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: ENST00000542120
Querying Taster for transcript #2: ENST00000539867
Querying Taster for transcript #3: ENST00000229088
MT speed 2.62 s - this script 3.887208 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
TBC1D30	polymorphism_automatic	1.23959953413078e-10	simple_aae				V475I	single base exchange	rs939875		show file
TBC1D30	polymorphism_automatic	1.23959953413078e-10	simple_aae				V589I	single base exchange	rs939875		show file
TBC1D30	polymorphism_automatic	1.23959953413078e-10	simple_aae				V752I	single base exchange	rs939875		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999987604 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:65269047G>AN/A show variant in all transcripts IGV

HGNC symbol

TBC1D30

Ensembl transcript ID

ENST00000542120

Genbank transcript ID

N/A

UniProt peptide

Q9Y2I9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1423G>A
cDNA.1668G>A
g.94459G>A

AA changes

V475I Score: 29 explain score(s)

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

475

frameshift

known variant

Reference ID: rs939875

database	homozygous (A/A)	heterozygous	allele carriers
1000G	368	346	714
ExAC	135	502	637

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.187	0.008
	-0.835	0.002
(flanking)	2.564	0.189

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 marginally increased	94456	wt: 0.5767 / mu: 0.6206 (marginal change - not scored)	wt: GGGACACCGTAGGGC mu: GGGACACCATAGGGC	GACA\|ccgt

distance from splice site

267

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

475

mutated

all conserved

475

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000003180

539

Fcatus

all identical

ENSFCAG00000007198

475

Mmusculus

all identical

ENSMUSG00000052302

590

Ggallus

all conserved

ENSGALG00000009859

538

Trubripes

not conserved

ENSTRUG00000012364

626

Drerio

all conserved

ENSDARG00000075281

740

Dmelanogaster

not conserved

FBgn0261928

1301

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000030378

763

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1944 / 1944

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

648 / 648

position of stopcodon in wt / mu cDNA

2189 / 2189

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

246 / 246

chromosome

strand

last intron/exon boundary

1402

theoretical NMD boundary in CDS

1106

length of CDS

1944

coding sequence (CDS) position

1423

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

1668

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

94459

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

65269047

original gDNA sequence snippet

ATCCGGGCTGTGGGGACACCGTAGGGCTGATAGATGAGCAG

altered gDNA sequence snippet

ATCCGGGCTGTGGGGACACCATAGGGCTGATAGATGAGCAG

original cDNA sequence snippet

ATCCGGGCTGTGGGGACACCGTAGGGCTGATAGATGAGCAG

altered cDNA sequence snippet

ATCCGGGCTGTGGGGACACCATAGGGCTGATAGATGAGCAG

wildtype AA sequence

MRFTFNERSN PDDDSMGIQI VKDLHRTGCS SYCGQEAEQD RVVLKRVLLA YARWNKTVGY
CQGFNILAAL ILEVMEGNEG DALKIMIYLI DKVLPESYFV NNLRALSVDM AVFRDLLRMK
LPELSQHLDT LQRTANKESG GGYEPPLTNV FTMQWFLTLF ATCLPNQTVL KIWDSVFFEG
SEIILRVSLA IWAKLGEQIE CCETADEFYS TMGRLTQEML ENDLLQSHEL MQTVYSMAPF
PFPQLAELRE KYTYNITPFP ATVKPTSVSG RHSKARDSDE ENDPDDEDAV VNAVGCLGPF
SGFLAPELQK YQKQIKEPNE EQSLRSNNIA ELSPGAINSC RSEYHAAFNS MMMERMTTDI
NALKRQYSRI KKKQQQQVHQ VYIRADKGPV TSILPSQVNS SPVINHLLLG KKMKMTNRAA
KNAVIHIPGH TGGKISPVPY EDLKTKLNSP WRTHIRVHKK NMPRTKSHPG CGDTVGLIDE
QNEASKTNGL GAAEAFPSGC TATAGREGSS PEGSTRRTIE GQSPEPVFGD ADVDVSAVQA
KLGALELNQR DAAAETELRV HPPCQRHCPE PPSAPEENKA TSKAPQGSNS KTPIFSPFPS
VKPLRKSATA RNLGLYGPTE RTPTVHFPQM SRSFSKPGGG NSGTKKR*

mutated AA sequence

MRFTFNERSN PDDDSMGIQI VKDLHRTGCS SYCGQEAEQD RVVLKRVLLA YARWNKTVGY
CQGFNILAAL ILEVMEGNEG DALKIMIYLI DKVLPESYFV NNLRALSVDM AVFRDLLRMK
LPELSQHLDT LQRTANKESG GGYEPPLTNV FTMQWFLTLF ATCLPNQTVL KIWDSVFFEG
SEIILRVSLA IWAKLGEQIE CCETADEFYS TMGRLTQEML ENDLLQSHEL MQTVYSMAPF
PFPQLAELRE KYTYNITPFP ATVKPTSVSG RHSKARDSDE ENDPDDEDAV VNAVGCLGPF
SGFLAPELQK YQKQIKEPNE EQSLRSNNIA ELSPGAINSC RSEYHAAFNS MMMERMTTDI
NALKRQYSRI KKKQQQQVHQ VYIRADKGPV TSILPSQVNS SPVINHLLLG KKMKMTNRAA
KNAVIHIPGH TGGKISPVPY EDLKTKLNSP WRTHIRVHKK NMPRTKSHPG CGDTIGLIDE
QNEASKTNGL GAAEAFPSGC TATAGREGSS PEGSTRRTIE GQSPEPVFGD ADVDVSAVQA
KLGALELNQR DAAAETELRV HPPCQRHCPE PPSAPEENKA TSKAPQGSNS KTPIFSPFPS
VKPLRKSATA RNLGLYGPTE RTPTVHFPQM SRSFSKPGGG NSGTKKR*

speed

0.82 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: 0.99999999987604 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:65269047G>AN/A show variant in all transcripts IGV

HGNC symbol

TBC1D30

Ensembl transcript ID

ENST00000539867

Genbank transcript ID

NM_015279

UniProt peptide

Q9Y2I9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1765G>A
cDNA.2073G>A
g.94459G>A

AA changes

V589I Score: 29 explain score(s)

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

589

frameshift

known variant

Reference ID: rs939875

database	homozygous (A/A)	heterozygous	allele carriers
1000G	368	346	714
ExAC	135	502	637

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.187	0.008
	-0.835	0.002
(flanking)	2.564	0.189

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 marginally increased	94456	wt: 0.5767 / mu: 0.6206 (marginal change - not scored)	wt: GGGACACCGTAGGGC mu: GGGACACCATAGGGC	GACA\|ccgt

distance from splice site

267

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

589

mutated

all conserved

589

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000003180

539

Fcatus

all identical

ENSFCAG00000007198

475

Mmusculus

all identical

ENSMUSG00000052302

590

Ggallus

all conserved

ENSGALG00000009859

538

Trubripes

not conserved

ENSTRUG00000012364

626

Drerio

all conserved

ENSDARG00000075281

740

Dmelanogaster

not conserved

FBgn0261928

1301

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000030378

763

protein features

no protein features affected

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

2594 / 2594

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

309 / 309

chromosome

strand

last intron/exon boundary

1807

theoretical NMD boundary in CDS

1448

length of CDS

2286

coding sequence (CDS) position

1765

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

2073

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

94459

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

65269047

original gDNA sequence snippet

ATCCGGGCTGTGGGGACACCGTAGGGCTGATAGATGAGCAG

altered gDNA sequence snippet

ATCCGGGCTGTGGGGACACCATAGGGCTGATAGATGAGCAG

original cDNA sequence snippet

ATCCGGGCTGTGGGGACACCGTAGGGCTGATAGATGAGCAG

altered cDNA sequence snippet

ATCCGGGCTGTGGGGACACCATAGGGCTGATAGATGAGCAG

wildtype AA sequence

MRQDKLTGSL RRGGRCLKRQ GGGVGTILSN VLKKRSCISR TAPRLLCTLE PGVDTKLKFT
LEPSLGQNGF QQWYDALKAV ARLSTGIPKE WRRKVWLTLA DHYLHSIAID WDKTMRFTFN
ERSNPDDDSM GIQIVKDLHR TGCSSYCGQE AEQDRVVLKR VLLAYARWNK TVGYCQGFNI
LAALILEVME GNEGDALKIM IYLIDKVLPE SYFVNNLRAL SVDMAVFRDL LRMKLPELSQ
HLDTLQRTAN KESGGGYEPP LTNVFTMQWF LTLFATCLPN QTVLKIWDSV FFEGSEIILR
VSLAIWAKLG EQIECCETAD EFYSTMGRLT QEMLENDLLQ SHELMQTVYS MAPFPFPQLA
ELREKYTYNI TPFPATVKPT SVSGRHSKAR DSDEENDPDD EDAVVNAVGC LGPFSGFLAP
ELQKYQKQIK EPNEEQSLRS NNIAELSPGA INSCRSEYHA AFNSMMMERM TTDINALKRQ
YSRIKKKQQQ QVHQVYIRAD KGPVTSILPS QVNSSPVINH LLLGKKMKMT NRAAKNAVIH
IPGHTGGKIS PVPYEDLKTK LNSPWRTHIR VHKKNMPRTK SHPGCGDTVG LIDEQNEASK
TNGLGAAEAF PSGCTATAGR EGSSPEGSTR RTIEGQSPEP VFGDADVDVS AVQAKLGALE
LNQRDAAAET ELRVHPPCQR HCPEPPSAPE ENKATSKAPQ GSNSKTPIFS PFPSVKPLRK
SATARNLGLY GPTERTPTVH FPQMSRSFSK PGGGNSGTKK R*

mutated AA sequence

MRQDKLTGSL RRGGRCLKRQ GGGVGTILSN VLKKRSCISR TAPRLLCTLE PGVDTKLKFT
LEPSLGQNGF QQWYDALKAV ARLSTGIPKE WRRKVWLTLA DHYLHSIAID WDKTMRFTFN
ERSNPDDDSM GIQIVKDLHR TGCSSYCGQE AEQDRVVLKR VLLAYARWNK TVGYCQGFNI
LAALILEVME GNEGDALKIM IYLIDKVLPE SYFVNNLRAL SVDMAVFRDL LRMKLPELSQ
HLDTLQRTAN KESGGGYEPP LTNVFTMQWF LTLFATCLPN QTVLKIWDSV FFEGSEIILR
VSLAIWAKLG EQIECCETAD EFYSTMGRLT QEMLENDLLQ SHELMQTVYS MAPFPFPQLA
ELREKYTYNI TPFPATVKPT SVSGRHSKAR DSDEENDPDD EDAVVNAVGC LGPFSGFLAP
ELQKYQKQIK EPNEEQSLRS NNIAELSPGA INSCRSEYHA AFNSMMMERM TTDINALKRQ
YSRIKKKQQQ QVHQVYIRAD KGPVTSILPS QVNSSPVINH LLLGKKMKMT NRAAKNAVIH
IPGHTGGKIS PVPYEDLKTK LNSPWRTHIR VHKKNMPRTK SHPGCGDTIG LIDEQNEASK
TNGLGAAEAF PSGCTATAGR EGSSPEGSTR RTIEGQSPEP VFGDADVDVS AVQAKLGALE
LNQRDAAAET ELRVHPPCQR HCPEPPSAPE ENKATSKAPQ GSNSKTPIFS PFPSVKPLRK
SATARNLGLY GPTERTPTVH FPQMSRSFSK PGGGNSGTKK R*

speed

0.92 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999987604 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:65269047G>AN/A show variant in all transcripts IGV

HGNC symbol

TBC1D30

Ensembl transcript ID

ENST00000229088

Genbank transcript ID

N/A

UniProt peptide

Q9Y2I9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2254G>A
cDNA.2254G>A
g.94459G>A

AA changes

V752I Score: 29 explain score(s)

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

752

frameshift

known variant

Reference ID: rs939875

database	homozygous (A/A)	heterozygous	allele carriers
1000G	368	346	714
ExAC	135	502	637

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.187	0.008
	-0.835	0.002
(flanking)	2.564	0.189

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 marginally increased	94456	wt: 0.5767 / mu: 0.6206 (marginal change - not scored)	wt: GGGACACCGTAGGGC mu: GGGACACCATAGGGC	GACA\|ccgt

distance from splice site

267

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

752

mutated

all conserved

752

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000003180

539

Fcatus

all identical

ENSFCAG00000007198

475

Mmusculus

all identical

ENSMUSG00000052302

590

Ggallus

all conserved

ENSGALG00000009859

538

Trubripes

not conserved

ENSTRUG00000012364

626

Drerio

all conserved

ENSDARG00000075281

740

Dmelanogaster

not conserved

FBgn0261928

1301

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000030378

763

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2775 / 2775

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

925 / 925

position of stopcodon in wt / mu cDNA

2775 / 2775

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

1 / 1

chromosome

strand

last intron/exon boundary

1988

theoretical NMD boundary in CDS

1937

length of CDS

2775

coding sequence (CDS) position

2254

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

2254

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

94459

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

65269047

original gDNA sequence snippet

ATCCGGGCTGTGGGGACACCGTAGGGCTGATAGATGAGCAG

altered gDNA sequence snippet

ATCCGGGCTGTGGGGACACCATAGGGCTGATAGATGAGCAG

original cDNA sequence snippet

ATCCGGGCTGTGGGGACACCGTAGGGCTGATAGATGAGCAG

altered cDNA sequence snippet

ATCCGGGCTGTGGGGACACCATAGGGCTGATAGATGAGCAG

wildtype AA sequence

MDVLPTGGGR PGLRTELEFR GGGGEARLES QEEETIPAAP PAPRLRGAAE RPRRSRDTWD
GDEDTEPGEA CGGRTSRTAS LVSGLLNELY SCTEEEEAAG GGRGAEGRRR RRDSLDSSTE
ASGSDVVLGG RSGAGDSRVL QELQERPSQR HQMLYLRQKD ANELKTILRE LKYRIGIQSA
KLLRHLKQKD RLLHKVQRNC DIVTACLQAV SQKRRVDTKL KFTLEPSLGQ NGFQQWYDAL
KAVARLSTGI PKEWRRKVWL TLADHYLHSI AIDWDKTMRF TFNERSNPDD DSMGIQIVKD
LHRTGCSSYC GQEAEQDRVV LKRVLLAYAR WNKTVGYCQG FNILAALILE VMEGNEGDAL
KIMIYLIDKV LPESYFVNNL RALSVDMAVF RDLLRMKLPE LSQHLDTLQR TANKESGGGY
EPPLTNVFTM QWFLTLFATC LPNQTVLKIW DSVFFEGSEI ILRVSLAIWA KLGEQIECCE
TADEFYSTMG RLTQEMLEND LLQSHELMQT VYSMAPFPFP QLAELREKYT YNITPFPATV
KPTSVSGRHS KARDSDEEND PDDEDAVVNA VGCLGPFSGF LAPELQKYQK QIKEPNEEQS
LRSNNIAELS PGAINSCRSE YHAAFNSMMM ERMTTDINAL KRQYSRIKKK QQQQVHQVYI
RADKGPVTSI LPSQVNSSPV INHLLLGKKM KMTNRAAKNA VIHIPGHTGG KISPVPYEDL
KTKLNSPWRT HIRVHKKNMP RTKSHPGCGD TVGLIDEQNE ASKTNGLGAA EAFPSGCTAT
AGREGSSPEG STRRTIEGQS PEPVFGDADV DVSAVQAKLG ALELNQRDAA AETELRVHPP
CQRHCPEPPS APEENKATSK APQGSNSKTP IFSPFPSVKP LRKSATARNL GLYGPTERTP
TVHFPQMSRS FSKPGGGNSG TKKR*

mutated AA sequence

MDVLPTGGGR PGLRTELEFR GGGGEARLES QEEETIPAAP PAPRLRGAAE RPRRSRDTWD
GDEDTEPGEA CGGRTSRTAS LVSGLLNELY SCTEEEEAAG GGRGAEGRRR RRDSLDSSTE
ASGSDVVLGG RSGAGDSRVL QELQERPSQR HQMLYLRQKD ANELKTILRE LKYRIGIQSA
KLLRHLKQKD RLLHKVQRNC DIVTACLQAV SQKRRVDTKL KFTLEPSLGQ NGFQQWYDAL
KAVARLSTGI PKEWRRKVWL TLADHYLHSI AIDWDKTMRF TFNERSNPDD DSMGIQIVKD
LHRTGCSSYC GQEAEQDRVV LKRVLLAYAR WNKTVGYCQG FNILAALILE VMEGNEGDAL
KIMIYLIDKV LPESYFVNNL RALSVDMAVF RDLLRMKLPE LSQHLDTLQR TANKESGGGY
EPPLTNVFTM QWFLTLFATC LPNQTVLKIW DSVFFEGSEI ILRVSLAIWA KLGEQIECCE
TADEFYSTMG RLTQEMLEND LLQSHELMQT VYSMAPFPFP QLAELREKYT YNITPFPATV
KPTSVSGRHS KARDSDEEND PDDEDAVVNA VGCLGPFSGF LAPELQKYQK QIKEPNEEQS
LRSNNIAELS PGAINSCRSE YHAAFNSMMM ERMTTDINAL KRQYSRIKKK QQQQVHQVYI
RADKGPVTSI LPSQVNSSPV INHLLLGKKM KMTNRAAKNA VIHIPGHTGG KISPVPYEDL
KTKLNSPWRT HIRVHKKNMP RTKSHPGCGD TIGLIDEQNE ASKTNGLGAA EAFPSGCTAT
AGREGSSPEG STRRTIEGQS PEPVFGDADV DVSAVQAKLG ALELNQRDAA AETELRVHPP
CQRHCPEPPS APEENKATSK APQGSNSKTP IFSPFPSVKP LRKSATARNL GLYGPTERTP
TVHFPQMSRS FSKPGGGNSG TKKR*

speed

0.88 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