MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000393540
Querying Taster for transcript #2: ENST00000307588
Querying Taster for transcript #3: ENST00000510617
MT speed 0 s - this script 4.327992 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CCDC110	polymorphism_automatic	2.73003841755326e-13	simple_aae		affected		L262M	single base exchange	rs7698680		show file
CCDC110	polymorphism_automatic	2.73003841755326e-13	simple_aae		affected		L299M	single base exchange	rs7698680		show file
CCDC110	polymorphism_automatic	2.73003841755326e-13	simple_aae		affected		L299M	single base exchange	rs7698680		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999727 (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)

chr4:186380846A>TN/A show variant in all transcripts IGV

HGNC symbol

CCDC110

Ensembl transcript ID

ENST00000393540

Genbank transcript ID

NM_001145411

UniProt peptide

Q8TBZ0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.784T>A
cDNA.795T>A
g.12068T>A

AA changes

L262M Score: 15 explain score(s)

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

262

frameshift

known variant

Reference ID: rs7698680

database	homozygous (T/T)	heterozygous	allele carriers
1000G	408	1115	1523
ExAC	14576	3615	18191

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.002	0.001
	-0.129	0.015
(flanking)	0.604	0.411

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	12073	wt: 0.6865 / mu: 0.7199 (marginal change - not scored)	wt: TTGGACGGTAACTTA mu: ATGGACGGTAACTTA	GGAC\|ggta
Donor gained	12068	0.60	mu: AAAACATGGACGGTA	AACA\|tgga
Donor gained	12064	0.56	mu: GAAGAAAACATGGAC	AGAA\|aaca

distance from splice site

547

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

262

mutated

all conserved

262

Ptroglodytes

all conserved

ENSPTRG00000016653

299

Mmulatta

all conserved

ENSMMUG00000000359

298

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000071104

306

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000075943

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
431	778	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

2391 / 2391

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

797 / 797

position of stopcodon in wt / mu cDNA

2402 / 2402

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

12 / 12

chromosome

strand

-1

last intron/exon boundary

2362

theoretical NMD boundary in CDS

2300

length of CDS

2391

coding sequence (CDS) position

784

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

795

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

12068

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

186380846

original gDNA sequence snippet

ACTTTATTAAGGAAGAAAACTTGGACGGTAACTTAAATGAA

altered gDNA sequence snippet

ACTTTATTAAGGAAGAAAACATGGACGGTAACTTAAATGAA

original cDNA sequence snippet

ACTTTATTAAGGAAGAAAACTTGGACGGTAACTTAAATGAA

altered cDNA sequence snippet

ACTTTATTAAGGAAGAAAACATGGACGGTAACTTAAATGAA

wildtype AA sequence

MSPEKQHREE DEVDSVLLSA SKILNSSEGV KESGCSDTEY GCIAESENQI QPQSALKVLQ
QQLESFQALR MQTLQNVSMP TENQEENLSM EKSHHFEDSK TLHSVEEKLS GDSVNSLPQS
VNVPSQIHSE DTLTLRTSTD NLSSNIIIHP SENSDILKNY NNFYRFLPTA PPNVMSQADT
VILDKSKITV PFLKHGFCEN LDDICHSIKQ MKEELQKSHD GEVALTNELQ TLQTDPDVHR
NGKYDMSPIH QDKMNFIKEE NLDGNLNEDI KSKRISELEA LVKKLLPFRE TVSKFHVHFC
RKCKKLSKSE MHRGKKNEKN NKEIPITGKN ITDLKFHSRV PRYTLSFLDQ TKHEMKDKER
QPFLVKQGSI ISENEKTSKV NSVTEQCVAK IQYLQNYLKE SVQIQKKVME LESENLNLKS
KMKPLIFTTQ SLIQKVETYE KQLKNLVEEK STIQSKLSKT EEYSKECLKE FKKIISKYNV
LQGQNKTLEE KNIQLSLEKQ QMMEALDQLK SKEHKTQSDM AIVNNENNRM SIEMEAMKTN
ILLIQDEKEM LEKKTHQLLK EKSSLGNELK ESQLEIIQLK EKERLAKTEQ ETLLQIIETV
KDEKLNLETT LQESTAARQI MEREIENIQT YQSTAEENFL QEIKNAKSEA SIYKNSLSEI
GKECEMLSKM VMETKTDNQI LKEELKKHSQ ENIKFENSIS RLTEDKILLE NYVRSIENER
DTLEFEMRHL QREYLSLSDK ICNQHNDPSK TTYISRREKF HFDNYTHEDT SSPQSRPLAS
DLKGYFKVKD RTLKHH*

mutated AA sequence

MSPEKQHREE DEVDSVLLSA SKILNSSEGV KESGCSDTEY GCIAESENQI QPQSALKVLQ
QQLESFQALR MQTLQNVSMP TENQEENLSM EKSHHFEDSK TLHSVEEKLS GDSVNSLPQS
VNVPSQIHSE DTLTLRTSTD NLSSNIIIHP SENSDILKNY NNFYRFLPTA PPNVMSQADT
VILDKSKITV PFLKHGFCEN LDDICHSIKQ MKEELQKSHD GEVALTNELQ TLQTDPDVHR
NGKYDMSPIH QDKMNFIKEE NMDGNLNEDI KSKRISELEA LVKKLLPFRE TVSKFHVHFC
RKCKKLSKSE MHRGKKNEKN NKEIPITGKN ITDLKFHSRV PRYTLSFLDQ TKHEMKDKER
QPFLVKQGSI ISENEKTSKV NSVTEQCVAK IQYLQNYLKE SVQIQKKVME LESENLNLKS
KMKPLIFTTQ SLIQKVETYE KQLKNLVEEK STIQSKLSKT EEYSKECLKE FKKIISKYNV
LQGQNKTLEE KNIQLSLEKQ QMMEALDQLK SKEHKTQSDM AIVNNENNRM SIEMEAMKTN
ILLIQDEKEM LEKKTHQLLK EKSSLGNELK ESQLEIIQLK EKERLAKTEQ ETLLQIIETV
KDEKLNLETT LQESTAARQI MEREIENIQT YQSTAEENFL QEIKNAKSEA SIYKNSLSEI
GKECEMLSKM VMETKTDNQI LKEELKKHSQ ENIKFENSIS RLTEDKILLE NYVRSIENER
DTLEFEMRHL QREYLSLSDK ICNQHNDPSK TTYISRREKF HFDNYTHEDT SSPQSRPLAS
DLKGYFKVKD RTLKHH*

speed

0.54 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: simple_aae, prob: 0.999999999999727 (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)

chr4:186380846A>TN/A show variant in all transcripts IGV

HGNC symbol

CCDC110

Ensembl transcript ID

ENST00000307588

Genbank transcript ID

NM_152775

UniProt peptide

Q8TBZ0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.895T>A
cDNA.971T>A
g.12068T>A

AA changes

L299M Score: 15 explain score(s)

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

299

frameshift

known variant

Reference ID: rs7698680

database	homozygous (T/T)	heterozygous	allele carriers
1000G	408	1115	1523
ExAC	14576	3615	18191

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.002	0.001
	-0.129	0.015
(flanking)	0.604	0.411

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	12073	wt: 0.6865 / mu: 0.7199 (marginal change - not scored)	wt: TTGGACGGTAACTTA mu: ATGGACGGTAACTTA	GGAC\|ggta
Donor gained	12068	0.60	mu: AAAACATGGACGGTA	AACA\|tgga
Donor gained	12064	0.56	mu: GAAGAAAACATGGAC	AGAA\|aaca

distance from splice site

547

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

299

mutated

all conserved

299

Ptroglodytes

all conserved

ENSPTRG00000016653

299

Mmulatta

all conserved

ENSMMUG00000000359

298

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000071104

306

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000075943

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
431	778	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

2502 / 2502

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

834 / 834

position of stopcodon in wt / mu cDNA

2578 / 2578

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

77 / 77

chromosome

strand

-1

last intron/exon boundary

2538

theoretical NMD boundary in CDS

2411

length of CDS

2502

coding sequence (CDS) position

895

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

971

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

12068

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

186380846

original gDNA sequence snippet

ACTTTATTAAGGAAGAAAACTTGGACGGTAACTTAAATGAA

altered gDNA sequence snippet

ACTTTATTAAGGAAGAAAACATGGACGGTAACTTAAATGAA

original cDNA sequence snippet

ACTTTATTAAGGAAGAAAACTTGGACGGTAACTTAAATGAA

altered cDNA sequence snippet

ACTTTATTAAGGAAGAAAACATGGACGGTAACTTAAATGAA

wildtype AA sequence

MSPEKQHREE DEVDSVLLSA SKILNSSEGV KESGCSDTEY GCIAESENQI QPQSALKVLQ
QQLESFQALR MQTLQNVSMV QSEISEILNK SIIEVENPQF SSEKNLVFGT RIEKDLPTEN
QEENLSMEKS HHFEDSKTLH SVEEKLSGDS VNSLPQSVNV PSQIHSEDTL TLRTSTDNLS
SNIIIHPSEN SDILKNYNNF YRFLPTAPPN VMSQADTVIL DKSKITVPFL KHGFCENLDD
ICHSIKQMKE ELQKSHDGEV ALTNELQTLQ TDPDVHRNGK YDMSPIHQDK MNFIKEENLD
GNLNEDIKSK RISELEALVK KLLPFRETVS KFHVHFCRKC KKLSKSEMHR GKKNEKNNKE
IPITGKNITD LKFHSRVPRY TLSFLDQTKH EMKDKERQPF LVKQGSIISE NEKTSKVNSV
TEQCVAKIQY LQNYLKESVQ IQKKVMELES ENLNLKSKMK PLIFTTQSLI QKVETYEKQL
KNLVEEKSTI QSKLSKTEEY SKECLKEFKK IISKYNVLQG QNKTLEEKNI QLSLEKQQMM
EALDQLKSKE HKTQSDMAIV NNENNRMSIE MEAMKTNILL IQDEKEMLEK KTHQLLKEKS
SLGNELKESQ LEIIQLKEKE RLAKTEQETL LQIIETVKDE KLNLETTLQE STAARQIMER
EIENIQTYQS TAEENFLQEI KNAKSEASIY KNSLSEIGKE CEMLSKMVME TKTDNQILKE
ELKKHSQENI KFENSISRLT EDKILLENYV RSIENERDTL EFEMRHLQRE YLSLSDKICN
QHNDPSKTTY ISRREKFHFD NYTHEDTSSP QSRPLASDLK GYFKVKDRTL KHH*

mutated AA sequence

MSPEKQHREE DEVDSVLLSA SKILNSSEGV KESGCSDTEY GCIAESENQI QPQSALKVLQ
QQLESFQALR MQTLQNVSMV QSEISEILNK SIIEVENPQF SSEKNLVFGT RIEKDLPTEN
QEENLSMEKS HHFEDSKTLH SVEEKLSGDS VNSLPQSVNV PSQIHSEDTL TLRTSTDNLS
SNIIIHPSEN SDILKNYNNF YRFLPTAPPN VMSQADTVIL DKSKITVPFL KHGFCENLDD
ICHSIKQMKE ELQKSHDGEV ALTNELQTLQ TDPDVHRNGK YDMSPIHQDK MNFIKEENMD
GNLNEDIKSK RISELEALVK KLLPFRETVS KFHVHFCRKC KKLSKSEMHR GKKNEKNNKE
IPITGKNITD LKFHSRVPRY TLSFLDQTKH EMKDKERQPF LVKQGSIISE NEKTSKVNSV
TEQCVAKIQY LQNYLKESVQ IQKKVMELES ENLNLKSKMK PLIFTTQSLI QKVETYEKQL
KNLVEEKSTI QSKLSKTEEY SKECLKEFKK IISKYNVLQG QNKTLEEKNI QLSLEKQQMM
EALDQLKSKE HKTQSDMAIV NNENNRMSIE MEAMKTNILL IQDEKEMLEK KTHQLLKEKS
SLGNELKESQ LEIIQLKEKE RLAKTEQETL LQIIETVKDE KLNLETTLQE STAARQIMER
EIENIQTYQS TAEENFLQEI KNAKSEASIY KNSLSEIGKE CEMLSKMVME TKTDNQILKE
ELKKHSQENI KFENSISRLT EDKILLENYV RSIENERDTL EFEMRHLQRE YLSLSDKICN
QHNDPSKTTY ISRREKFHFD NYTHEDTSSP QSRPLASDLK GYFKVKDRTL KHH*

speed

1.30 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999727 (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)

chr4:186380846A>TN/A show variant in all transcripts IGV

HGNC symbol

CCDC110

Ensembl transcript ID

ENST00000510617

Genbank transcript ID

N/A

UniProt peptide

Q8TBZ0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.895T>A
cDNA.956T>A
g.12068T>A

AA changes

L299M Score: 15 explain score(s)

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

299

frameshift

known variant

Reference ID: rs7698680

database	homozygous (T/T)	heterozygous	allele carriers
1000G	408	1115	1523
ExAC	14576	3615	18191

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.002	0.001
	-0.129	0.015
(flanking)	0.604	0.411

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	12073	wt: 0.6865 / mu: 0.7199 (marginal change - not scored)	wt: TTGGACGGTAACTTA mu: ATGGACGGTAACTTA	GGAC\|ggta
Donor gained	12068	0.60	mu: AAAACATGGACGGTA	AACA\|tgga
Donor gained	12064	0.56	mu: GAAGAAAACATGGAC	AGAA\|aaca

distance from splice site

547

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

299

mutated

all conserved

299

Ptroglodytes

all conserved

ENSPTRG00000016653

299

Mmulatta

all conserved

ENSMMUG00000000359

298

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000071104

306

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000075943

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
431	778	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

2511 / 2511

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

837 / 837

position of stopcodon in wt / mu cDNA

2572 / 2572

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

62 / 62

chromosome

strand

-1

last intron/exon boundary

2523

theoretical NMD boundary in CDS

2411

length of CDS

2511

coding sequence (CDS) position

895

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

956

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

12068

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

186380846

original gDNA sequence snippet

ACTTTATTAAGGAAGAAAACTTGGACGGTAACTTAAATGAA

altered gDNA sequence snippet

ACTTTATTAAGGAAGAAAACATGGACGGTAACTTAAATGAA

original cDNA sequence snippet

ACTTTATTAAGGAAGAAAACTTGGACGGTAACTTAAATGAA

altered cDNA sequence snippet

ACTTTATTAAGGAAGAAAACATGGACGGTAACTTAAATGAA

wildtype AA sequence

mutated AA sequence

MSPEKQHREE DEVDSVLLSA SKILNSSEGV KESGCSDTEY GCIAESENQI QPQSALKVLQ
QQLESFQALR MQTLQNVSMV QSEISEILNK SIIEVENPQF SSEKNLVFGT RIEKDLPTEN
QEENLSMEKS HHFEDSKTLH SVEEKLSGDS VNSLPQSVNV PSQIHSEDTL TLRTSTDNLS
SNIIIHPSEN SDILKNYNNF YRFLPTAPPN VMSQADTVIL DKSKITVPFL KHGFCENLDD
ICHSIKQMKE ELQKSHDGEV ALTNELQTLQ TDPDVHRNGK YDMSPIHQDK MNFIKEENMD
GNLNEDIKSK RISELEALVK KLLPFRETVS KFHVHFCRKC KKLSKSEMHR GKKNEKNNKE
IPITGKNITD LKFHSRVPRY TLSFLDQTKH EMKDKERQPF LVKQGSIISE NEKTSKVNSV
TEQCVAKIQY LQNYLKESVQ IQKKVMELES ENLNLKSKMK PLIFTTQSLI QKVETYEKQL
KNLVEEKSTI QSKLSKTEEY SKECLKEFKK IISKYNVLQG QNKTLEEKNI QLSLEKQQMM
EALDQLKSKE HKTQSDMAIV NNENNRMSIE MEAMKTNILL IQDEKEMLEK KTHQLLKEKS
SLGNELKESQ LEIIQLKEKE RLAKTEQETL LQIIETVKDE KLNLETTLQE STAARQIMER
EIENIQTYQS TAEENFLQEI KNAKSEASIY KNSLSEIGKE CEMLSKMVME TKTDNQILKE
ELKKHSQENI KFENSISRLT EDKILLENYV RSIENERDTL EFEMRHLQRE YLSLSDKICN
QHNDPSKTTY ISRREKFHFD NYTHEDTSSP QSRPLASDLK GIPSKLYHLL PSKIYK*

speed

1.00 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems