MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000315489
Querying Taster for transcript #2: ENST00000382696
MT speed 0 s - this script 4.131633 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ODF3L2	polymorphism_automatic	4.54283899387065e-09	simple_aae				V135A	single base exchange	rs34551779		show file
ODF3L2	polymorphism_automatic	1.34855170363934e-08	simple_aae				V99A	single base exchange	rs34551779		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999995457161 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:464310A>GN/A show variant in all transcripts IGV

HGNC symbol

ODF3L2

Ensembl transcript ID

ENST00000315489

Genbank transcript ID

NM_182577

UniProt peptide

Q3SX64

alteration type

single base exchange

alteration region

CDS

DNA changes

c.404T>C
cDNA.640T>C
g.10674T>C

AA changes

V135A Score: 64 explain score(s)

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

135

frameshift

known variant

Reference ID: rs34551779

database	homozygous (G/G)	heterozygous	allele carriers
1000G	548	1092	1640
ExAC	1396	3800	5196

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.73	0.284
	-0.107	0.01
(flanking)	-0.582	0

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

135

mutated

not conserved

135

Ptroglodytes

all identical

ENSPTRG00000010148

Mmulatta

all identical

ENSMMUG00000032205

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000035963

135

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000009610

107

Drerio

all conserved

ENSDARG00000014209

111

Dmelanogaster

not conserved

FBgn0039104

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
118	245	COMPBIAS	Pro-rich.	lost
122	148	REPEAT	STPGR 1.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

870 / 870

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

290 / 290

position of stopcodon in wt / mu cDNA

1106 / 1106

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

237 / 237

chromosome

strand

-1

last intron/exon boundary

586

theoretical NMD boundary in CDS

299

length of CDS

870

coding sequence (CDS) position

404

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

640

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

10674

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

464310

original gDNA sequence snippet

CCCAGAGAAGGTGCCCCCTGTGCGCCATCGGACACCGCCGG

altered gDNA sequence snippet

CCCAGAGAAGGTGCCCCCTGCGCGCCATCGGACACCGCCGG

original cDNA sequence snippet

CCCAGAGAAGGTGCCCCCTGTGCGCCATCGGACACCGCCGG

altered cDNA sequence snippet

CCCAGAGAAGGTGCCCCCTGCGCGCCATCGGACACCGCCGG

wildtype AA sequence

MGTLSCDSTP RLATAPLGRR VTEGQIPETG LRKSCGTATL ENGSGPGLYV LPSTVGFINH
DCTRVASPAY SLVRRPSEAP PQDTSPGPIY FLDPKVTRFG RSCTPAYSMQ GRAKSRGPEV
TPGPGAYSPE KVPPVRHRTP PAFTLGCRLP LKPLDTSAPA PNAYTMPPLW GSQIFTKPSS
PSYTVVGRTP PARPPQDPAE IPGPGQYDSP DANTYRQRLP AFTMLGRPRA PRPLEETPGP
GAHCPEQVTV NKARAPAFSM GIRHSKRAST MAATTPSRPA GHRLPGRCC*

mutated AA sequence

MGTLSCDSTP RLATAPLGRR VTEGQIPETG LRKSCGTATL ENGSGPGLYV LPSTVGFINH
DCTRVASPAY SLVRRPSEAP PQDTSPGPIY FLDPKVTRFG RSCTPAYSMQ GRAKSRGPEV
TPGPGAYSPE KVPPARHRTP PAFTLGCRLP LKPLDTSAPA PNAYTMPPLW GSQIFTKPSS
PSYTVVGRTP PARPPQDPAE IPGPGQYDSP DANTYRQRLP AFTMLGRPRA PRPLEETPGP
GAHCPEQVTV NKARAPAFSM GIRHSKRAST MAATTPSRPA GHRLPGRCC*

speed

1.30 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: 0.999999986514483 (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)

chr19:464310A>GN/A show variant in all transcripts IGV

HGNC symbol

ODF3L2

Ensembl transcript ID

ENST00000382696

Genbank transcript ID

N/A

UniProt peptide

Q3SX64

alteration type

single base exchange

alteration region

CDS

DNA changes

c.296T>C
cDNA.429T>C
g.10674T>C

AA changes

V99A Score: 64 explain score(s)

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

frameshift

known variant

Reference ID: rs34551779

database	homozygous (G/G)	heterozygous	allele carriers
1000G	548	1092	1640
ExAC	1396	3800	5196

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.73	0.284
	-0.107	0.01
(flanking)	-0.582	0

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000010148

Mmulatta

all identical

ENSMMUG00000032205

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000035963

135

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000009610

107

Drerio

all conserved

ENSDARG00000014209

111

Dmelanogaster

not conserved

FBgn0039104

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

762 / 762

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

254 / 254

position of stopcodon in wt / mu cDNA

895 / 895

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

134 / 134

chromosome

strand

-1

last intron/exon boundary

375

theoretical NMD boundary in CDS

191

length of CDS

762

coding sequence (CDS) position

296

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

429

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

10674

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

464310

original gDNA sequence snippet

CCCAGAGAAGGTGCCCCCTGTGCGCCATCGGACACCGCCGG

altered gDNA sequence snippet

CCCAGAGAAGGTGCCCCCTGCGCGCCATCGGACACCGCCGG

original cDNA sequence snippet

CCCAGAGAAGGTGCCCCCTGTGCGCCATCGGACACCGCCGG

altered cDNA sequence snippet

CCCAGAGAAGGTGCCCCCTGCGCGCCATCGGACACCGCCGG

wildtype AA sequence

MGTLSCDSTP RLATAPLGRR VTEGQIPETG LRKSCGTATL ENAPPQDTSP GPIYFLDPKV
TRFGRSCTPA YSMQGRAKSR GPEVTPGPGA YSPEKVPPVR HRTPPAFTLG CRLPLKPLDT
SAPAPNAYTM PPLWGSQIFT KPSSPSYTVV GRTPPARPPQ DPAEIPGPGQ YDSPDANTYR
QRLPAFTMLG RPRAPRPLEE TPGPGAHCPE QVTVNKARAP AFSMGIRHSK RASTMAATTP
SRPAGHRLPG RCC*

mutated AA sequence

MGTLSCDSTP RLATAPLGRR VTEGQIPETG LRKSCGTATL ENAPPQDTSP GPIYFLDPKV
TRFGRSCTPA YSMQGRAKSR GPEVTPGPGA YSPEKVPPAR HRTPPAFTLG CRLPLKPLDT
SAPAPNAYTM PPLWGSQIFT KPSSPSYTVV GRTPPARPPQ DPAEIPGPGQ YDSPDANTYR
QRLPAFTMLG RPRAPRPLEE TPGPGAHCPE QVTVNKARAP AFSMGIRHSK RASTMAATTP
SRPAGHRLPG RCC*

speed

0.89 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems