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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000444636
Querying Taster for transcript #2: ENST00000415673
Querying Taster for transcript #3: ENST00000243810
Querying Taster for transcript #4: ENST00000396563
MT speed 0 s - this script 4.711791 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SP140L	polymorphism_automatic	1.88572538029064e-07	simple_aae				P377S	single base exchange	rs7590429		show file
SP140L	polymorphism_automatic	1.88572538029064e-07	simple_aae				P377S	single base exchange	rs7590429		show file
SP140L	polymorphism_automatic	1.88572538029064e-07	simple_aae				P377S	single base exchange	rs7590429		show file
SP140L	polymorphism_automatic	3.13143209029754e-07	simple_aae				P342S	single base exchange	rs7590429		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999811427462 (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)

chr2:231258150C>TN/A show variant in all transcripts IGV

HGNC symbol

SP140L

Ensembl transcript ID

ENST00000415673

Genbank transcript ID

NM_138402

UniProt peptide

Q9H930

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1129C>T
cDNA.1215C>T
g.66252C>T

AA changes

P377S Score: 74 explain score(s)

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

377

frameshift

known variant

Reference ID: rs7590429

database	homozygous (T/T)	heterozygous	allele carriers
1000G	472	1143	1615
ExAC	8569	15629	24198

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.35	0.334
	0.605	0.34
(flanking)	1.092	0.338

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	66255	wt: 0.5465 / mu: 0.5489 (marginal change - not scored)	wt: GATCTCTACCTAATCCTCCAAGAATATATTACAGGAACAAA mu: GATCTCTACCTAATCCTTCAAGAATATATTACAGGAACAAA	ccaa\|GAAT
Acc marginally increased	66257	wt: 0.5452 / mu: 0.5653 (marginal change - not scored)	wt: TCTCTACCTAATCCTCCAAGAATATATTACAGGAACAAAAA mu: TCTCTACCTAATCCTTCAAGAATATATTACAGGAACAAAAA	aaga\|ATAT
Donor marginally increased	66254	wt: 0.3417 / mu: 0.3453 (marginal change - not scored)	wt: CCTCCAAGAATATAT mu: CCTTCAAGAATATAT	TCCA\|agaa
Donor marginally increased	66250	wt: 0.9412 / mu: 0.9511 (marginal change - not scored)	wt: TAATCCTCCAAGAAT mu: TAATCCTTCAAGAAT	ATCC\|tcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

377

mutated

not conserved

377

Ptroglodytes

all identical

ENSPTRG00000013011

377

Mmulatta

all identical

ENSMMUG00000016575

289

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000055359

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000032669

176

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1743 / 1743

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

581 / 581

position of stopcodon in wt / mu cDNA

1829 / 1829

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

87 / 87

chromosome

strand

last intron/exon boundary

1731

theoretical NMD boundary in CDS

1594

length of CDS

1743

coding sequence (CDS) position

1129

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

1215

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

66252

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

231258150

original gDNA sequence snippet

AAGGATCTCTACCTAATCCTCCAAGAATATATTACAGGAAC

altered gDNA sequence snippet

AAGGATCTCTACCTAATCCTTCAAGAATATATTACAGGAAC

original cDNA sequence snippet

AAGGATCTCTACCTAATCCTCCAAGAATATATTACAGGAAC

altered cDNA sequence snippet

AAGGATCTCTACCTAATCCTTCAAGAATATATTACAGGAAC

wildtype AA sequence

MAGGGSDLST RGLNGGVSQV ANEMNHLPAH SQSLQRLFTE DQDVDEGLVY DTVFKHFKRH
KLEISNAIKK TFPFLEGLRD RELITNKMFE DSEDSCRNLV PVQRVVYNVL SELEKTFNLS
VLEALFSEVN MQEYPDLIHI YKSFKNAIQD KLSFQESDRK EREERPDIKL SLKQGEVPES
PEARKESDQA CGKMDTVDIA NNSTLGKPKR KRRKKKGHGW SRMGTRTQKN NQQNDNSKAD
GQLVSSEKKA NMNLKDLSKI RGRKRGKPGT HFTQSDRAPQ KRVRSRASRK HKDETVDFQA
PLLPVTCGGV KGILHKEKLE QGTLAKCIQT EDGKWFTPME FEIKGGYARS KNWRLSVRCG
GWPLRRLMEE GSLPNPPRIY YRNKKRILKS QNNSSVDPCM RNLDECEVCR DGGELFCCDT
CSRVFHEDCH IPPVESEKTP WNCIFCRMKE SPGSQQCCQE SEVLERQMCP EEQLKCEFLL
LKVYCCSESS FFAKIPYYYY IREACQGLKE PMWLDKIKKR LNEHGYPQVE GFVQDMRLIF
QNHRASYKYK DFGQMGLRLE AEFEKDFKEV FAIQETNGNS *

mutated AA sequence

MAGGGSDLST RGLNGGVSQV ANEMNHLPAH SQSLQRLFTE DQDVDEGLVY DTVFKHFKRH
KLEISNAIKK TFPFLEGLRD RELITNKMFE DSEDSCRNLV PVQRVVYNVL SELEKTFNLS
VLEALFSEVN MQEYPDLIHI YKSFKNAIQD KLSFQESDRK EREERPDIKL SLKQGEVPES
PEARKESDQA CGKMDTVDIA NNSTLGKPKR KRRKKKGHGW SRMGTRTQKN NQQNDNSKAD
GQLVSSEKKA NMNLKDLSKI RGRKRGKPGT HFTQSDRAPQ KRVRSRASRK HKDETVDFQA
PLLPVTCGGV KGILHKEKLE QGTLAKCIQT EDGKWFTPME FEIKGGYARS KNWRLSVRCG
GWPLRRLMEE GSLPNPSRIY YRNKKRILKS QNNSSVDPCM RNLDECEVCR DGGELFCCDT
CSRVFHEDCH IPPVESEKTP WNCIFCRMKE SPGSQQCCQE SEVLERQMCP EEQLKCEFLL
LKVYCCSESS FFAKIPYYYY IREACQGLKE PMWLDKIKKR LNEHGYPQVE GFVQDMRLIF
QNHRASYKYK DFGQMGLRLE AEFEKDFKEV FAIQETNGNS *

speed

0.97 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: 0.999999811427462 (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)

chr2:231258150C>TN/A show variant in all transcripts IGV

HGNC symbol

SP140L

Ensembl transcript ID

ENST00000444636

Genbank transcript ID

N/A

UniProt peptide

Q9H930

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1129C>T
cDNA.1215C>T
g.66252C>T

AA changes

P377S Score: 74 explain score(s)

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

377

frameshift

known variant

Reference ID: rs7590429

database	homozygous (T/T)	heterozygous	allele carriers
1000G	472	1143	1615
ExAC	8569	15629	24198

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.35	0.334
	0.605	0.34
(flanking)	1.092	0.338

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	66255	wt: 0.5465 / mu: 0.5489 (marginal change - not scored)	wt: GATCTCTACCTAATCCTCCAAGAATATATTACAGGAACAAA mu: GATCTCTACCTAATCCTTCAAGAATATATTACAGGAACAAA	ccaa\|GAAT
Acc marginally increased	66257	wt: 0.5452 / mu: 0.5653 (marginal change - not scored)	wt: TCTCTACCTAATCCTCCAAGAATATATTACAGGAACAAAAA mu: TCTCTACCTAATCCTTCAAGAATATATTACAGGAACAAAAA	aaga\|ATAT
Donor marginally increased	66254	wt: 0.3417 / mu: 0.3453 (marginal change - not scored)	wt: CCTCCAAGAATATAT mu: CCTTCAAGAATATAT	TCCA\|agaa
Donor marginally increased	66250	wt: 0.9412 / mu: 0.9511 (marginal change - not scored)	wt: TAATCCTCCAAGAAT mu: TAATCCTTCAAGAAT	ATCC\|tcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

377

mutated

not conserved

377

Ptroglodytes

all identical

ENSPTRG00000013011

377

Mmulatta

all identical

ENSMMUG00000016575

289

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000055359

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000032669

176

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1317 / 1317

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

439 / 439

position of stopcodon in wt / mu cDNA

1403 / 1403

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

87 / 87

chromosome

strand

last intron/exon boundary

1284

theoretical NMD boundary in CDS

1147

length of CDS

1317

coding sequence (CDS) position

1129

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

1215

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

66252

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

231258150

original gDNA sequence snippet

AAGGATCTCTACCTAATCCTCCAAGAATATATTACAGGAAC

altered gDNA sequence snippet

AAGGATCTCTACCTAATCCTTCAAGAATATATTACAGGAAC

original cDNA sequence snippet

AAGGATCTCTACCTAATCCTCCAAGAATATATTACAGGAAC

altered cDNA sequence snippet

AAGGATCTCTACCTAATCCTTCAAGAATATATTACAGGAAC

wildtype AA sequence

mutated AA sequence

MAGGGSDLST RGLNGGVSQV ANEMNHLPAH SQSLQRLFTE DQDVDEGLVY DTVFKHFKRH
KLEISNAIKK TFPFLEGLRD RELITNKMFE DSEDSCRNLV PVQRVVYNVL SELEKTFNLS
VLEALFSEVN MQEYPDLIHI YKSFKNAIQD KLSFQESDRK EREERPDIKL SLKQGEVPES
PEARKESDQA CGKMDTVDIA NNSTLGKPKR KRRKKKGHGW SRMGTRTQKN NQQNDNSKAD
GQLVSSEKKA NMNLKDLSKI RGRKRGKPGT HFTQSDRAPQ KRVRSRASRK HKDETVDFQA
PLLPVTCGGV KGILHKEKLE QGTLAKCIQT EDGKWFTPME FEIKGGYARS KNWRLSVRCG
GWPLRRLMEE GSLPNPSRIY YRNKKRILKS QNNSSVDPCM RNLDECEVCR DGGELFCCDT
CSRVFHEDCH IPPVESEK*

speed

0.89 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999811427462 (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)

chr2:231258150C>TN/A show variant in all transcripts IGV

HGNC symbol

SP140L

Ensembl transcript ID

ENST00000243810

Genbank transcript ID

N/A

UniProt peptide

Q9H930

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1129C>T
cDNA.1129C>T
g.66252C>T

AA changes

P377S Score: 74 explain score(s)

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

377

frameshift

known variant

Reference ID: rs7590429

database	homozygous (T/T)	heterozygous	allele carriers
1000G	472	1143	1615
ExAC	8569	15629	24198

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.35	0.334
	0.605	0.34
(flanking)	1.092	0.338

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	66255	wt: 0.5465 / mu: 0.5489 (marginal change - not scored)	wt: GATCTCTACCTAATCCTCCAAGAATATATTACAGGAACAAA mu: GATCTCTACCTAATCCTTCAAGAATATATTACAGGAACAAA	ccaa\|GAAT
Acc marginally increased	66257	wt: 0.5452 / mu: 0.5653 (marginal change - not scored)	wt: TCTCTACCTAATCCTCCAAGAATATATTACAGGAACAAAAA mu: TCTCTACCTAATCCTTCAAGAATATATTACAGGAACAAAAA	aaga\|ATAT
Donor marginally increased	66254	wt: 0.3417 / mu: 0.3453 (marginal change - not scored)	wt: CCTCCAAGAATATAT mu: CCTTCAAGAATATAT	TCCA\|agaa
Donor marginally increased	66250	wt: 0.9412 / mu: 0.9511 (marginal change - not scored)	wt: TAATCCTCCAAGAAT mu: TAATCCTTCAAGAAT	ATCC\|tcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

377

mutated

not conserved

377

Ptroglodytes

all identical

ENSPTRG00000013011

377

Mmulatta

all identical

ENSMMUG00000016575

289

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000055359

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000032669

176

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1317 / 1317

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

439 / 439

position of stopcodon in wt / mu cDNA

1317 / 1317

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

2659

theoretical NMD boundary in CDS

2608

length of CDS

1317

coding sequence (CDS) position

1129

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

1129

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

66252

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

231258150

original gDNA sequence snippet

AAGGATCTCTACCTAATCCTCCAAGAATATATTACAGGAAC

altered gDNA sequence snippet

AAGGATCTCTACCTAATCCTTCAAGAATATATTACAGGAAC

original cDNA sequence snippet

AAGGATCTCTACCTAATCCTCCAAGAATATATTACAGGAAC

altered cDNA sequence snippet

AAGGATCTCTACCTAATCCTTCAAGAATATATTACAGGAAC

wildtype AA sequence

mutated AA sequence

MAGGGSDLST RGLNGGVSQV ANEMNHLPAH SQSLQRLFTE DQDVDEGLVY DTVFKHFKRH
KLEISNAIKK TFPFLEGLRD RELITNKMFE DSEDSCRNLV PVQRVVYNVL SELEKTFNLS
VLEALFSEVN MQEYPDLIHI YKSFKNAIQD KLSFQESDRK EREERPDIKL SLKQGEVPES
PEARKESDQA CGKMDTVDIA NNSTLGKPKR KRRKKKGHGW SRMGTRTQKN NQQNDNSKAD
GQLVSSEKKA NMNLKDLSKI RGRKRGKPGT HFTQSDRAPQ KRVRSRASRK HKDETVDFQA
PLLPVTCGGV KGILHKEKLE QGTLAKCIQT EDGKWFTPME FEIKGGYARS KNWRLSVRCG
GWPLRRLMEE GSLPNPSRIY YRNKKRILKS QNNSSVDPCM RNLDECEVCR DGGELFCCDT
CSRVFHEDCH IPPVESEK*

speed

0.84 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999686856791 (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)

chr2:231258150C>TN/A show variant in all transcripts IGV

HGNC symbol

SP140L

Ensembl transcript ID

ENST00000396563

Genbank transcript ID

N/A

UniProt peptide

Q9H930

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1024C>T
cDNA.1024C>T
g.66252C>T

AA changes

P342S Score: 74 explain score(s)

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

342

frameshift

known variant

Reference ID: rs7590429

database	homozygous (T/T)	heterozygous	allele carriers
1000G	472	1143	1615
ExAC	8569	15629	24198

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.35	0.334
	0.605	0.34
(flanking)	1.092	0.338

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	66255	wt: 0.5465 / mu: 0.5489 (marginal change - not scored)	wt: GATCTCTACCTAATCCTCCAAGAATATATTACAGGAACAAA mu: GATCTCTACCTAATCCTTCAAGAATATATTACAGGAACAAA	ccaa\|GAAT
Acc marginally increased	66257	wt: 0.5452 / mu: 0.5653 (marginal change - not scored)	wt: TCTCTACCTAATCCTCCAAGAATATATTACAGGAACAAAAA mu: TCTCTACCTAATCCTTCAAGAATATATTACAGGAACAAAAA	aaga\|ATAT
Donor marginally increased	66254	wt: 0.3417 / mu: 0.3453 (marginal change - not scored)	wt: CCTCCAAGAATATAT mu: CCTTCAAGAATATAT	TCCA\|agaa
Donor marginally increased	66250	wt: 0.9412 / mu: 0.9511 (marginal change - not scored)	wt: TAATCCTCCAAGAAT mu: TAATCCTTCAAGAAT	ATCC\|tcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

342

mutated

not conserved

342

Ptroglodytes

all identical

ENSPTRG00000013011

377

Mmulatta

all identical

ENSMMUG00000016575

289

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000055359

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000032669

177

protein features

start (aa)	end (aa)	feature	details
293	374	DOMAIN	SAND.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1212 / 1212

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

404 / 404

position of stopcodon in wt / mu cDNA

1212 / 1212

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

2554

theoretical NMD boundary in CDS

2503

length of CDS

1212

coding sequence (CDS) position

1024

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

1024

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

66252

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

231258150

original gDNA sequence snippet

AAGGATCTCTACCTAATCCTCCAAGAATATATTACAGGAAC

altered gDNA sequence snippet

AAGGATCTCTACCTAATCCTTCAAGAATATATTACAGGAAC

original cDNA sequence snippet

AAGGATCTCTACCTAATCCTCCAAGAATATATTACAGGAAC

altered cDNA sequence snippet

AAGGATCTCTACCTAATCCTTCAAGAATATATTACAGGAAC

wildtype AA sequence

mutated AA sequence

speed

0.87 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems