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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000392455
Querying Taster for transcript #2: ENST00000392456
MT speed 0 s - this script 4.315699 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CCDC50	polymorphism_automatic	2.99760216648792e-15	simple_aae		affected		M156T	single base exchange	rs293813		show file
CCDC50	polymorphism_automatic	6.99440505513849e-15	simple_aae		affected		M332T	single base exchange	rs293813		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999997 (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)

chr3:191097966T>CN/A show variant in all transcripts IGV

HGNC symbol

CCDC50

Ensembl transcript ID

ENST00000392455

Genbank transcript ID

NM_174908

UniProt peptide

Q8IVM0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.467T>C
cDNA.1065T>C
g.51101T>C

AA changes

M156T Score: 81 explain score(s)

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

156

frameshift

known variant

Reference ID: rs293813

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1099	1030	2129
ExAC	17770	-2773	14997

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.078	0
	-0.04	0.002
(flanking)	-0.171	0.027

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	51100	wt: 0.9502 / mu: 0.9801 (marginal change - not scored)	wt: GAGTGATGAAAGAAG mu: GAGTGACGAAAGAAG	GTGA\|tgaa
Donor increased	51105	wt: 0.21 / mu: 0.26	wt: ATGAAAGAAGCTGTA mu: ACGAAAGAAGCTGTA	GAAA\|gaag
Donor marginally increased	51096	wt: 0.9966 / mu: 0.9975 (marginal change - not scored)	wt: CCAAGAGTGATGAAA mu: CCAAGAGTGACGAAA	AAGA\|gtga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

156

mutated

not conserved

156

Ptroglodytes

not conserved

ENSPTRG00000015745

332

Mmulatta

not conserved

ENSMMUG00000015330

332

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000038127

156

Ggallus

not conserved

ENSGALG00000020813

157

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000002145

157

protein features

start (aa)	end (aa)	feature	details
214	250	COMPBIAS	Lys-rich.	might get lost (downstream of altered splice site)
266	269	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
279	279	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

921 / 921

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

307 / 307

position of stopcodon in wt / mu cDNA

1519 / 1519

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

599 / 599

chromosome

strand

last intron/exon boundary

1500

theoretical NMD boundary in CDS

851

length of CDS

921

coding sequence (CDS) position

467

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

1065

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

51101

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

191097966

original gDNA sequence snippet

AGGAATGAAGCCAAGAGTGATGAAAGAAGCTGTATCTACTC

altered gDNA sequence snippet

AGGAATGAAGCCAAGAGTGACGAAAGAAGCTGTATCTACTC

original cDNA sequence snippet

AGGAATGAAGCCAAGAGTGATGAAAGAAGCTGTATCTACTC

altered cDNA sequence snippet

AGGAATGAAGCCAAGAGTGACGAAAGAAGCTGTATCTACTC

wildtype AA sequence

MAEVSIDQSK LPGVKEVCRD FAVLEDHTLA HSLQEQEIEH HLASNVQRNR LVQHDLQVAK
QLQEEDLKAQ AQLQKRYKDL EQQDCEIAQE IQEKLAIEAE RRRIQEKKDE DIARLLQEKE
LQEEKKRKKH FPEFPATRAY ADSYYYEDGG MKPRVMKEAV STPSRMAHRD QEWYDAEIAR
KLQEEELLAT QVDMRAAQVA QDEEIARLLM AEEKKAYKKA KEREKSSLDK RKQDPEWKPK
TAKAANSKSK ESDEPHHSKN ERPARPPPPI MTDGEDADYT HFTNQQSSTR HFSKSESSHK
GFHYKH*

mutated AA sequence

MAEVSIDQSK LPGVKEVCRD FAVLEDHTLA HSLQEQEIEH HLASNVQRNR LVQHDLQVAK
QLQEEDLKAQ AQLQKRYKDL EQQDCEIAQE IQEKLAIEAE RRRIQEKKDE DIARLLQEKE
LQEEKKRKKH FPEFPATRAY ADSYYYEDGG MKPRVTKEAV STPSRMAHRD QEWYDAEIAR
KLQEEELLAT QVDMRAAQVA QDEEIARLLM AEEKKAYKKA KEREKSSLDK RKQDPEWKPK
TAKAANSKSK ESDEPHHSKN ERPARPPPPI MTDGEDADYT HFTNQQSSTR HFSKSESSHK
GFHYKH*

speed

1.20 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: 0.999999999999993 (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)

chr3:191097966T>CN/A show variant in all transcripts IGV

HGNC symbol

CCDC50

Ensembl transcript ID

ENST00000392456

Genbank transcript ID

NM_178335

UniProt peptide

Q8IVM0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.995T>C
cDNA.1585T>C
g.51101T>C

