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: ENST00000356509
Querying Taster for transcript #2: ENST00000230056
MT speed 0 s - this script 4.161628 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GMNN	polymorphism_automatic	0.846068065593201	simple_aae		affected		N18T	single base exchange	rs1923185		show file
GMNN	polymorphism_automatic	0.846068065593201	simple_aae		affected		N18T	single base exchange	rs1923185		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.153931934406799 (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)

chr6:24780892A>CN/A show variant in all transcripts IGV

HGNC symbol

GMNN

Ensembl transcript ID

ENST00000356509

Genbank transcript ID

NM_001251989

UniProt peptide

O75496

alteration type

single base exchange

alteration region

CDS

DNA changes

c.53A>C
cDNA.260A>C
g.5734A>C

AA changes

N18T Score: 65 explain score(s)

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

frameshift

known variant

Reference ID: rs1923185

database	homozygous (C/C)	heterozygous	allele carriers
1000G	207	645	852
ExAC	2570	9486	12056

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.046	1
	0.175	0.977
(flanking)	0.449	0.97

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	5732	sequence motif lost	-	wt: ttag\|AATA mu: ttag.ACTA
Acc marginally increased	5731	wt: 0.6363 / mu: 0.6917 (marginal change - not scored)	wt: ATGAATTATGCTGACTTTTTAGAATAGTTCTGTCCCAAGAA mu: ATGAATTATGCTGACTTTTTAGACTAGTTCTGTCCCAAGAA	ttta\|GAAT
Donor marginally increased	5736	wt: 0.7817 / mu: 0.7874 (marginal change - not scored)	wt: AGAATAGTTCTGTCC mu: AGACTAGTTCTGTCC	AATA\|gttc
Donor marginally increased	5731	wt: 0.9392 / mu: 0.9409 (marginal change - not scored)	wt: TTTTTAGAATAGTTC mu: TTTTTAGACTAGTTC	TTTA\|gaat
Acc gained	5736	0.85	mu: TTATGCTGACTTTTTAGACTAGTTCTGTCCCAAGAAGAACT	acta\|GTTC
Acc gained	5741	0.53	mu: CTGACTTTTTAGACTAGTTCTGTCCCAAGAAGAACTCTGAA	ttct\|GTCC

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

ENSPTRG00000017781

Mmulatta

all identical

ENSMMUG00000017495

Fcatus

no alignment

ENSFCAG00000002800

n/a

Mmusculus

all identical

ENSMUSG00000006715

Ggallus

no homologue

Trubripes

no alignment

ENSTRUG00000014406

n/a

Drerio

not conserved

ENSDARG00000035957

KFLVAPTSG

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000014814

DAEQPTM

TNEAL

protein features

start (aa)	end (aa)	feature	details
27	27	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
63	63	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
64	64	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
82	161	REGION	Necessary and sufficient for interaction with IDAS.	might get lost (downstream of altered splice site)
94	144	COILED		might get lost (downstream of altered splice site)
110	142	HELIX		might get lost (downstream of altered splice site)
177	179	TURN		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

630 / 630

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

210 / 210

position of stopcodon in wt / mu cDNA

837 / 837

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

208 / 208

chromosome

strand

last intron/exon boundary

676

theoretical NMD boundary in CDS

418

length of CDS

630

coding sequence (CDS) position

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

260

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

5734

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

24780892

original gDNA sequence snippet

AATTATGCTGACTTTTTAGAATAGTTCTGTCCCAAGAAGAA

altered gDNA sequence snippet

AATTATGCTGACTTTTTAGACTAGTTCTGTCCCAAGAAGAA

original cDNA sequence snippet

AATCAAAGAGAATATAAAGAATAGTTCTGTCCCAAGAAGAA

altered cDNA sequence snippet

AATCAAAGAGAATATAAAGACTAGTTCTGTCCCAAGAAGAA

wildtype AA sequence

MNPSMKQKQE EIKENIKNSS VPRRTLKMIQ PSASGSLVGR ENELSAGLSK RKHRNDHLTS
TTSSPGVIVP ESSENKNLGG VTQESFDLMI KENPSSQYWK EVAEKRRKAL YEALKENEKL
HKEIEQKDNE IARLKKENKE LAEVAEHVQY MAELIERLNG EPLDNFESLD NQEFDSEEET
VEDSLVEDSE IGTCAEGTVS SSTDAKPCI*

mutated AA sequence

MNPSMKQKQE EIKENIKTSS VPRRTLKMIQ PSASGSLVGR ENELSAGLSK RKHRNDHLTS
TTSSPGVIVP ESSENKNLGG VTQESFDLMI KENPSSQYWK EVAEKRRKAL YEALKENEKL
HKEIEQKDNE IARLKKENKE LAEVAEHVQY MAELIERLNG EPLDNFESLD NQEFDSEEET
VEDSLVEDSE IGTCAEGTVS SSTDAKPCI*

speed

0.91 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: 0.153931934406799 (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)

chr6:24780892A>CN/A show variant in all transcripts IGV

HGNC symbol

GMNN

Ensembl transcript ID

ENST00000230056

Genbank transcript ID

NM_001251990

UniProt peptide

O75496

alteration type

single base exchange

alteration region

CDS

DNA changes

c.53A>C
cDNA.385A>C
g.5734A>C

AA changes

N18T Score: 65 explain score(s)

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

frameshift

known variant

Reference ID: rs1923185

database	homozygous (C/C)	heterozygous	allele carriers
1000G	207	645	852
ExAC	2570	9486	12056

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.046	1
	0.175	0.977
(flanking)	0.449	0.97

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	5732	sequence motif lost	-	wt: ttag\|AATA mu: ttag.ACTA
Acc marginally increased	5731	wt: 0.6363 / mu: 0.6917 (marginal change - not scored)	wt: ATGAATTATGCTGACTTTTTAGAATAGTTCTGTCCCAAGAA mu: ATGAATTATGCTGACTTTTTAGACTAGTTCTGTCCCAAGAA	ttta\|GAAT
Donor marginally increased	5736	wt: 0.7817 / mu: 0.7874 (marginal change - not scored)	wt: AGAATAGTTCTGTCC mu: AGACTAGTTCTGTCC	AATA\|gttc
Donor marginally increased	5731	wt: 0.9392 / mu: 0.9409 (marginal change - not scored)	wt: TTTTTAGAATAGTTC mu: TTTTTAGACTAGTTC	TTTA\|gaat
Acc gained	5736	0.85	mu: TTATGCTGACTTTTTAGACTAGTTCTGTCCCAAGAAGAACT	acta\|GTTC
Acc gained	5741	0.53	mu: CTGACTTTTTAGACTAGTTCTGTCCCAAGAAGAACTCTGAA	ttct\|GTCC

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

ENSPTRG00000017781

Mmulatta

all identical

ENSMMUG00000017495

Fcatus

no alignment

ENSFCAG00000002800

n/a

Mmusculus

all identical

ENSMUSG00000006715

Ggallus

no homologue

Trubripes

no alignment

ENSTRUG00000014406

n/a

Drerio

not conserved

ENSDARG00000035957

KFLVAPTSG

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000014814

DAEQPTM

TNEAL

protein features

start (aa)	end (aa)	feature	details
27	27	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
63	63	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
64	64	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
82	161	REGION	Necessary and sufficient for interaction with IDAS.	might get lost (downstream of altered splice site)
94	144	COILED		might get lost (downstream of altered splice site)
110	142	HELIX		might get lost (downstream of altered splice site)
177	179	TURN		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

630 / 630

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

210 / 210

position of stopcodon in wt / mu cDNA

962 / 962

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

333 / 333

chromosome

strand

last intron/exon boundary

801

theoretical NMD boundary in CDS

418

length of CDS

630

coding sequence (CDS) position

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

385

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

5734

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

24780892

original gDNA sequence snippet

AATTATGCTGACTTTTTAGAATAGTTCTGTCCCAAGAAGAA

altered gDNA sequence snippet

AATTATGCTGACTTTTTAGACTAGTTCTGTCCCAAGAAGAA

original cDNA sequence snippet

AATCAAAGAGAATATAAAGAATAGTTCTGTCCCAAGAAGAA

altered cDNA sequence snippet

AATCAAAGAGAATATAAAGACTAGTTCTGTCCCAAGAAGAA

wildtype AA sequence

mutated AA sequence

speed

1.18 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems