MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000393215
Querying Taster for transcript #2: ENST00000343036
Querying Taster for transcript #3: ENST00000393216
MT speed 0 s - this script 3.520001 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CFAP77	polymorphism_automatic	0.996715619882218	simple_aae		affected		G101R	single base exchange	rs7047726		show file
CFAP77	polymorphism_automatic	0.996715619882218	simple_aae		affected		G137R	single base exchange	rs7047726		show file
CFAP77	polymorphism_automatic	0.996715619882218	simple_aae		affected		G101R	single base exchange	rs7047726		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.00328438011778205 (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)

chr9:135374764G>AN/A show variant in all transcripts IGV

HGNC symbol

CFAP77

Ensembl transcript ID

ENST00000393215

Genbank transcript ID

N/A

UniProt peptide

Q6ZQR2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.301G>A
cDNA.530G>A
g.89335G>A

AA changes

G101R Score: 125 explain score(s)

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

101

frameshift

known variant

Reference ID: rs7047726

database	homozygous (A/A)	heterozygous	allele carriers
1000G	149	635	784
ExAC	1617	12019	13636

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.257	0.54
	3.978	0.998
(flanking)	3.978	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 decreased	89329	wt: 0.7579 / mu: 0.7311 (marginal change - not scored)	wt: TGGGTCTCTCCCTGCCCTCAGCCATCGGACGCTGGAACGTG mu: TGGGTCTCTCCCTGCCCTCAGCCATCAGACGCTGGAACGTG	tcag\|CCAT
Acc marginally increased	89335	wt: 0.8551 / mu: 0.8717 (marginal change - not scored)	wt: TCTCCCTGCCCTCAGCCATCGGACGCTGGAACGTGTTCAAG mu: TCTCCCTGCCCTCAGCCATCAGACGCTGGAACGTGTTCAAG	atcg\|GACG
Acc marginally increased	89326	wt: 0.3157 / mu: 0.3255 (marginal change - not scored)	wt: CCGTGGGTCTCTCCCTGCCCTCAGCCATCGGACGCTGGAAC mu: CCGTGGGTCTCTCCCTGCCCTCAGCCATCAGACGCTGGAAC	ccct\|CAGC
Acc marginally increased	89332	wt: 0.5791 / mu: 0.6016 (marginal change - not scored)	wt: GTCTCTCCCTGCCCTCAGCCATCGGACGCTGGAACGTGTTC mu: GTCTCTCCCTGCCCTCAGCCATCAGACGCTGGAACGTGTTC	gcca\|TCGG
Donor marginally increased	89328	wt: 0.7208 / mu: 0.7385 (marginal change - not scored)	wt: CCCTCAGCCATCGGA mu: CCCTCAGCCATCAGA	CTCA\|gcca
Donor gained	89335	0.40	mu: CCATCAGACGCTGGA	ATCA\|gacg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

101

mutated

not conserved

101

Ptroglodytes

all identical

ENSPTRG00000021497

137

Mmulatta

all identical

ENSMMUG00000004588

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000079502

101

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000068122

Dmelanogaster

no homologue

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

597 / 597

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

199 / 199

position of stopcodon in wt / mu cDNA

826 / 826

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

230 / 230

chromosome

strand

last intron/exon boundary

754

theoretical NMD boundary in CDS

474

length of CDS

597

coding sequence (CDS) position

301

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

530

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

89335

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

135374764

original gDNA sequence snippet

TCTCCCTGCCCTCAGCCATCGGACGCTGGAACGTGTTCAAG

altered gDNA sequence snippet

TCTCCCTGCCCTCAGCCATCAGACGCTGGAACGTGTTCAAG

original cDNA sequence snippet

GAGGAGTCCCTGAAGCCATCGGACGCTGGAACGTGTTCAAG

altered cDNA sequence snippet

GAGGAGTCCCTGAAGCCATCAGACGCTGGAACGTGTTCAAG

wildtype AA sequence

mutated AA sequence

speed

0.74 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: 0.00328438011778205 (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)

chr9:135374764G>AN/A show variant in all transcripts IGV

HGNC symbol

CFAP77

Ensembl transcript ID

ENST00000343036

Genbank transcript ID

NM_207417

UniProt peptide

Q6ZQR2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.409G>A
cDNA.457G>A
g.89335G>A

AA changes

G137R Score: 125 explain score(s)

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

137

frameshift

known variant

Reference ID: rs7047726

database	homozygous (A/A)	heterozygous	allele carriers
1000G	149	635	784
ExAC	1617	12019	13636

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.257	0.54
	3.978	0.998
(flanking)	3.978	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 decreased	89329	wt: 0.7579 / mu: 0.7311 (marginal change - not scored)	wt: TGGGTCTCTCCCTGCCCTCAGCCATCGGACGCTGGAACGTG mu: TGGGTCTCTCCCTGCCCTCAGCCATCAGACGCTGGAACGTG	tcag\|CCAT
Acc marginally increased	89335	wt: 0.8551 / mu: 0.8717 (marginal change - not scored)	wt: TCTCCCTGCCCTCAGCCATCGGACGCTGGAACGTGTTCAAG mu: TCTCCCTGCCCTCAGCCATCAGACGCTGGAACGTGTTCAAG	atcg\|GACG
Acc marginally increased	89326	wt: 0.3157 / mu: 0.3255 (marginal change - not scored)	wt: CCGTGGGTCTCTCCCTGCCCTCAGCCATCGGACGCTGGAAC mu: CCGTGGGTCTCTCCCTGCCCTCAGCCATCAGACGCTGGAAC	ccct\|CAGC
Acc marginally increased	89332	wt: 0.5791 / mu: 0.6016 (marginal change - not scored)	wt: GTCTCTCCCTGCCCTCAGCCATCGGACGCTGGAACGTGTTC mu: GTCTCTCCCTGCCCTCAGCCATCAGACGCTGGAACGTGTTC	gcca\|TCGG
Donor marginally increased	89328	wt: 0.7208 / mu: 0.7385 (marginal change - not scored)	wt: CCCTCAGCCATCGGA mu: CCCTCAGCCATCAGA	CTCA\|gcca
Donor gained	89335	0.40	mu: CCATCAGACGCTGGA	ATCA\|gacg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

137

mutated

not conserved

137

Ptroglodytes

all identical

ENSPTRG00000021497

137

Mmulatta

all identical

ENSMMUG00000004588

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000079502

101

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000068122

Dmelanogaster

no homologue

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

963 / 963

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

321 / 321

position of stopcodon in wt / mu cDNA

1011 / 1011

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

49 / 49

chromosome

strand

last intron/exon boundary

889

theoretical NMD boundary in CDS

790

length of CDS

963

coding sequence (CDS) position

409

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

457

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

89335

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

135374764

original gDNA sequence snippet

TCTCCCTGCCCTCAGCCATCGGACGCTGGAACGTGTTCAAG

altered gDNA sequence snippet

TCTCCCTGCCCTCAGCCATCAGACGCTGGAACGTGTTCAAG

original cDNA sequence snippet

GAGGAGTCCCTGAAGCCATCGGACGCTGGAACGTGTTCAAG

altered cDNA sequence snippet

GAGGAGTCCCTGAAGCCATCAGACGCTGGAACGTGTTCAAG

wildtype AA sequence

MPEARSSGPD LTRWRKQQQP VRRTVSQVCP PPRRPLTVAD IRSGMENERL GVVRDSMFQN
PLIVKAAGPA SVGTSYSVYD SSAVQKVIPS LAGHHIKGGP QAELGKPRER SYSLPGINFN
YGLYIRGLDG GVPEAIGRWN VFKQQPTCPH ELTRNYIAMN RGAVKAGLVT ARENLLYRQL
NDIRISDQDD RRMKKEPPPL PPNMTFGIRA RPSTPFFDLL QHRYLQLWVQ EQKATQKAIK
LEKKQKVVLG KLYETRSSQL RKYKPPVKLD TLWHMPHFQK VGRHLDTFPT EADRQRALKA
HREECAVRQG TLRMGNYTHP *

mutated AA sequence

MPEARSSGPD LTRWRKQQQP VRRTVSQVCP PPRRPLTVAD IRSGMENERL GVVRDSMFQN
PLIVKAAGPA SVGTSYSVYD SSAVQKVIPS LAGHHIKGGP QAELGKPRER SYSLPGINFN
YGLYIRGLDG GVPEAIRRWN VFKQQPTCPH ELTRNYIAMN RGAVKAGLVT ARENLLYRQL
NDIRISDQDD RRMKKEPPPL PPNMTFGIRA RPSTPFFDLL QHRYLQLWVQ EQKATQKAIK
LEKKQKVVLG KLYETRSSQL RKYKPPVKLD TLWHMPHFQK VGRHLDTFPT EADRQRALKA
HREECAVRQG TLRMGNYTHP *

speed

0.78 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.00328438011778205 (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)

chr9:135374764G>AN/A show variant in all transcripts IGV

HGNC symbol

CFAP77

Ensembl transcript ID

ENST00000393216

Genbank transcript ID

N/A

UniProt peptide

Q6ZQR2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.301G>A
cDNA.345G>A
g.89335G>A

AA changes

G101R Score: 125 explain score(s)

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

101

frameshift

known variant

Reference ID: rs7047726

database	homozygous (A/A)	heterozygous	allele carriers
1000G	149	635	784
ExAC	1617	12019	13636

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.257	0.54
	3.978	0.998
(flanking)	3.978	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 decreased	89329	wt: 0.7579 / mu: 0.7311 (marginal change - not scored)	wt: TGGGTCTCTCCCTGCCCTCAGCCATCGGACGCTGGAACGTG mu: TGGGTCTCTCCCTGCCCTCAGCCATCAGACGCTGGAACGTG	tcag\|CCAT
Acc marginally increased	89335	wt: 0.8551 / mu: 0.8717 (marginal change - not scored)	wt: TCTCCCTGCCCTCAGCCATCGGACGCTGGAACGTGTTCAAG mu: TCTCCCTGCCCTCAGCCATCAGACGCTGGAACGTGTTCAAG	atcg\|GACG
Acc marginally increased	89326	wt: 0.3157 / mu: 0.3255 (marginal change - not scored)	wt: CCGTGGGTCTCTCCCTGCCCTCAGCCATCGGACGCTGGAAC mu: CCGTGGGTCTCTCCCTGCCCTCAGCCATCAGACGCTGGAAC	ccct\|CAGC
Acc marginally increased	89332	wt: 0.5791 / mu: 0.6016 (marginal change - not scored)	wt: GTCTCTCCCTGCCCTCAGCCATCGGACGCTGGAACGTGTTC mu: GTCTCTCCCTGCCCTCAGCCATCAGACGCTGGAACGTGTTC	gcca\|TCGG
Donor marginally increased	89328	wt: 0.7208 / mu: 0.7385 (marginal change - not scored)	wt: CCCTCAGCCATCGGA mu: CCCTCAGCCATCAGA	CTCA\|gcca
Donor gained	89335	0.40	mu: CCATCAGACGCTGGA	ATCA\|gacg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

101

mutated

not conserved

101

Ptroglodytes

all identical

ENSPTRG00000021497

137

Mmulatta

all identical

ENSMMUG00000004588

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000079502

101

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000068122

Dmelanogaster

no homologue

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

855 / 855

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

285 / 285

position of stopcodon in wt / mu cDNA

899 / 899

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

45 / 45

chromosome

strand

last intron/exon boundary

777

theoretical NMD boundary in CDS

682

length of CDS

855

coding sequence (CDS) position

301

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

345

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

89335

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

135374764

original gDNA sequence snippet

TCTCCCTGCCCTCAGCCATCGGACGCTGGAACGTGTTCAAG

altered gDNA sequence snippet

TCTCCCTGCCCTCAGCCATCAGACGCTGGAACGTGTTCAAG

original cDNA sequence snippet

GAGGAGTCCCTGAAGCCATCGGACGCTGGAACGTGTTCAAG

altered cDNA sequence snippet

GAGGAGTCCCTGAAGCCATCAGACGCTGGAACGTGTTCAAG

wildtype AA sequence

MPEARSSGPD LTRWRKQQQP VRRTVSQVCP PPRRPLTVAD IRSGMENERL GVVRDSMFQN
PLIVKAELGK PRERSYSLPG INFNYGLYIR GLDGGVPEAI GRWNVFKQQP TCPHELTRNY
IAMNRGAVKA GLVTARENLL YRQLNDIRIS DQDDRRMKKE PPPLPPNMTF GIRARPSTPF
FDLLQHRYLQ LWVQEQKATQ KAIKLEKKQK VVLGKLYETR SSQLRKYKPP VKLDTLWHMP
HFQKVGRHLD TFPTEADRQR ALKAHREECA VRQGTLRMGN YTHP*

mutated AA sequence

MPEARSSGPD LTRWRKQQQP VRRTVSQVCP PPRRPLTVAD IRSGMENERL GVVRDSMFQN
PLIVKAELGK PRERSYSLPG INFNYGLYIR GLDGGVPEAI RRWNVFKQQP TCPHELTRNY
IAMNRGAVKA GLVTARENLL YRQLNDIRIS DQDDRRMKKE PPPLPPNMTF GIRARPSTPF
FDLLQHRYLQ LWVQEQKATQ KAIKLEKKQK VVLGKLYETR SSQLRKYKPP VKLDTLWHMP
HFQKVGRHLD TFPTEADRQR ALKAHREECA VRQGTLRMGN YTHP*

speed

0.71 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