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: ENST00000361976
Querying Taster for transcript #2: ENST00000369080
MT speed 0 s - this script 2.893707 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
INPP5F	polymorphism_automatic	0	simple_aae		affected		N997D	single base exchange	rs3188055		show file
INPP5F	polymorphism_automatic	9.99200722162641e-16	simple_aae		affected		N387D	single base exchange	rs3188055		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1 (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)

chr10:121586882A>GN/A show variant in all transcripts IGV

HGNC symbol

INPP5F

Ensembl transcript ID

ENST00000361976

Genbank transcript ID

NM_001243194

UniProt peptide

Q9Y2H2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2989A>G
cDNA.3155A>G
g.101274A>G

AA changes

N997D Score: 23 explain score(s)

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

997

frameshift

known variant

Reference ID: rs3188055

database	homozygous (G/G)	heterozygous	allele carriers
1000G	206	935	1141
ExAC	5294	22179	27473

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.973	0
	0.979	0.001
(flanking)	0.54	0.001

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 gained	101273	0.60	mu: GTTTCAGATGAAACC	TTCA\|gatg

distance from splice site

740

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

997

mutated

all conserved

997

Ptroglodytes

not conserved

ENSPTRG00000022873

997

Mmulatta

not conserved

ENSMMUG00000009558

1015

Fcatus

not conserved

ENSFCAG00000019160

964

Mmusculus

not conserved

ENSMUSG00000042105

998

Ggallus

not conserved

ENSGALG00000009445

1009

KKA

Trubripes

not conserved

ENSTRUG00000017919

994

KSSADTD

Drerio

not conserved

ENSDARG00000061437

1002

Dmelanogaster

not conserved

FBgn0038890

1130

Celegans

no alignment

W09C5.7

n/a

Xtropicalis

not conserved

ENSXETG00000010235

982

protein features

start (aa)	end (aa)	feature	details
1069	1069	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3399 / 3399

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

1133 / 1133

position of stopcodon in wt / mu cDNA

3565 / 3565

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

167 / 167

chromosome

strand

last intron/exon boundary

2416

theoretical NMD boundary in CDS

2199

length of CDS

3399

coding sequence (CDS) position

2989

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

3155

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

101274

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

121586882

original gDNA sequence snippet

AAATGACCAATCAAGTTTCAAATGAAACCCAATCAGAATCA

altered gDNA sequence snippet

AAATGACCAATCAAGTTTCAGATGAAACCCAATCAGAATCA

original cDNA sequence snippet

AAATGACCAATCAAGTTTCAAATGAAACCCAATCAGAATCA

altered cDNA sequence snippet

AAATGACCAATCAAGTTTCAGATGAAACCCAATCAGAATCA

wildtype AA sequence

MELFQAKDHY ILQQGERALW CSRRDGGLQL RPATDLLLAW NPICLGLVEG VIGKIQLHSD
LPWWLILIRQ KALVGKLPGD HEVCKVTKIA VLSLSEMEPQ DLELELCKKH HFGINKPEKI
IPSPDDSKFL LKTFTHIKSN VSAPNKKKVK ESKEKEKLER RLLEELLKMF MDSESFYYSL
TYDLTNSVQR QSTGERDGRP LWQKVDDRFF WNKYMIQDLT EIGTPDVDFW IIPMIQGFVQ
IEELVVNYTE SSDDEKSSPE TPPQESTCVD DIHPRFLVAL ISRRSRHRAG MRYKRRGVDK
NGNVANYVET EQLIHVHNHT LSFVQTRGSV PVFWSQVGYR YNPRPRLDRS EKETVAYFCA
HFEEQLNIYK KQVIINLVDQ AGREKIIGDA YLKQVLLFNN SHLTYVSFDF HEHCRGMKFE
NVQTLTDAIY DIILDMKWCW VDEAGVICKQ EGIFRVNCMD CLDRTNVVQA AIARVVMEQQ
LKKLGVMPPE QPLPVKCNRI YQIMWANNGD SISRQYAGTA ALKGDFTRTG ERKLAGVMKD
GVNSANRYYL NRFKDAYRQA VIDLMQGIPV TEDLYSIFTK EKEHEALHKE NQRSHQELIS
QLLQSYMKLL LPDDEKFHGG WALIDCDPSL IDATHRDVDV LLLLSNSAYY VAYYDDEVDK
VNQYQRLSLE NLEKIEIGPE PTLFGKPKFS CMRLHYRYKE ASGYFHTLRA VMRNPEEDGK
DTLQCIAEML QITKQAMGSD LPIIEKKLER KSSKPHEDII GIRSQNQGSL AQGKNFLMSK
FSSLNQKVKQ TKSNVNIGNL RKLGNFTKPE MKVNFLKPNL KVNLWKSDSS LETMENTGVM
DKVQAESDGD MSSDNDSYHS DEFLTNSKSD EDRQLANSLE SVGPIDYVLP SCGIIASAPR
LGSRSQSLSS TDSSVHAPSE ITVAHGSGLG KGQESPLKKS PSAGDVHILT GFAKPMDIYC
HRFVQDAQNK VTHLSETRSV SQQASQERNQ MTNQVSNETQ SESTEQTPSR PSQLDVSLSA
TGPQFLSVEP AHSVASQKTP TSASSMLELE TGLHVTPSPS ESSSSRAVSP FAKIRSSMVQ
VASITQAGLT HGINFAVSKV QKSPPEPEII NQVQQNELKK MFIQCQTRII QI*

mutated AA sequence

MELFQAKDHY ILQQGERALW CSRRDGGLQL RPATDLLLAW NPICLGLVEG VIGKIQLHSD
LPWWLILIRQ KALVGKLPGD HEVCKVTKIA VLSLSEMEPQ DLELELCKKH HFGINKPEKI
IPSPDDSKFL LKTFTHIKSN VSAPNKKKVK ESKEKEKLER RLLEELLKMF MDSESFYYSL
TYDLTNSVQR QSTGERDGRP LWQKVDDRFF WNKYMIQDLT EIGTPDVDFW IIPMIQGFVQ
IEELVVNYTE SSDDEKSSPE TPPQESTCVD DIHPRFLVAL ISRRSRHRAG MRYKRRGVDK
NGNVANYVET EQLIHVHNHT LSFVQTRGSV PVFWSQVGYR YNPRPRLDRS EKETVAYFCA
HFEEQLNIYK KQVIINLVDQ AGREKIIGDA YLKQVLLFNN SHLTYVSFDF HEHCRGMKFE
NVQTLTDAIY DIILDMKWCW VDEAGVICKQ EGIFRVNCMD CLDRTNVVQA AIARVVMEQQ
LKKLGVMPPE QPLPVKCNRI YQIMWANNGD SISRQYAGTA ALKGDFTRTG ERKLAGVMKD
GVNSANRYYL NRFKDAYRQA VIDLMQGIPV TEDLYSIFTK EKEHEALHKE NQRSHQELIS
QLLQSYMKLL LPDDEKFHGG WALIDCDPSL IDATHRDVDV LLLLSNSAYY VAYYDDEVDK
VNQYQRLSLE NLEKIEIGPE PTLFGKPKFS CMRLHYRYKE ASGYFHTLRA VMRNPEEDGK
DTLQCIAEML QITKQAMGSD LPIIEKKLER KSSKPHEDII GIRSQNQGSL AQGKNFLMSK
FSSLNQKVKQ TKSNVNIGNL RKLGNFTKPE MKVNFLKPNL KVNLWKSDSS LETMENTGVM
DKVQAESDGD MSSDNDSYHS DEFLTNSKSD EDRQLANSLE SVGPIDYVLP SCGIIASAPR
LGSRSQSLSS TDSSVHAPSE ITVAHGSGLG KGQESPLKKS PSAGDVHILT GFAKPMDIYC
HRFVQDAQNK VTHLSETRSV SQQASQERNQ MTNQVSDETQ SESTEQTPSR PSQLDVSLSA
TGPQFLSVEP AHSVASQKTP TSASSMLELE TGLHVTPSPS ESSSSRAVSP FAKIRSSMVQ
VASITQAGLT HGINFAVSKV QKSPPEPEII NQVQQNELKK MFIQCQTRII QI*

speed

0.46 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)

chr10:121586882A>GN/A show variant in all transcripts IGV

HGNC symbol

INPP5F

Ensembl transcript ID

ENST00000369080

Genbank transcript ID

N/A

UniProt peptide

Q9Y2H2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1159A>G
cDNA.1927A>G
g.101274A>G

AA changes

N387D Score: 23 explain score(s)

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

387

frameshift

known variant

Reference ID: rs3188055

database	homozygous (G/G)	heterozygous	allele carriers
1000G	206	935	1141
ExAC	5294	22179	27473

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.973	0
	0.979	0.001
(flanking)	0.54	0.001

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 gained	101273	0.60	mu: GTTTCAGATGAAACC	TTCA\|gatg

distance from splice site

740

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

387

mutated

all conserved

387

Ptroglodytes

not conserved

ENSPTRG00000022873

997

Mmulatta

not conserved

ENSMMUG00000009558

1015

Fcatus

not conserved

ENSFCAG00000019160

964

Mmusculus

not conserved

ENSMUSG00000042105

997

Ggallus

not conserved

ENSGALG00000009445

1009

KKA

Trubripes

not conserved

ENSTRUG00000017919

997

KSSADTDDC

Drerio

not conserved

ENSDARG00000061437

1002

Dmelanogaster

not conserved

FBgn0038890

1125

Celegans

no alignment

W09C5.7

n/a

Xtropicalis

not conserved

ENSXETG00000010235

981

protein features

start (aa)	end (aa)	feature	details
167	518	DOMAIN	SAC.	lost
386	386	CONFLICT	I -> V (in Ref. 5; AAI11494).	might get lost (downstream of altered splice site)
460	460	MUTAGEN	D->A: Loss of phosphatase activity.	might get lost (downstream of altered splice site)
829	829	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
905	905	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
909	909	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
942	942	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
1069	1069	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1569 / 1569

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

523 / 523

position of stopcodon in wt / mu cDNA

2337 / 2337

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

769 / 769

chromosome

strand

last intron/exon boundary

1188

theoretical NMD boundary in CDS

369

length of CDS

1569

coding sequence (CDS) position

1159

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

1927

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

101274

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

121586882

original gDNA sequence snippet

AAATGACCAATCAAGTTTCAAATGAAACCCAATCAGAATCA

altered gDNA sequence snippet

AAATGACCAATCAAGTTTCAGATGAAACCCAATCAGAATCA

original cDNA sequence snippet

AAATGACCAATCAAGTTTCAAATGAAACCCAATCAGAATCA

altered cDNA sequence snippet

AAATGACCAATCAAGTTTCAGATGAAACCCAATCAGAATCA

wildtype AA sequence

MCHDVIFMAW LKQQFSECTL IDATHRDVDV LLLLSNSAYY VAYYDDEVDK VNQYQRLSLE
NLEKIEIGPE PTLFGKPKFS CMRLHYRYKE ASGYFHTLRA VMRNPEEDGK DTLQCIAEML
QITKQAMGSD LPIIEKKLER KSSKPHEDII GIRSQNQGSL AQGKNFLMSK FSSLNQKVKQ
TKSNVNIGNL RKLGNFTKPE MKVNFLKPNL KVNLWKSDSS LETMENTGVM DKVQAESDGD
MSSDNDSYHS DEFLTNSKSD EDRQLANSLE SVGPIDYVLP SCGIIASAPR LGSRSQSLSS
TDSSVHAPSE ITVAHGSGLG KGQESPLKKS PSAGDVHILT GFAKPMDIYC HRFVQDAQNK
VTHLSETRSV SQQASQERNQ MTNQVSNETQ SESTEQTPSR PSQLDVSLSA TGPQFLSVEP
AHSVASQKTP TSASSMLELE TGLHVTPSPS ESSSSRAVSP FAKIRSSMVQ VASITQAGLT
HGINFAVSKV QKSPPEPEII NQVQQNELKK MFIQCQTRII QI*

mutated AA sequence

MCHDVIFMAW LKQQFSECTL IDATHRDVDV LLLLSNSAYY VAYYDDEVDK VNQYQRLSLE
NLEKIEIGPE PTLFGKPKFS CMRLHYRYKE ASGYFHTLRA VMRNPEEDGK DTLQCIAEML
QITKQAMGSD LPIIEKKLER KSSKPHEDII GIRSQNQGSL AQGKNFLMSK FSSLNQKVKQ
TKSNVNIGNL RKLGNFTKPE MKVNFLKPNL KVNLWKSDSS LETMENTGVM DKVQAESDGD
MSSDNDSYHS DEFLTNSKSD EDRQLANSLE SVGPIDYVLP SCGIIASAPR LGSRSQSLSS
TDSSVHAPSE ITVAHGSGLG KGQESPLKKS PSAGDVHILT GFAKPMDIYC HRFVQDAQNK
VTHLSETRSV SQQASQERNQ MTNQVSDETQ SESTEQTPSR PSQLDVSLSA TGPQFLSVEP
AHSVASQKTP TSASSMLELE TGLHVTPSPS ESSSSRAVSP FAKIRSSMVQ VASITQAGLT
HGINFAVSKV QKSPPEPEII NQVQQNELKK MFIQCQTRII QI*

speed

0.44 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems