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: ENST00000264870
Querying Taster for transcript #2: ENST00000445223
MT speed 0 s - this script 2.634584 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
F13A1	disease_causing_automatic	0.999999199513853	simple_aae			0	Y284C	single base exchange	rs121913074		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999199513853 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM011781)
known disease mutation: rs16535 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:6225041T>CN/A show variant in all transcripts IGV

HGNC symbol

F13A1

Ensembl transcript ID

ENST00000264870

Genbank transcript ID

NM_000129

UniProt peptide

P00488

alteration type

single base exchange

alteration region

CDS

DNA changes

c.851A>G
cDNA.1117A>G
g.96206A>G

AA changes

Y284C Score: 194 explain score(s)

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

284

frameshift

known variant

Reference ID: rs121913074
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs16535 (pathogenic for Factor XIII subunit A deficiency) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM011781)

known disease mutation at this position, please check HGMD for details (HGMD ID CM011781)
known disease mutation at this position, please check HGMD for details (HGMD ID CM011781)

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.993	1
	2.946	1
(flanking)	4.512	1

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
Acc marginally increased	96215	wt: 0.2637 / mu: 0.3085 (marginal change - not scored)	wt: GGACAATATCTATGCCTATGGCGTCCCCCCATCGGCCTGGA mu: GGACAATATCTGTGCCTATGGCGTCCCCCCATCGGCCTGGA	atgg\|CGTC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

284

mutated

not conserved

284

Ptroglodytes

all identical

ENSPTRG00000017694

284

Mmulatta

all identical

ENSMMUG00000001248

284

Fcatus

all identical

ENSFCAG00000015505

284

Mmusculus

all identical

ENSMUSG00000039109

284

Ggallus

all identical

ENSGALG00000012802

291

Trubripes

all identical

ENSTRUG00000018071

302

Drerio

all identical

ENSDARG00000036893

301

Dmelanogaster

all conserved

FBgn0031975

298

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

2199 / 2199

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

733 / 733

position of stopcodon in wt / mu cDNA

2465 / 2465

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

267 / 267

chromosome

strand

-1

last intron/exon boundary

2312

theoretical NMD boundary in CDS

1995

length of CDS

2199

coding sequence (CDS) position

851

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

1117

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

96206

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

6225041

original gDNA sequence snippet

TGGATCCTGGGACAATATCTATGCCTATGGCGTCCCCCCAT

altered gDNA sequence snippet

TGGATCCTGGGACAATATCTGTGCCTATGGCGTCCCCCCAT

original cDNA sequence snippet

TGGATCCTGGGACAATATCTATGCCTATGGCGTCCCCCCAT

altered cDNA sequence snippet

TGGATCCTGGGACAATATCTGTGCCTATGGCGTCCCCCCAT

wildtype AA sequence

MSETSRTAFG GRRAVPPNNS NAAEDDLPTV ELQGVVPRGV NLQEFLNVTS VHLFKERWDT
NKVDHHTDKY ENNKLIVRRG QSFYVQIDFS RPYDPRRDLF RVEYVIGRYP QENKGTYIPV
PIVSELQSGK WGAKIVMRED RSVRLSIQSS PKCIVGKFRM YVAVWTPYGV LRTSRNPETD
TYILFNPWCE DDAVYLDNEK EREEYVLNDI GVIFYGEVND IKTRSWSYGQ FEDGILDTCL
YVMDRAQMDL SGRGNPIKVS RVGSAMVNAK DDEGVLVGSW DNIYAYGVPP SAWTGSVDIL
LEYRSSENPV RYGQCWVFAG VFNTFLRCLG IPARIVTNYF SAHDNDANLQ MDIFLEEDGN
VNSKLTKDSV WNYHCWNEAW MTRPDLPVGF GGWQAVDSTP QENSDGMYRC GPASVQAIKH
GHVCFQFDAP FVFAEVNSDL IYITAKKDGT HVVENVDATH IGKLIVTKQI GGDGMMDITD
TYKFQEGQEE ERLALETALM YGAKKPLNTE GVMKSRSNVD MDFEVENAVL GKDFKLSITF
RNNSHNRYTI TAYLSANITF YTGVPKAEFK KETFDVTLEP LSFKKEAVLI QAGEYMGQLL
EQASLHFFVT ARINETRDVL AKQKSTVLTI PEIIIKVRGT QVVGSDMTVT VEFTNPLKET
LRNVWVHLDG PGVTRPMKKM FREIRPNSTV QWEEVCRPWV SGHRKLIASM SSDSLRHVYG
ELDVQIQRRP SM*

mutated AA sequence

MSETSRTAFG GRRAVPPNNS NAAEDDLPTV ELQGVVPRGV NLQEFLNVTS VHLFKERWDT
NKVDHHTDKY ENNKLIVRRG QSFYVQIDFS RPYDPRRDLF RVEYVIGRYP QENKGTYIPV
PIVSELQSGK WGAKIVMRED RSVRLSIQSS PKCIVGKFRM YVAVWTPYGV LRTSRNPETD
TYILFNPWCE DDAVYLDNEK EREEYVLNDI GVIFYGEVND IKTRSWSYGQ FEDGILDTCL
YVMDRAQMDL SGRGNPIKVS RVGSAMVNAK DDEGVLVGSW DNICAYGVPP SAWTGSVDIL
LEYRSSENPV RYGQCWVFAG VFNTFLRCLG IPARIVTNYF SAHDNDANLQ MDIFLEEDGN
VNSKLTKDSV WNYHCWNEAW MTRPDLPVGF GGWQAVDSTP QENSDGMYRC GPASVQAIKH
GHVCFQFDAP FVFAEVNSDL IYITAKKDGT HVVENVDATH IGKLIVTKQI GGDGMMDITD
TYKFQEGQEE ERLALETALM YGAKKPLNTE GVMKSRSNVD MDFEVENAVL GKDFKLSITF
RNNSHNRYTI TAYLSANITF YTGVPKAEFK KETFDVTLEP LSFKKEAVLI QAGEYMGQLL
EQASLHFFVT ARINETRDVL AKQKSTVLTI PEIIIKVRGT QVVGSDMTVT VEFTNPLKET
LRNVWVHLDG PGVTRPMKKM FREIRPNSTV QWEEVCRPWV SGHRKLIASM SSDSLRHVYG
ELDVQIQRRP SM*

speed

0.65 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
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Problems

annotation problem

The chosen transcript ENST00000445223 on chromosome 6 has no correct in-frame stop codon (TGA, TAA or TAG) annotated
This is likely to cause a false prediction. You should choose another transcript.

back to results table