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 3.02559 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
F13A1	disease_causing_automatic	0.999999999505713	simple_aae		affected	0	V317F	single base exchange	rs121913073		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999505713 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM010241)
known disease mutation: rs16534 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:6224943C>AN/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.949G>T
cDNA.1215G>T
g.96304G>T

AA changes

V317F Score: 50 explain score(s)

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

317

frameshift

known variant

Reference ID: rs121913073
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs16534 (pathogenic for Factor XIII subunit A deficiency) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM010241)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010241)
known disease mutation at this position, please check HGMD for details (HGMD ID CM010241)

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.512	1
	5.444	1
(flanking)	5.444	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 increased	96313	wt: 0.38 / mu: 0.81	wt: GCCAATGCTGGGTTTTTGCTGGTGTCTTTAACACATGTAAG mu: GCCAATGCTGGTTTTTTGCTGGTGTCTTTAACACATGTAAG	gctg\|GTGT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

317

mutated

not conserved

317

Ptroglodytes

all identical

ENSPTRG00000017694

317

Mmulatta

all identical

ENSMMUG00000001248

317

Fcatus

all identical

ENSFCAG00000015505

317

Mmusculus

all identical

ENSMUSG00000039109

317

Ggallus

all identical

ENSGALG00000012802

324

Trubripes

all identical

ENSTRUG00000018071

335

Drerio

all identical

ENSDARG00000036893

335

Dmelanogaster

not conserved

FBgn0031975

332

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
315	329	HELIX		lost
333	341	STRAND		might get lost (downstream of altered splice site)
350	355	STRAND		might get lost (downstream of altered splice site)
357	359	STRAND		might get lost (downstream of altered splice site)
363	365	TURN		might get lost (downstream of altered splice site)
371	381	STRAND		might get lost (downstream of altered splice site)
374	374	ACT_SITE		might get lost (downstream of altered splice site)
384	386	STRAND		might get lost (downstream of altered splice site)
392	402	STRAND		might get lost (downstream of altered splice site)
397	397	ACT_SITE		might get lost (downstream of altered splice site)
404	414	STRAND		might get lost (downstream of altered splice site)
415	420	HELIX		might get lost (downstream of altered splice site)
425	428	STRAND		might get lost (downstream of altered splice site)
429	437	HELIX		might get lost (downstream of altered splice site)
437	437	METAL	Calcium.	might get lost (downstream of altered splice site)
439	439	METAL	Calcium.	might get lost (downstream of altered splice site)
439	445	STRAND		might get lost (downstream of altered splice site)
447	449	TURN		might get lost (downstream of altered splice site)
451	457	STRAND		might get lost (downstream of altered splice site)
464	468	STRAND		might get lost (downstream of altered splice site)
470	473	STRAND		might get lost (downstream of altered splice site)
475	477	STRAND		might get lost (downstream of altered splice site)
479	482	HELIX		might get lost (downstream of altered splice site)
486	486	METAL	Calcium.	might get lost (downstream of altered splice site)
489	499	HELIX		might get lost (downstream of altered splice site)
491	491	METAL	Calcium.	might get lost (downstream of altered splice site)
500	502	TURN		might get lost (downstream of altered splice site)
519	525	STRAND		might get lost (downstream of altered splice site)
534	542	STRAND		might get lost (downstream of altered splice site)
544	546	STRAND		might get lost (downstream of altered splice site)
548	559	STRAND		might get lost (downstream of altered splice site)
565	578	STRAND		might get lost (downstream of altered splice site)
582	590	STRAND		might get lost (downstream of altered splice site)
592	595	HELIX		might get lost (downstream of altered splice site)
596	598	TURN		might get lost (downstream of altered splice site)
604	613	STRAND		might get lost (downstream of altered splice site)
614	614	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
614	616	TURN		might get lost (downstream of altered splice site)
619	627	STRAND		might get lost (downstream of altered splice site)
634	639	STRAND		might get lost (downstream of altered splice site)
647	654	STRAND		might get lost (downstream of altered splice site)
657	659	STRAND		might get lost (downstream of altered splice site)
661	670	STRAND		might get lost (downstream of altered splice site)
671	673	TURN		might get lost (downstream of altered splice site)
674	684	STRAND		might get lost (downstream of altered splice site)
689	696	STRAND		might get lost (downstream of altered splice site)
702	711	STRAND		might get lost (downstream of altered splice site)
718	727	STRAND		might get lost (downstream of altered splice site)

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

949

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

1215

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

96304

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

6224943

original gDNA sequence snippet

TCCGGTATGGCCAATGCTGGGTTTTTGCTGGTGTCTTTAAC

altered gDNA sequence snippet

TCCGGTATGGCCAATGCTGGTTTTTTGCTGGTGTCTTTAAC

original cDNA sequence snippet

TCCGGTATGGCCAATGCTGGGTTTTTGCTGGTGTCTTTAAC

altered cDNA sequence snippet

TCCGGTATGGCCAATGCTGGTTTTTTGCTGGTGTCTTTAAC

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 DNIYAYGVPP SAWTGSVDIL
LEYRSSENPV RYGQCWFFAG 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

0.80 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.

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