MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000301659
MT speed 0 s - this script 2.449488 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GSDMA	polymorphism_automatic	0.382759085122379	simple_aae				T314N	single base exchange	rs56030650		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.617240914877621 (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)

chr17:38131187C>AN/A show variant in all transcripts IGV

HGNC symbol

GSDMA

Ensembl transcript ID

ENST00000301659

Genbank transcript ID

NM_178171

UniProt peptide

Q96QA5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.941C>A
cDNA.1059C>A
g.11962C>A

AA changes

T314N Score: 65 explain score(s)

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

314

frameshift

known variant

Reference ID: rs56030650

database	homozygous (A/A)	heterozygous	allele carriers
1000G	373	1171	1544
ExAC	10588	11591	22179

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.472	0.996
	1.227	0.996
(flanking)	-0.03	0.991

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 marginally increased	11954	wt: 0.5740 / mu: 0.6090 (marginal change - not scored)	wt: GGACATGAAGTGACC mu: GGACATGAAGTGAAC	ACAT\|gaag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

314

mutated

not conserved

314

Ptroglodytes

all identical

ENSPTRG00000009108

314

Mmulatta

all identical

ENSMMUG00000020381

314

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000017204

315

Ggallus

all identical

ENSGALG00000013495

308

DDP

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

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

1338 / 1338

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

446 / 446

position of stopcodon in wt / mu cDNA

1456 / 1456

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

119 / 119

chromosome

strand

last intron/exon boundary

1214

theoretical NMD boundary in CDS

1045

length of CDS

1338

coding sequence (CDS) position

941

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

1059

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

11962

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

38131187

original gDNA sequence snippet

AGACAAGGGACATGAAGTGACCCTGGAGGCACTCCCAAAAG

altered gDNA sequence snippet

AGACAAGGGACATGAAGTGAACCTGGAGGCACTCCCAAAAG

original cDNA sequence snippet

AGACAAGGGACATGAAGTGACCCTGGAGGCACTCCCAAAAG

altered cDNA sequence snippet

AGACAAGGGACATGAAGTGAACCTGGAGGCACTCCCAAAAG

wildtype AA sequence

MTMFENVTRA LARQLNPRGD LTPLDSLIDF KRFHPFCLVL RKRKSTLFWG ARYVRTDYTL
LDVLEPGSSP SDPTDTGNFG FKNMLDTRVE GDVDVPKTVK VKGTAGLSQN STLEVQTLSV
APKALETVQE RKLAADHPFL KEMQDQGENL YVVMEVVETV QEVTLERAGK AEACFSLPFF
APLGLQGSIN HKEAVTIPKG CVLAFRVRQL MVKGKDEWDI PHICNDNMQT FPPGEKSGEE
KVILIQASDV GDVHEGFRTL KEEVQRETQQ VEKLSRVGQS SLLSSLSKLL GKKKELQDLE
LALEGALDKG HEVTLEALPK DVLLSKEAVG AILYFVGALT ELSEAQQKLL VKSMEKKILP
VQLKLVESTM EQNFLLDKEG VFPLQPELLS SLGDEELTLT EALVGLSGLE VQRSGPQYMW
DPDTLPRLCA LYAGLSLLQQ LTKAS*

mutated AA sequence

MTMFENVTRA LARQLNPRGD LTPLDSLIDF KRFHPFCLVL RKRKSTLFWG ARYVRTDYTL
LDVLEPGSSP SDPTDTGNFG FKNMLDTRVE GDVDVPKTVK VKGTAGLSQN STLEVQTLSV
APKALETVQE RKLAADHPFL KEMQDQGENL YVVMEVVETV QEVTLERAGK AEACFSLPFF
APLGLQGSIN HKEAVTIPKG CVLAFRVRQL MVKGKDEWDI PHICNDNMQT FPPGEKSGEE
KVILIQASDV GDVHEGFRTL KEEVQRETQQ VEKLSRVGQS SLLSSLSKLL GKKKELQDLE
LALEGALDKG HEVNLEALPK DVLLSKEAVG AILYFVGALT ELSEAQQKLL VKSMEKKILP
VQLKLVESTM EQNFLLDKEG VFPLQPELLS SLGDEELTLT EALVGLSGLE VQRSGPQYMW
DPDTLPRLCA LYAGLSLLQQ LTKAS*

speed

0.44 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

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

Problems