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: ENST00000356987
Querying Taster for transcript #2: ENST00000528880
MT speed 0 s - this script 3.426194 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
HCAR3	polymorphism_automatic	1.04705133452399e-12	simple_aae				T173P	single base exchange	rs1798192		show file
HCAR1	polymorphism_automatic	8.45261179938106e-08	without_aae					single base exchange	rs1798192		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999998953 (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)

chr12:123200768T>GN/A show variant in all transcripts IGV

HGNC symbol

HCAR3

Ensembl transcript ID

ENST00000528880

Genbank transcript ID

NM_006018

UniProt peptide

N/A

alteration type

single base exchange

alteration region

CDS

DNA changes

c.517A>C
cDNA.672A>C
g.672A>C

AA changes

T173P Score: 38 explain score(s)

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

173

frameshift

known variant

Reference ID: rs1798192

database	homozygous (G/G)	heterozygous	allele carriers
1000G	555	1214	1769
ExAC	16145	477	16622

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.266	0
	-0.113	0
(flanking)	0.256	0

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

splice sites

no abrogation of potential splice sites

distance from splice site

672

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

173

mutated

not conserved

173

Ptroglodytes

all identical

ENSPTRG00000032447

173

Mmulatta

no homologue

Fcatus

not conserved

ENSFCAG00000016311

173

Mmusculus

not conserved

ENSMUSG00000045502

170

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

N/A

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1164 / 1164

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

388 / 388

position of stopcodon in wt / mu cDNA

1319 / 1319

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

156 / 156

chromosome

strand

-1

last intron/exon boundary

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

1164

coding sequence (CDS) position

517

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

672

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

672

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

123200768

original gDNA sequence snippet

AGTTGCTGATCCAGAATGGCACTGCAAATGTGTGCATCAGC

altered gDNA sequence snippet

AGTTGCTGATCCAGAATGGCCCTGCAAATGTGTGCATCAGC

original cDNA sequence snippet

AGTTGCTGATCCAGAATGGCACTGCAAATGTGTGCATCAGC

altered cDNA sequence snippet

AGTTGCTGATCCAGAATGGCCCTGCAAATGTGTGCATCAGC

wildtype AA sequence

MNRHHLQDHF LEIDKKNCCV FRDDFIAKVL PPVLGLEFIF GLLGNGLALW IFCFHLKSWK
SSRIFLFNLA VADFLLIICL PFVMDYYVRR SDWKFGDIPC RLVLFMFAMN RQGSIIFLTV
VAVDRYFRVV HPHHALNKIS NWTAAIISCL LWGITVGLTV HLLKKKLLIQ NGTANVCISF
SICHTFRWHE AMFLLEFFLP LGIILFCSAR IIWSLRQRQM DRHAKIKRAI TFIMVVAIVF
VICFLPSVVV RIHIFWLLHT SGTQNCEVYR SVDLAFFITL SFTYMNSMLD PVVYYFSSPS
FPNFFSTLIN RCLQRKITGE PDNNRSTSVE LTGDPNKTRG APEALIANSG EPWSPSYLGP
TSNNHSKKGH CHQEPASLEK QLGCCIE*

mutated AA sequence

MNRHHLQDHF LEIDKKNCCV FRDDFIAKVL PPVLGLEFIF GLLGNGLALW IFCFHLKSWK
SSRIFLFNLA VADFLLIICL PFVMDYYVRR SDWKFGDIPC RLVLFMFAMN RQGSIIFLTV
VAVDRYFRVV HPHHALNKIS NWTAAIISCL LWGITVGLTV HLLKKKLLIQ NGPANVCISF
SICHTFRWHE AMFLLEFFLP LGIILFCSAR IIWSLRQRQM DRHAKIKRAI TFIMVVAIVF
VICFLPSVVV RIHIFWLLHT SGTQNCEVYR SVDLAFFITL SFTYMNSMLD PVVYYFSSPS
FPNFFSTLIN RCLQRKITGE PDNNRSTSVE LTGDPNKTRG APEALIANSG EPWSPSYLGP
TSNNHSKKGH CHQEPASLEK QLGCCIE*

speed

0.83 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: without_aae, prob: 0.999999915473882 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:123200768T>GN/A show variant in all transcripts IGV

HGNC symbol

HCAR1

Ensembl transcript ID

ENST00000356987

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.14623A>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs1798192

database	homozygous (G/G)	heterozygous	allele carriers
1000G	555	1214	1769
ExAC	16145	477	16622

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.266	0
	-0.113	0
(flanking)	0.256	0

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

splice sites

no abrogation of potential splice sites

distance from splice site

6376

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

505 / 505

chromosome

strand

-1

last intron/exon boundary

2322

theoretical NMD boundary in CDS

1767

length of CDS

1041

coding sequence (CDS) position

N/A

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

N/A

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

14623

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

123200768

original gDNA sequence snippet

AGTTGCTGATCCAGAATGGCACTGCAAATGTGTGCATCAGC

altered gDNA sequence snippet

AGTTGCTGATCCAGAATGGCCCTGCAAATGTGTGCATCAGC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MYNGSCCRIE GDTISQVMPP LLIVAFVLGA LGNGVALCGF CFHMKTWKPS TVYLFNLAVA
DFLLMICLPF RTDYYLRRRH WAFGDIPCRV GLFTLAMNRA GSIVFLTVVA ADRYFKVVHP
HHAVNTISTR VAAGIVCTLW ALVILGTVYL LLENHLCVQE TAVSCESFIM ESANGWHDIM
FQLEFFMPLG IILFCSFKIV WSLRRRQQLA RQARMKKATR FIMVVAIVFI TCYLPSVSAR
LYFLWTVPSS ACDPSVHGAL HITLSFTYMN SMLDPLVYYF SSPSFPKFYN KLKICSLKPK
QPGHSKTQRP EEMPISNLGR RSCISVANSF QSQSDGQWDP HIVEWH*

mutated AA sequence

N/A

speed

0.65 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems