MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000288350
Querying Taster for transcript #2: ENST00000358268
Querying Taster for transcript #3: ENST00000380671
MT speed 0 s - this script 3.838965 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
LCA5L	polymorphism_automatic	9.99200722162641e-16	simple_aae		affected		G17S	single base exchange	rs2837029		show file
LCA5L	polymorphism_automatic	9.99200722162641e-16	simple_aae		affected		G17S	single base exchange	rs2837029		show file
LCA5L	polymorphism_automatic	9.99200722162641e-16	simple_aae		affected		G17S	single base exchange	rs2837029		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999999 (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)

chr21:40800371C>TN/A show variant in all transcripts IGV

HGNC symbol

LCA5L

Ensembl transcript ID

ENST00000288350

Genbank transcript ID

NM_152505

UniProt peptide

O95447

alteration type

single base exchange

alteration region

CDS

DNA changes

c.49G>A
cDNA.414G>A
g.17361G>A

AA changes

G17S Score: 56 explain score(s)

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

frameshift

known variant

Reference ID: rs2837029

database	homozygous (T/T)	heterozygous	allele carriers
1000G	172	752	924
ExAC	2713	17934	20647

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.297	0
	-0.421	0
(flanking)	0.348	0.002

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	17361	wt: 0.4765 / mu: 0.5485 (marginal change - not scored)	wt: ATATAGATGAGCATTTCTTCGGCGTGGCATTAGAAAACAAT mu: ATATAGATGAGCATTTCTTCAGCGTGGCATTAGAAAACAAT	ttcg\|GCGT
Donor gained	17361	0.81	mu: TCTTCAGCGTGGCAT	TTCA\|gcgt

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

not conserved

ENSPTRG00000013916

Mmulatta

not conserved

ENSMMUG00000010407

Fcatus

not conserved

ENSFCAG00000008508

Mmusculus

not conserved

ENSMUSG00000045275

Ggallus

not conserved

ENSGALG00000016125

302

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000076153

n/a

Dmelanogaster

no alignment

FBgn0036687

n/a

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
148	259	COILED	Potential.	might get lost (downstream of altered splice site)
305	336	COILED	Potential.	might get lost (downstream of altered splice site)
420	440	COILED	Potential.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2013 / 2013

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

671 / 671

position of stopcodon in wt / mu cDNA

2378 / 2378

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

366 / 366

chromosome

strand

-1

last intron/exon boundary

1648

theoretical NMD boundary in CDS

1232

length of CDS

2013

coding sequence (CDS) position

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

414

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

17361

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

40800371

original gDNA sequence snippet

ATATAGATGAGCATTTCTTCGGCGTGGCATTAGAAAACAAT

altered gDNA sequence snippet

ATATAGATGAGCATTTCTTCAGCGTGGCATTAGAAAACAAT

original cDNA sequence snippet

ATATAGATGAGCATTTCTTCGGCGTGGCATTAGAAAACAAT

altered cDNA sequence snippet

ATATAGATGAGCATTTCTTCAGCGTGGCATTAGAAAACAAT

wildtype AA sequence

MSLADLTKTN IDEHFFGVAL ENNRRSAACK RSPGTGDFSR NSNASNKSVD YSRSQCSCGS
LSSQYDYSED FLCDCSEKAI NRNYLKQPVV KEKEKKKYNV SKISQSKGQK EISVEKKHTW
NASLFNSQIH MIAQRRDAMA HRILSARLHK IKGLKNELAD MHHKLEAILT ENQFLKQLQL
RHLKAIGKYE NSQNNLPQIM AKHQNEVKNL RQLLRKSQEK ERTLSRKLRE TDSQLLKTKD
ILQALQKLSE DKNLAEREEL THKLSIITTK MDANDKKIQS LEKQLRLNCR AFSRQLAIET
RKTLAAQTAT KTLQVEVKHL QQKLKEKDRE LEIKNIYSHR ILKNLHDTED YPKVSSTKSV
QADRKILPFT SMRHQGTQKS DVPPLTTKGK KATGNIDHKE KSTEINHEIP HCVNKLPKQE
DSKRKYEDLS GEEKHLEVQI LLENTGRQKD KKEDQEKKNI FVKEEQELPP KIIEVIHPER
ESNQEDVLVR EKFKRSMQRN GVDDTLGKGT APYTKGPLRQ RRHYSFTEAT ENLHHGLPAS
GGPANAGNMR YSHSTGKHLS NREEMELEHS DSGYEPSFGK SSRIKVKDTT FRDKKSSLME
ELFGSGYVLK TDQSSPGVAK GSEEPLQSKE SHPLPPSQAS TSHAFGDSKV TVVNSIKPSS
PTEGKRKIII *

mutated AA sequence

MSLADLTKTN IDEHFFSVAL ENNRRSAACK RSPGTGDFSR NSNASNKSVD YSRSQCSCGS
LSSQYDYSED FLCDCSEKAI NRNYLKQPVV KEKEKKKYNV SKISQSKGQK EISVEKKHTW
NASLFNSQIH MIAQRRDAMA HRILSARLHK IKGLKNELAD MHHKLEAILT ENQFLKQLQL
RHLKAIGKYE NSQNNLPQIM AKHQNEVKNL RQLLRKSQEK ERTLSRKLRE TDSQLLKTKD
ILQALQKLSE DKNLAEREEL THKLSIITTK MDANDKKIQS LEKQLRLNCR AFSRQLAIET
RKTLAAQTAT KTLQVEVKHL QQKLKEKDRE LEIKNIYSHR ILKNLHDTED YPKVSSTKSV
QADRKILPFT SMRHQGTQKS DVPPLTTKGK KATGNIDHKE KSTEINHEIP HCVNKLPKQE
DSKRKYEDLS GEEKHLEVQI LLENTGRQKD KKEDQEKKNI FVKEEQELPP KIIEVIHPER
ESNQEDVLVR EKFKRSMQRN GVDDTLGKGT APYTKGPLRQ RRHYSFTEAT ENLHHGLPAS
GGPANAGNMR YSHSTGKHLS NREEMELEHS DSGYEPSFGK SSRIKVKDTT FRDKKSSLME
ELFGSGYVLK TDQSSPGVAK GSEEPLQSKE SHPLPPSQAS TSHAFGDSKV TVVNSIKPSS
PTEGKRKIII *

speed

0.72 s

All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999999 (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)

chr21:40800371C>TN/A show variant in all transcripts IGV

HGNC symbol

LCA5L

Ensembl transcript ID

ENST00000358268

Genbank transcript ID

N/A

UniProt peptide

O95447

alteration type

single base exchange

alteration region

CDS

DNA changes

c.49G>A
cDNA.578G>A
g.17361G>A

AA changes

G17S Score: 56 explain score(s)

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

frameshift

known variant

Reference ID: rs2837029

database	homozygous (T/T)	heterozygous	allele carriers
1000G	172	752	924
ExAC	2713	17934	20647

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.297	0
	-0.421	0
(flanking)	0.348	0.002

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	17361	wt: 0.4765 / mu: 0.5485 (marginal change - not scored)	wt: ATATAGATGAGCATTTCTTCGGCGTGGCATTAGAAAACAAT mu: ATATAGATGAGCATTTCTTCAGCGTGGCATTAGAAAACAAT	ttcg\|GCGT
Donor gained	17361	0.81	mu: TCTTCAGCGTGGCAT	TTCA\|gcgt

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

not conserved

ENSPTRG00000013916

Mmulatta

not conserved

ENSMMUG00000010407

Fcatus

not conserved

ENSFCAG00000008508

Mmusculus

not conserved

ENSMUSG00000045275

Ggallus

not conserved

ENSGALG00000016125

302

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000076153

n/a

Dmelanogaster

no alignment

FBgn0036687

n/a

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
148	259	COILED	Potential.	might get lost (downstream of altered splice site)
305	336	COILED	Potential.	might get lost (downstream of altered splice site)
420	440	COILED	Potential.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2013 / 2013

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

671 / 671

position of stopcodon in wt / mu cDNA

2542 / 2542

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

530 / 530

chromosome

strand

-1

last intron/exon boundary

1812

theoretical NMD boundary in CDS

1232

length of CDS

2013

coding sequence (CDS) position

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

578

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

17361

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

40800371

original gDNA sequence snippet

ATATAGATGAGCATTTCTTCGGCGTGGCATTAGAAAACAAT

altered gDNA sequence snippet

ATATAGATGAGCATTTCTTCAGCGTGGCATTAGAAAACAAT

original cDNA sequence snippet

ATATAGATGAGCATTTCTTCGGCGTGGCATTAGAAAACAAT

altered cDNA sequence snippet

ATATAGATGAGCATTTCTTCAGCGTGGCATTAGAAAACAAT

wildtype AA sequence

mutated AA sequence

speed

1.05 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999999 (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)

chr21:40800371C>TN/A show variant in all transcripts IGV

HGNC symbol

LCA5L

Ensembl transcript ID

ENST00000380671

Genbank transcript ID

NM_152505

UniProt peptide

O95447

alteration type

single base exchange

alteration region

CDS

DNA changes

c.49G>A
cDNA.362G>A
g.17361G>A

AA changes

G17S Score: 56 explain score(s)

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

frameshift

known variant

Reference ID: rs2837029

database	homozygous (T/T)	heterozygous	allele carriers
1000G	172	752	924
ExAC	2713	17934	20647

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.297	0
	-0.421	0
(flanking)	0.348	0.002

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	17361	wt: 0.4765 / mu: 0.5485 (marginal change - not scored)	wt: ATATAGATGAGCATTTCTTCGGCGTGGCATTAGAAAACAAT mu: ATATAGATGAGCATTTCTTCAGCGTGGCATTAGAAAACAAT	ttcg\|GCGT
Donor gained	17361	0.81	mu: TCTTCAGCGTGGCAT	TTCA\|gcgt

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

not conserved

ENSPTRG00000013916

Mmulatta

not conserved

ENSMMUG00000010407

Fcatus

not conserved

ENSFCAG00000008508

Mmusculus

not conserved

ENSMUSG00000045275

Ggallus

not conserved

ENSGALG00000016125

302

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000076153

n/a

Dmelanogaster

no alignment

FBgn0036687

n/a

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
148	259	COILED	Potential.	might get lost (downstream of altered splice site)
305	336	COILED	Potential.	might get lost (downstream of altered splice site)
420	440	COILED	Potential.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2013 / 2013

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

671 / 671

position of stopcodon in wt / mu cDNA

2326 / 2326

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

314 / 314

chromosome

strand

-1

last intron/exon boundary

1596

theoretical NMD boundary in CDS

1232

length of CDS

2013

coding sequence (CDS) position

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

362

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

17361

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

40800371

original gDNA sequence snippet

ATATAGATGAGCATTTCTTCGGCGTGGCATTAGAAAACAAT

altered gDNA sequence snippet

ATATAGATGAGCATTTCTTCAGCGTGGCATTAGAAAACAAT

original cDNA sequence snippet

ATATAGATGAGCATTTCTTCGGCGTGGCATTAGAAAACAAT

altered cDNA sequence snippet

ATATAGATGAGCATTTCTTCAGCGTGGCATTAGAAAACAAT

wildtype AA sequence

mutated AA sequence

speed

0.74 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