDNWL AARNAERNLN DLRKENAHNR QKLTETELKF
ELLEKDPYAL DVPNTAFGRE HSPYGPSPLG WPSSETRAFL SPPTLLEGPL RLSPLLPGGG
GRGSRGPGNP LDHQITNERG ESSCDRLTDP HRAPSDTGSL SPPWDQDRRM MFPPPGQSYP
DSALPPQRQD RFCSNSGRLS GPAELRSFNM PSLDKMDGSM PSEMESSRND TKDDLGNLNV
PDSSLPAENE ATGPGFVPPP LAPIRGPLFP VDARGPFLRR GPPFPPPPPG AMFGASRDYF
PPGDFPGPPP APFAMRNVYP PRGFPPYLPP RPGFFPPPPH SEGRSEFPSG LIPPSNEPAT
EHPEPQQET*

mutated AA sequence

MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE ATEAQSLEVE NQMATCEKLN
RSNSELEDEI LCLEKELKEE KSKHSEQDEL MADISKRIQS LEDESKSLKS QVAEAKMTFK
IFQMNEERLK IAIKDALNEN SQLQESQKQL LQEAEVWKEQ VSELNKQKVT FEDSKVHAEQ
VLNDKESHIK TLTERLLKMK DWAAMLGEDI TDDDNLELEM NSESENGAYL DNPPKGALKK
LIHAAKLNAS LKTLEGERNQ IYIQLSEVDK TKEELTEHIK NLQTEQASLQ SENTHFENEN
QKLQQKLKVM TELYQENEMK LHRKLTVEEN YRLEKEEKLS KVDEKISHAT EELETYRKRA
KDLEEELERT IHSYQGQIIS HEKKAHDNWL AARNAERNLN DLRKENAHNR QKLTETELKF
ELLEKDPYAL DVPNTAFGRE HSPYGPSPLG WPSSETRAFL SPPTLLEGPL RLSPLLPGGG
GRGSRGPGNP LDHQITNERG ESSCDRLTDP HRAPSDTGSL SPPWDQDRRM MFPPPGQSYP
DSALPPQRQD RFCSNSGRLS GPAELRSFNM PSLDKMDGSM PSEMESSRND TKDDLGNLNV
PDSSLPAENE ATGPGFVPPP LAPIRGPLFP VDARGPFLRR GPPFPPPPPG AMFGASRDYF
PPRDFPGPPP APFAMRNVYP PRGFPPYLPP RPGFFPPPPH SEGRSEFPSG LIPPSNEPAT
EHPEPQQET*

speed

0.65 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999728047416 (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)

chr14:39818145G>AN/A show variant in all transcripts IGV

HGNC symbol

MIA2

Ensembl transcript ID

ENST00000553352

Genbank transcript ID

N/A

UniProt peptide

O15320

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2125G>A
cDNA.2857G>A
g.83658G>A

AA changes

G709R Score: 125 explain score(s)

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

709

frameshift

known variant

Reference ID: rs1060878

database	homozygous (A/A)	heterozygous	allele carriers
1000G	259	1038	1297
ExAC	7734	17299	25033

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.362	0.999
	0.326	0.999
(flanking)	3.54	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	83658	wt: 0.6961 / mu: 0.7634 (marginal change - not scored)	wt: CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA mu: CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA	ccag\|GGGA
Acc increased	83655	wt: 0.24 / mu: 0.37	wt: CTTCTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCA mu: CTTCTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCA	ccac\|CAGG
Donor increased	83654	wt: 0.22 / mu: 0.85	wt: TTTCCACCAGGGGAT mu: TTTCCACCAAGGGAT	TCCA\|ccag
Donor increased	83658	wt: 0.65 / mu: 0.95	wt: CACCAGGGGATTTCC mu: CACCAAGGGATTTCC	CCAG\|ggga
Acc gained	83660	0.60	mu: CGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCACC	aagg\|GATT
Donor gained	83653	0.94	mu: TTTTCCACCAAGGGA	TTCC\|acca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

709

mutated

not conserved

709

Ptroglodytes

not conserved

ENSPTRG00000006297

738

Mmulatta

not conserved

ENSMMUG00000021121

739

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000021000

740

Ggallus

not conserved

ENSGALG00000010189

1258

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000023516

623

Dmelanogaster

no alignment

FBgn0031842

n/a

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
502	804	COMPBIAS	Pro-rich.	lost
776	776	CONFLICT	S -> F (in Ref. 2; AAN77610).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2328 / 2328

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

776 / 776

position of stopcodon in wt / mu cDNA

3060 / 3060

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

733 / 733

chromosome

strand

last intron/exon boundary

2894

theoretical NMD boundary in CDS

2111

length of CDS

2328

coding sequence (CDS) position

2125

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

2857

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

83658

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

39818145

original gDNA sequence snippet

CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA

altered gDNA sequence snippet

CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA

original cDNA sequence snippet

CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA

altered cDNA sequence snippet

CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA

wildtype AA sequence

mutated AA sequence

MRPDSNLYGF PWELVICAAV VGFFAVLFFL WRSFRSVRSR LYVGREKKLA LMLSGLIEEK
SKLLEKFSLV QKEYEGYEVE SSLKDASFEK EATEAQSLEA TCEKLNRSNS ELEDEILCLE
KELKEEKSKH SEQDELMADI SKRIQSLEDE SKSLKSQVAE AKMTFKIFQM NEERLKIAIK
DALNENSQLQ ESQKQLLQEA EVWKEQVSEL NKQKVTFEDS KVHAEQVLND KESHIKTLTE
RLLKMKDWAA MLGEDITDDD NLELEMNSES ENGAYLDNPP KGALKKLIHA AKLNASLKTL
EGERNQIYIQ LSEVDKTKEE LTEHIKNLQT EQASLQSENT HFENENQKLQ QKLKVMTELY
QENEMKLHRK LTVEENYRLE KEEKLSKVDE KISHATEELE TYRKRAKDLE EELERTIHSY
QGQIISHEKK AHDNWLAARN AERNLNDLRK ENAHNRQKLT ETELKFELLE KDPYALDVPN
TAFGREHSPY GPSPLGWPSS ETRAFLSPPT LLEGPLRLSP LLPGGGGRGS RGPGNPLDHQ
ITNERGESSC DRLTDPHRAP SDTGSLSPPW DQDRRMMFPP PGQSYPDSAL PPQRQDRFCS
NSGRLSGPAE LRSFNMPSLD KMDGSMPSEM ESSRNDTKDD LGNLNVPDSS LPAENEATGP
GFVPPPLAPI RGPLFPVDAR GPFLRRGPPF PPPPPGAMFG ASRDYFPPRD FPGPPPAPFA
MRNVYPPRGF PPYLPPRPGF FPPPPHSEGR SEFPSGLIPP SNEPATEHPE PQQET*

speed

0.44 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999728047416 (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)

chr14:39818145G>AN/A show variant in all transcripts IGV

HGNC symbol

MIA2

Ensembl transcript ID

ENST00000396158

Genbank transcript ID

NM_001247989

UniProt peptide

O15320

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2227G>A
cDNA.2563G>A
g.83658G>A

AA changes

G743R Score: 125 explain score(s)

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

743

frameshift

known variant

Reference ID: rs1060878

database	homozygous (A/A)	heterozygous	allele carriers
1000G	259	1038	1297
ExAC	7734	17299	25033

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.362	0.999
	0.326	0.999
(flanking)	3.54	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	83658	wt: 0.6961 / mu: 0.7634 (marginal change - not scored)	wt: CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA mu: CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA	ccag\|GGGA
Acc increased	83655	wt: 0.24 / mu: 0.37	wt: CTTCTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCA mu: CTTCTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCA	ccac\|CAGG
Donor increased	83654	wt: 0.22 / mu: 0.85	wt: TTTCCACCAGGGGAT mu: TTTCCACCAAGGGAT	TCCA\|ccag
Donor increased	83658	wt: 0.65 / mu: 0.95	wt: CACCAGGGGATTTCC mu: CACCAAGGGATTTCC	CCAG\|ggga
Acc gained	83660	0.60	mu: CGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCACC	aagg\|GATT
Donor gained	83653	0.94	mu: TTTTCCACCAAGGGA	TTCC\|acca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

743

mutated

not conserved

743

Ptroglodytes

not conserved

ENSPTRG00000006297

738

Mmulatta

not conserved

ENSMMUG00000021121

739

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000021000

740

Ggallus

not conserved

ENSGALG00000010189

1259

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000023516

625

Dmelanogaster

no alignment

FBgn0031842

n/a

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
502	804	COMPBIAS	Pro-rich.	lost
776	776	CONFLICT	S -> F (in Ref. 2; AAN77610).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2430 / 2430

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

810 / 810

position of stopcodon in wt / mu cDNA

2766 / 2766

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

337 / 337

chromosome

strand

last intron/exon boundary

2600

theoretical NMD boundary in CDS

2213

length of CDS

2430

coding sequence (CDS) position

2227

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

2563

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

83658

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

39818145

original gDNA sequence snippet

CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA

altered gDNA sequence snippet

CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA

original cDNA sequence snippet

CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA

altered cDNA sequence snippet

CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA

wildtype AA sequence

MEEPGVTPQP YLGLLLEELR RVVAALPEGM RPDSNLYGFP WELVICAAVV GFFAVLFFLW
RSFRSVRSRL YVGREKKLAL MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE
ATEAQSLEVE NQMATCEKLN RSNSELEDEI LCLEKELKEE KSKHSEQDEL MADISKRIQS
LEDESKSLKS QVAEAKMTFK IFQMNEERLK IAIKDALNEN SQLQESQKQL LQEAEVWKEQ
VSELNKQKVT FEDSKVHAEQ VLNDKESHIK TLTERLLKMK DWAAMLGEDI TDDDNLELEM
NSESENGAYL DNPPKGALKK LIHAAKLNAS LKTLEGERNQ IYIQLSEVDK TKEELTEHIK
NLQTEQASLQ SENTHFENEN QKLQQKLKVM TELYQENEMK LHRKLTVEEN YRLEKEEKLS
KVDEKISHAT EELETYRKRA KDLEEELERT IHSYQGQIIS HEKKAHDNWL AARNAERNLN
DLRKENAHNR QKLTETELKF ELLEKDPYAL DVPNTAFGRE HSPYGPSPLG WPSSETRAFL
SPPTLLEGPL RLSPLLPGGG GRGSRGPGNP LDHQITNERG ESSCDRLTDP HRAPSDTGSL
SPPWDQDRRM MFPPPGQSYP DSALPPQRQD RFCSNSGRLS GPAELRSFNM PSLDKMDGSM
PSEMESSRND TKDDLGNLNV PDSSLPAENE ATGPGFVPPP LAPIRGPLFP VDARGPFLRR
GPPFPPPPPG AMFGASRDYF PPGDFPGPPP APFAMRNVYP PRGFPPYLPP RPGFFPPPPH
SEGRSEFPSG LIPPSNEPAT EHPEPQQET*

mutated AA sequence

MEEPGVTPQP YLGLLLEELR RVVAALPEGM RPDSNLYGFP WELVICAAVV GFFAVLFFLW
RSFRSVRSRL YVGREKKLAL MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE
ATEAQSLEVE NQMATCEKLN RSNSELEDEI LCLEKELKEE KSKHSEQDEL MADISKRIQS
LEDESKSLKS QVAEAKMTFK IFQMNEERLK IAIKDALNEN SQLQESQKQL LQEAEVWKEQ
VSELNKQKVT FEDSKVHAEQ VLNDKESHIK TLTERLLKMK DWAAMLGEDI TDDDNLELEM
NSESENGAYL DNPPKGALKK LIHAAKLNAS LKTLEGERNQ IYIQLSEVDK TKEELTEHIK
NLQTEQASLQ SENTHFENEN QKLQQKLKVM TELYQENEMK LHRKLTVEEN YRLEKEEKLS
KVDEKISHAT EELETYRKRA KDLEEELERT IHSYQGQIIS HEKKAHDNWL AARNAERNLN
DLRKENAHNR QKLTETELKF ELLEKDPYAL DVPNTAFGRE HSPYGPSPLG WPSSETRAFL
SPPTLLEGPL RLSPLLPGGG GRGSRGPGNP LDHQITNERG ESSCDRLTDP HRAPSDTGSL
SPPWDQDRRM MFPPPGQSYP DSALPPQRQD RFCSNSGRLS GPAELRSFNM PSLDKMDGSM
PSEMESSRND TKDDLGNLNV PDSSLPAENE ATGPGFVPPP LAPIRGPLFP VDARGPFLRR
GPPFPPPPPG AMFGASRDYF PPRDFPGPPP APFAMRNVYP PRGFPPYLPP RPGFFPPPPH
SEGRSEFPSG LIPPSNEPAT EHPEPQQET*

speed

0.18 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999994276299178 (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)

chr14:39818145G>AN/A show variant in all transcripts IGV

HGNC symbol

MIA2

Ensembl transcript ID

ENST00000348007

Genbank transcript ID

NM_001247988

UniProt peptide

O15320

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2083G>A
cDNA.2129G>A
g.83658G>A

AA changes

G695R Score: 125 explain score(s)

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

695

frameshift

known variant

Reference ID: rs1060878

database	homozygous (A/A)	heterozygous	allele carriers
1000G	259	1038	1297
ExAC	7734	17299	25033

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.362	0.999
	0.326	0.999
(flanking)	3.54	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	83658	wt: 0.6961 / mu: 0.7634 (marginal change - not scored)	wt: CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA mu: CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA	ccag\|GGGA
Acc increased	83655	wt: 0.24 / mu: 0.37	wt: CTTCTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCA mu: CTTCTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCA	ccac\|CAGG
Donor increased	83654	wt: 0.22 / mu: 0.85	wt: TTTCCACCAGGGGAT mu: TTTCCACCAAGGGAT	TCCA\|ccag
Donor increased	83658	wt: 0.65 / mu: 0.95	wt: CACCAGGGGATTTCC mu: CACCAAGGGATTTCC	CCAG\|ggga
Acc gained	83660	0.60	mu: CGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCACC	aagg\|GATT
Donor gained	83653	0.94	mu: TTTTCCACCAAGGGA	TTCC\|acca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

695

mutated

not conserved

695

Ptroglodytes

not conserved

ENSPTRG00000006297

738

Mmulatta

not conserved

ENSMMUG00000021121

739

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000021000

740

Ggallus

not conserved

ENSGALG00000010189

1259

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000023516

635

Dmelanogaster

not conserved

FBgn0031842

1329

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
502	804	COMPBIAS	Pro-rich.	lost
776	776	CONFLICT	S -> F (in Ref. 2; AAN77610).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2286 / 2286

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

762 / 762

position of stopcodon in wt / mu cDNA

2332 / 2332

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

47 / 47

chromosome

strand

last intron/exon boundary

2166

theoretical NMD boundary in CDS

2069

length of CDS

2286

coding sequence (CDS) position

2083

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

2129

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

83658

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

39818145

original gDNA sequence snippet

CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA

altered gDNA sequence snippet

CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA

original cDNA sequence snippet

CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA

altered cDNA sequence snippet

CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA

wildtype AA sequence

MEEPGVTPQP YLGLLLEELR RVVAALPEGM RPDSNLYGFP WELVICAAVV GFFAVLFFLW
RSFRSVRSRL YVGREKKLAL MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE
ATEAQSLEAT CEKLNRSNSE LEDEILCLEK ELKEEKSKHS EQDELMADIS KRIQSLEDES
KSLKSQVAEA KMTFKIFQMN EERLKIAIKD ALNENSQLQE SQKQLLQEAE VWKEQVSELN
KQKVTFEDSK VHAEQVLNDK ESHIKTLTER LLKMKDWAAM LGEDITDDDN LELEMNSESE
NGAYLDNPPK GALKKLIHAA KLNASLKTLE GERNQIYIQL SEVDKTKEEL TEHIKNLQTE
QASLQSENTH FENENQKLQQ KLKVMTELYQ ENEMKLHRKL TVEENYRLEK EEKLSKVDEK
ISHATEELET YRKRAKDLEE ELERTIHSYQ GQIISHEKKA HDNWLAARNA ERNLNDLRKE
NAHNRQKLTE TELKFELLEK DPYALDVPNT AFGRGSRGPG NPLDHQITNE RGESSCDRLT
DPHRAPSDTG SLSPPWDQDR RMMFPPPGQS YPDSALPPQR QDRFCSNSGR LSGPAELRSF
NMPSLDKMDG SMPSEMESSR NDTKDDLGNL NVPDSSLPAE NEATGPGFVP PPLAPIRGPL
FPVDARGPFL RRGPPFPPPP PGAMFGASRD YFPPGDFPGP PPAPFAMRNV YPPRGFPPYL
PPRPGFFPPP PHSEGRSEFP SGLIPPSNEP ATEHPEPQQE T*

mutated AA sequence

MEEPGVTPQP YLGLLLEELR RVVAALPEGM RPDSNLYGFP WELVICAAVV GFFAVLFFLW
RSFRSVRSRL YVGREKKLAL MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE
ATEAQSLEAT CEKLNRSNSE LEDEILCLEK ELKEEKSKHS EQDELMADIS KRIQSLEDES
KSLKSQVAEA KMTFKIFQMN EERLKIAIKD ALNENSQLQE SQKQLLQEAE VWKEQVSELN
KQKVTFEDSK VHAEQVLNDK ESHIKTLTER LLKMKDWAAM LGEDITDDDN LELEMNSESE
NGAYLDNPPK GALKKLIHAA KLNASLKTLE GERNQIYIQL SEVDKTKEEL TEHIKNLQTE
QASLQSENTH FENENQKLQQ KLKVMTELYQ ENEMKLHRKL TVEENYRLEK EEKLSKVDEK
ISHATEELET YRKRAKDLEE ELERTIHSYQ GQIISHEKKA HDNWLAARNA ERNLNDLRKE
NAHNRQKLTE TELKFELLEK DPYALDVPNT AFGRGSRGPG NPLDHQITNE RGESSCDRLT
DPHRAPSDTG SLSPPWDQDR RMMFPPPGQS YPDSALPPQR QDRFCSNSGR LSGPAELRSF
NMPSLDKMDG SMPSEMESSR NDTKDDLGNL NVPDSSLPAE NEATGPGFVP PPLAPIRGPL
FPVDARGPFL RRGPPFPPPP PGAMFGASRD YFPPRDFPGP PPAPFAMRNV YPPRGFPPYL
PPRPGFFPPP PHSEGRSEFP SGLIPPSNEP ATEHPEPQQE T*

speed

0.70 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999948942066861 (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)

chr14:39818145G>AN/A show variant in all transcripts IGV

HGNC symbol

MIA2

Ensembl transcript ID

ENST00000341502

Genbank transcript ID

N/A

UniProt peptide

O15320

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2212G>A
cDNA.2548G>A
g.83658G>A

AA changes

G738R Score: 125 explain score(s)

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

738

frameshift

known variant

Reference ID: rs1060878

database	homozygous (A/A)	heterozygous	allele carriers
1000G	259	1038	1297
ExAC	7734	17299	25033

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.362	0.999
	0.326	0.999
(flanking)	3.54	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	83658	wt: 0.6961 / mu: 0.7634 (marginal change - not scored)	wt: CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA mu: CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA	ccag\|GGGA
Acc increased	83655	wt: 0.24 / mu: 0.37	wt: CTTCTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCA mu: CTTCTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCA	ccac\|CAGG
Donor increased	83654	wt: 0.22 / mu: 0.85	wt: TTTCCACCAGGGGAT mu: TTTCCACCAAGGGAT	TCCA\|ccag
Donor increased	83658	wt: 0.65 / mu: 0.95	wt: CACCAGGGGATTTCC mu: CACCAAGGGATTTCC	CCAG\|ggga
Acc gained	83660	0.60	mu: CGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCACC	aagg\|GATT
Donor gained	83653	0.94	mu: TTTTCCACCAAGGGA	TTCC\|acca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

738

mutated

not conserved

738

Ptroglodytes

not conserved

ENSPTRG00000006297

738

Mmulatta

not conserved

ENSMMUG00000021121

739

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000021000

740

Ggallus

not conserved

ENSGALG00000010189

1259

Trubripes

no homologue

Drerio

all identical

ENSDARG00000023516

639

PRAPVPFPQHMGFLPPRAPSDSFTH

Dmelanogaster

no alignment

FBgn0031842

n/a

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
502	804	COMPBIAS	Pro-rich.	lost
776	776	CONFLICT	S -> F (in Ref. 2; AAN77610).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2316 / 2316

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

772 / 772

position of stopcodon in wt / mu cDNA

2652 / 2652

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

337 / 337

chromosome

strand

last intron/exon boundary

2585

theoretical NMD boundary in CDS

2198

length of CDS

2316

coding sequence (CDS) position

2212

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

2548

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

83658

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

39818145

original gDNA sequence snippet

CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA

altered gDNA sequence snippet

CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA

original cDNA sequence snippet

CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA

altered cDNA sequence snippet

CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA

wildtype AA sequence

mutated AA sequence

speed

0.47 s

Problems

data problem

No NCBI gene ID found for this transcript

back to results table