AA changes

M332T Score: 81 explain score(s)

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

332

frameshift

known variant

Reference ID: rs293813

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1099	1030	2129
ExAC	17770	-2773	14997

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.078	0
	-0.04	0.002
(flanking)	-0.171	0.027

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	51100	wt: 0.9502 / mu: 0.9801 (marginal change - not scored)	wt: GAGTGATGAAAGAAG mu: GAGTGACGAAAGAAG	GTGA\|tgaa
Donor increased	51105	wt: 0.21 / mu: 0.26	wt: ATGAAAGAAGCTGTA mu: ACGAAAGAAGCTGTA	GAAA\|gaag
Donor marginally increased	51096	wt: 0.9966 / mu: 0.9975 (marginal change - not scored)	wt: CCAAGAGTGATGAAA mu: CCAAGAGTGACGAAA	AAGA\|gtga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

332

mutated

not conserved

332

Ptroglodytes

not conserved

ENSPTRG00000015745

332

Mmulatta

not conserved

ENSMMUG00000015330

332

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000038127

156

Ggallus

no alignment

ENSGALG00000020813

n/a

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000002145

312

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1449 / 1449

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

483 / 483

position of stopcodon in wt / mu cDNA

2039 / 2039

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

591 / 591

chromosome

strand

last intron/exon boundary

2020

theoretical NMD boundary in CDS

1379

length of CDS

1449

coding sequence (CDS) position

995

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

1585

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

51101

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

191097966

original gDNA sequence snippet

AGGAATGAAGCCAAGAGTGATGAAAGAAGCTGTATCTACTC

altered gDNA sequence snippet

AGGAATGAAGCCAAGAGTGACGAAAGAAGCTGTATCTACTC

original cDNA sequence snippet

AGGAATGAAGCCAAGAGTGATGAAAGAAGCTGTATCTACTC

altered cDNA sequence snippet

AGGAATGAAGCCAAGAGTGACGAAAGAAGCTGTATCTACTC

wildtype AA sequence

MAEVSIDQSK LPGVKEVCRD FAVLEDHTLA HSLQEQEIEH HLASNVQRNR LVQHDLQVAK
QLQEEDLKAQ AQLQKRYKDL EQQDCEIAQE IQEKLAIEAE RRRIQEKKDE DIARLLQEKE
LQEEKKRKKH FPEFPATRAY ADSYYYEDGD QPGSRRAREL GSGFSRPCRL QRDGKTVKHK
KEKPEHPLEN LEEPEQHCSS KRSLSSSSSG KGRDNPHINN EQHERKRSTQ ERPRRPLLPT
ISGEVFLSTE CDDWETKINH QTRNWEKQSR HQDRLSPKSS QKAGLHCKEV VYGRDHGQGE
HRKRRHRPRT PPFSESEEQL HLHDAGMKPR VMKEAVSTPS RMAHRDQEWY DAEIARKLQE
EELLATQVDM RAAQVAQDEE IARLLMAEEK KAYKKAKERE KSSLDKRKQD PEWKPKTAKA
ANSKSKESDE PHHSKNERPA RPPPPIMTDG EDADYTHFTN QQSSTRHFSK SESSHKGFHY
KH*

mutated AA sequence

MAEVSIDQSK LPGVKEVCRD FAVLEDHTLA HSLQEQEIEH HLASNVQRNR LVQHDLQVAK
QLQEEDLKAQ AQLQKRYKDL EQQDCEIAQE IQEKLAIEAE RRRIQEKKDE DIARLLQEKE
LQEEKKRKKH FPEFPATRAY ADSYYYEDGD QPGSRRAREL GSGFSRPCRL QRDGKTVKHK
KEKPEHPLEN LEEPEQHCSS KRSLSSSSSG KGRDNPHINN EQHERKRSTQ ERPRRPLLPT
ISGEVFLSTE CDDWETKINH QTRNWEKQSR HQDRLSPKSS QKAGLHCKEV VYGRDHGQGE
HRKRRHRPRT PPFSESEEQL HLHDAGMKPR VTKEAVSTPS RMAHRDQEWY DAEIARKLQE
EELLATQVDM RAAQVAQDEE IARLLMAEEK KAYKKAKERE KSSLDKRKQD PEWKPKTAKA
ANSKSKESDE PHHSKNERPA RPPPPIMTDG EDADYTHFTN QQSSTRHFSK SESSHKGFHY
KH*

speed

1.11 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems