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: ENST00000374268
MT speed 0.86 s - this script 2.905305 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FAM110D	polymorphism_automatic	0.106238749497373	simple_aae		affected		H53R	single base exchange	rs3748856		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.893761250502627 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:26487940A>GN/A show variant in all transcripts IGV

HGNC symbol

FAM110D

Ensembl transcript ID

ENST00000374268

Genbank transcript ID

NM_024869

UniProt peptide

Q8TAY7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.158A>G
cDNA.345A>G
g.2430A>G

AA changes

H53R Score: 29 explain score(s)

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

frameshift

known variant

Reference ID: rs3748856

database	homozygous (G/G)	heterozygous	allele carriers
1000G	108	724	832
ExAC	1672	8838	10510

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.434	0.907
	1.791	0.848
(flanking)	1.135	0.786

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	2435	wt: 0.9917 / mu: 0.9921 (marginal change - not scored)	wt: ACCCCTGCAACGAGC mu: GCCCCTGCAACGAGC	CCCT\|gcaa
Donor gained	2424	0.94	mu: GCTCACGCCGCGCCC	TCAC\|gccg

distance from splice site

238

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000022777

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000050105

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000007360

LVPCATPPPQPR

VSL

RLPPRS

Drerio

not conserved

ENSDARG00000062517

VPC

VPRRNLTTS

STPVLL

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000009193

163

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

816 / 816

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

272 / 272

position of stopcodon in wt / mu cDNA

1003 / 1003

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

188 / 188

chromosome

strand

last intron/exon boundary

108

theoretical NMD boundary in CDS

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

length of CDS

816

coding sequence (CDS) position

158

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

345

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

2430

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

26487940

original gDNA sequence snippet

TCCTGGGCCGCTCACGCCGCACCCCTGCAACGAGCTGGGGC

altered gDNA sequence snippet

TCCTGGGCCGCTCACGCCGCGCCCCTGCAACGAGCTGGGGC

original cDNA sequence snippet

TCCTGGGCCGCTCACGCCGCACCCCTGCAACGAGCTGGGGC

altered cDNA sequence snippet

TCCTGGGCCGCTCACGCCGCGCCCCTGCAACGAGCTGGGGC

wildtype AA sequence

MLLAPPSTPS RGRTPSAVER LEADKAKYVK THQVIARRQE PALRGSPGPL TPHPCNELGP
PASPRTPRPV RRGSGRRLPR PDSLIFYRQK RDCKASVNKE NAKGQGLVRR LFLGAPRDAA
PSSPASTERP AASGGWAAPQ DAPEAAGKRA LCPTCSLPLS EKERFFNYCG LERALVEVLG
AERFSPQSWG ADASPQAGTS PPPGSGDASD WTSSDRGVDS PGGAGGGGGS EAAGSARDRR
PPVSVVERNA RVIQWLYGCQ RARGPPRESE V*

mutated AA sequence

MLLAPPSTPS RGRTPSAVER LEADKAKYVK THQVIARRQE PALRGSPGPL TPRPCNELGP
PASPRTPRPV RRGSGRRLPR PDSLIFYRQK RDCKASVNKE NAKGQGLVRR LFLGAPRDAA
PSSPASTERP AASGGWAAPQ DAPEAAGKRA LCPTCSLPLS EKERFFNYCG LERALVEVLG
AERFSPQSWG ADASPQAGTS PPPGSGDASD WTSSDRGVDS PGGAGGGGGS EAAGSARDRR
PPVSVVERNA RVIQWLYGCQ RARGPPRESE V*

speed

0.86 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