mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.970233197181046 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr15:40914177T>CN/A show variant in all transcripts IGV

HGNC symbol

KNL1

Ensembl transcript ID

ENST00000399668

Genbank transcript ID

NM_144508

UniProt peptide

Q8NG31

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1715T>C
cDNA.1876T>C
g.27960T>C

AA changes

M572T Score: 81 explain score(s)

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

572

frameshift

known variant

Reference ID: rs11858113

database	homozygous (C/C)	heterozygous	allele carriers
1000G	326	1108	1434
ExAC	9787	13193	22980

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.135	1
	0.242	1
(flanking)	3.847	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
Donor increased	27952	wt: 0.47 / mu: 0.73	wt: TCAGGTGAAAATATG mu: TCAGGTGAAAATACG	AGGT\|gaaa
Donor marginally increased	27951	wt: 0.4935 / mu: 0.5449 (marginal change - not scored)	wt: ATCAGGTGAAAATAT mu: ATCAGGTGAAAATAC	CAGG\|tgaa

distance from splice site

1340

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

572

mutated

not conserved

572

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000027326

552

Ggallus

no homologue

Trubripes

no alignment

ENSTRUG00000013401

n/a

Drerio

no alignment

ENSDARG00000070239

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
1	728	REGION	Interaction with BUB1 and BUB1B.	lost
578	578	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
601	601	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
682	682	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
765	765	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
767	767	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
855	1201	REGION	2 X 104 AA approximate repeats.	might get lost (downstream of altered splice site)
885	989	REPEAT	1.	might get lost (downstream of altered splice site)
954	954	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
956	956	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1039	1039	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1042	1042	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
1076	1076	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1099	1201	REPEAT	2.	might get lost (downstream of altered splice site)
1232	1232	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1332	1332	CONFLICT	P -> A (in Ref. 2; BAC05691).	might get lost (downstream of altered splice site)
1357	1357	CONFLICT	N -> H (in Ref. 2; BAC05691).	might get lost (downstream of altered splice site)
1720	1720	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1756	1756	CONFLICT	N -> Y (in Ref. 2; BAC05691).	might get lost (downstream of altered splice site)
1773	1773	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1789	1803	MOTIF	Nuclear localization signal (Potential).	might get lost (downstream of altered splice site)
1818	1819	SITE	Breakpoint for translocation to form MLL- CASC5.	might get lost (downstream of altered splice site)
1834	2316	REGION	Necessary for kinetochore localization and for interaction with NSL1 and DSN1.	might get lost (downstream of altered splice site)
1845	1845	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1869	1869	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1879	1879	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
1942	2133	COILED	Potential.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

6951 / 6951

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

2317 / 2317

position of stopcodon in wt / mu cDNA

7112 / 7112

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

162 / 162

chromosome

strand

last intron/exon boundary

6998

theoretical NMD boundary in CDS

6786

length of CDS

6951

coding sequence (CDS) position

1715

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

1876

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

27960

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

40914177

original gDNA sequence snippet

ACTCTTATCAGGTGAAAATATGGATTTGACTGAAAGTCACA

altered gDNA sequence snippet

ACTCTTATCAGGTGAAAATACGGATTTGACTGAAAGTCACA

original cDNA sequence snippet

ACTCTTATCAGGTGAAAATATGGATTTGACTGAAAGTCACA

altered cDNA sequence snippet

ACTCTTATCAGGTGAAAATACGGATTTGACTGAAAGTCACA

wildtype AA sequence

MDGVSSEANE ENDNIERPVR RRHSSILKPP RSPLQDLRGG NERVQESNAL RNKKNSRRVS
FADTIKVFQT ESHMKIVRKS EMEETETGEN LLLIQNKKLE DNYCEITGMN TLLSAPIHTQ
MQQKEFSIIE HTRERKHAND QTVIFSDENQ MDLTSSHTVM ITKGLLDNPI SEKSTKIDTT
SFLANLKLHT EDSRMKKEVN FSVDQNTSSE NKIDFNDFIK RLKTGKCSAF PDVPDKENFE
IPIYSKEPNS ASSTHQMHVS LKEDENNSNI TRLFREKDDG MNFTQCHTAN IQTLIPTSSE
TNSRESKGND ITIYGNDFMD LTFNHTLQIL PATGNFSEIE NQTQNAMDVT TGYGTKASGN
KTVFKSKQNT AFQDLSINSA DKIHITRSHI MGAETHIVSQ TCNQDARILA MTPESIYSNP
SIQGCKTVFY SSCNDAMEMT KCLSNMREEK NLLKHDSNYA KMYCNPDAMS SLTEKTIYSG
EENMDITKSH TVAIDNQIFK QDQSNVQIAA APTPEKEMML QNLMTTSEDG KMNVNCNSVP
HVSKERIQQS LSNPLSISLT DRKTELLSGE NMDLTESHTS NLGSQVPLAA YNLAPESTSE
SHSQSKSSSD ECEEITKSRN EPFQRSDIIA KNSLTDTWNK DKDWVLKILP YLDKDSPQSA
DCNQEIATSH NIVYCGGVLD KQITNRNTVS WEQSLFSTTK PLFSSGQFSM KNHDTAISSH
TVKSVLGQNS KLAEPLRKSL SNPTPDYCHD KMIICSEEEQ NMDLTKSHTV VIGFGPSELQ
ELGKTNLEHT TGQLTTMNRQ IAVKVEKCGK SPIEKSGVLK SNCIMDVLED ESVQKPKFPK
EKQNVKIWGR KSVGGPKIDK TIVFSEDDKN DMDITKSYTI EINHRPLLEK RDCHLVPLAG
TSETILYTCR QDDMEITRSH TTALECKTVS PDEITTRPMD KTVVFVDNHV ELEMTESHTV
FIDYQEKERT DRPNFELSQR KSLGTPTVIC TPTEESVFFP GNGESDRLVA NDSQLTPLEE
WSNNRGPVEV ADNMELSKSA TCKNIKDVQS PGFLNEPLSS KSQRRKSLKL KNDKTIVFSE
NHKNDMDITQ SCMVEIDNES ALEDKEDFHL AGASKTILYS CGQDDMEITR SHTTALECKT
LLPNEIAIRP MDKTVLFTDN YSDLEVTDSH TVFIDCQATE KILEENPKFG IGKGKNLGVS
FPKDNSCVQE IAEKQALAVG NKIVLHTEQK QQLFAATNRT TNEIIKFHSA AMDEKVIGKV
VDQACTLEKA QVESCQLNNR DRRNVDFTSS HATAVCGSSD NYSCLPNVIS CTDNLEGSAM
LLCDKDEEKA NYCPVQNDLA YANDFASEYY LESEGQPLSA PCPLLEKEEV IQTSTKGQLD
CVITLHKDQD LIKDPRNLLA NQTLVYSQDL GEMTKLNSKR VSFKLPKDQM KVYVDDIYVI
PQPHFSTDQP PLPKKGQSSI NKEEVILSKA GNKSLNIIEN SSAPICENKP KILNSEEWFA
AACKKELKEN IQTTNYNTAL DFHSNSDVTK QVIQTHVNAG EAPDPVITSN VPCFHSIKPN
LNNLNGKTGE FLAFQTVHLP PLPEQLLELG NKAHNDMHIV QATEIHNINI ISSNAKDSRD
EENKKSHNGA ETTSLPPKTV FKDKVRRCSL GIFLPRLPNK RNCSVTGIDD LEQIPADTTD
INHLETQPVS SKDSGIGSVA GKLNLSPSQY INEENLPVYP DEINSSDSIN IETEEKALIE
TYQKEISPYE NKMGKTCNSQ KRTWVQEEED IHKEKKIRKN EIKFSDTTQD REIFDHHTEE
DIDKSANSVL IKNLSRTPSS CSSSLDSIKA DGTSLDFSTY RSSQMESQFL RDTICEESLR
EKLQDGRITI REFFILLQVH ILIQKPRQSN LPGNFTVNTP PTPEDLMLSQ YVYRPKIQIY
REDCEARRQK IEELKLSASN QDKLLVDINK NLWEKMRHCS DKELKAFGIY LNKIKSCFTK
MTKVFTHQGK VALYGKLVQS AQNEREKLQI KIDEMDKILK KIDNCLTEME TETKNLEDEE
KNNPVEEWDS EMRAAEKELE QLKTEEEELQ RNLLELEVQK EQTLAQIDFM QKQRNRTEEL
LDQLSLSEWD VVEWSDDQAV FTFVYDTIQL TITFEESVVG FPFLDKRYRK IVDVNFQSLL
DEDQAPPSSL LVHKLIFQYV EEKESWKKTC TTQHQLPKML EEFSLVVHHC RLLGEEIEYL
KRWGPNYNLM NIDINNNELR LLFSSSAAFA KFEITLFLSA YYPSVPLPST IQNHVGNTSQ
DDIATILSKV PLENNYLKNV VKQIYQDLFQ DCHFYH*

mutated AA sequence

MDGVSSEANE ENDNIERPVR RRHSSILKPP RSPLQDLRGG NERVQESNAL RNKKNSRRVS
FADTIKVFQT ESHMKIVRKS EMEETETGEN LLLIQNKKLE DNYCEITGMN TLLSAPIHTQ
MQQKEFSIIE HTRERKHAND QTVIFSDENQ MDLTSSHTVM ITKGLLDNPI SEKSTKIDTT
SFLANLKLHT EDSRMKKEVN FSVDQNTSSE NKIDFNDFIK RLKTGKCSAF PDVPDKENFE
IPIYSKEPNS ASSTHQMHVS LKEDENNSNI TRLFREKDDG MNFTQCHTAN IQTLIPTSSE
TNSRESKGND ITIYGNDFMD LTFNHTLQIL PATGNFSEIE NQTQNAMDVT TGYGTKASGN
KTVFKSKQNT AFQDLSINSA DKIHITRSHI MGAETHIVSQ TCNQDARILA MTPESIYSNP
SIQGCKTVFY SSCNDAMEMT KCLSNMREEK NLLKHDSNYA KMYCNPDAMS SLTEKTIYSG
EENMDITKSH TVAIDNQIFK QDQSNVQIAA APTPEKEMML QNLMTTSEDG KMNVNCNSVP
HVSKERIQQS LSNPLSISLT DRKTELLSGE NTDLTESHTS NLGSQVPLAA YNLAPESTSE
SHSQSKSSSD ECEEITKSRN EPFQRSDIIA KNSLTDTWNK DKDWVLKILP YLDKDSPQSA
DCNQEIATSH NIVYCGGVLD KQITNRNTVS WEQSLFSTTK PLFSSGQFSM KNHDTAISSH
TVKSVLGQNS KLAEPLRKSL SNPTPDYCHD KMIICSEEEQ NMDLTKSHTV VIGFGPSELQ
ELGKTNLEHT TGQLTTMNRQ IAVKVEKCGK SPIEKSGVLK SNCIMDVLED ESVQKPKFPK
EKQNVKIWGR KSVGGPKIDK TIVFSEDDKN DMDITKSYTI EINHRPLLEK RDCHLVPLAG
TSETILYTCR QDDMEITRSH TTALECKTVS PDEITTRPMD KTVVFVDNHV ELEMTESHTV
FIDYQEKERT DRPNFELSQR KSLGTPTVIC TPTEESVFFP GNGESDRLVA NDSQLTPLEE
WSNNRGPVEV ADNMELSKSA TCKNIKDVQS PGFLNEPLSS KSQRRKSLKL KNDKTIVFSE
NHKNDMDITQ SCMVEIDNES ALEDKEDFHL AGASKTILYS CGQDDMEITR SHTTALECKT
LLPNEIAIRP MDKTVLFTDN YSDLEVTDSH TVFIDCQATE KILEENPKFG IGKGKNLGVS
FPKDNSCVQE IAEKQALAVG NKIVLHTEQK QQLFAATNRT TNEIIKFHSA AMDEKVIGKV
VDQACTLEKA QVESCQLNNR DRRNVDFTSS HATAVCGSSD NYSCLPNVIS CTDNLEGSAM
LLCDKDEEKA NYCPVQNDLA YANDFASEYY LESEGQPLSA PCPLLEKEEV IQTSTKGQLD
CVITLHKDQD LIKDPRNLLA NQTLVYSQDL GEMTKLNSKR VSFKLPKDQM KVYVDDIYVI
PQPHFSTDQP PLPKKGQSSI NKEEVILSKA GNKSLNIIEN SSAPICENKP KILNSEEWFA
AACKKELKEN IQTTNYNTAL DFHSNSDVTK QVIQTHVNAG EAPDPVITSN VPCFHSIKPN
LNNLNGKTGE FLAFQTVHLP PLPEQLLELG NKAHNDMHIV QATEIHNINI ISSNAKDSRD
EENKKSHNGA ETTSLPPKTV FKDKVRRCSL GIFLPRLPNK RNCSVTGIDD LEQIPADTTD
INHLETQPVS SKDSGIGSVA GKLNLSPSQY INEENLPVYP DEINSSDSIN IETEEKALIE
TYQKEISPYE NKMGKTCNSQ KRTWVQEEED IHKEKKIRKN EIKFSDTTQD REIFDHHTEE
DIDKSANSVL IKNLSRTPSS CSSSLDSIKA DGTSLDFSTY RSSQMESQFL RDTICEESLR
EKLQDGRITI REFFILLQVH ILIQKPRQSN LPGNFTVNTP PTPEDLMLSQ YVYRPKIQIY
REDCEARRQK IEELKLSASN QDKLLVDINK NLWEKMRHCS DKELKAFGIY LNKIKSCFTK
MTKVFTHQGK VALYGKLVQS AQNEREKLQI KIDEMDKILK KIDNCLTEME TETKNLEDEE
KNNPVEEWDS EMRAAEKELE QLKTEEEELQ RNLLELEVQK EQTLAQIDFM QKQRNRTEEL
LDQLSLSEWD VVEWSDDQAV FTFVYDTIQL TITFEESVVG FPFLDKRYRK IVDVNFQSLL
DEDQAPPSSL LVHKLIFQYV EEKESWKKTC TTQHQLPKML EEFSLVVHHC RLLGEEIEYL
KRWGPNYNLM NIDINNNELR LLFSSSAAFA KFEITLFLSA YYPSVPLPST IQNHVGNTSQ
DDIATILSKV PLENNYLKNV VKQIYQDLFQ DCHFYH*

speed

0.63 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