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: ENST00000294543
Querying Taster for transcript #2: ENST00000375127
Querying Taster for transcript #3: ENST00000375122
MT speed 0 s - this script 3.591708 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
TMCO4	polymorphism_automatic	1.60119454909458e-05	simple_aae		affected		R478H	single base exchange	rs4515815		show file
TMCO4	polymorphism_automatic	1.60119454909458e-05	simple_aae		affected		R478H	single base exchange	rs4515815		show file
TMCO4	polymorphism_automatic	1.60119454909458e-05	simple_aae		affected		R438H	single base exchange	rs4515815		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999983988054509 (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)

chr1:20020994C>TN/A show variant in all transcripts IGV

HGNC symbol

TMCO4

Ensembl transcript ID

ENST00000294543

Genbank transcript ID

NM_181719

UniProt peptide

Q5TGY1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1433G>A
cDNA.1675G>A
g.105445G>A

AA changes

R478H Score: 29 explain score(s)

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

478

frameshift

known variant

Reference ID: rs4515815

database	homozygous (T/T)	heterozygous	allele carriers
1000G	576	1002	1578
ExAC	21356	-9945	11411

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-3.003	0.001
	-0.639	0.002
(flanking)	1.167	0.442

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 gained	105441	0.82	mu: TGCAGCTCCATGTCG	CAGC\|tcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

478

mutated

not conserved

478

Ptroglodytes

all identical

ENSPTRG00000000272

478

Mmulatta

all identical

ENSMMUG00000002492

478

Fcatus

all identical

ENSFCAG00000014732

475

Mmusculus

all identical

ENSMUSG00000041143

475

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000078924

478

Dmelanogaster

no homologue

Celegans

all identical

F35D11.3

508

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
605	605	CONFLICT	P -> S (in Ref. 1; CAE45994).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1905 / 1905

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

635 / 635

position of stopcodon in wt / mu cDNA

2147 / 2147

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

243 / 243

chromosome

strand

-1

last intron/exon boundary

1743

theoretical NMD boundary in CDS

1450

length of CDS

1905

coding sequence (CDS) position

1433

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

1675

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

105445

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

20020994

original gDNA sequence snippet

CACATCCTCGGTGCAGCTCCGTGTCGCCGGCCTACAGCCCG

altered gDNA sequence snippet

CACATCCTCGGTGCAGCTCCATGTCGCCGGCCTACAGCCCG

original cDNA sequence snippet

CACATCCTCGGTGCAGCTCCGTGTCGCCGGCCTACAGCCCG

altered cDNA sequence snippet

CACATCCTCGGTGCAGCTCCATGTCGCCGGCCTACAGCCCG

wildtype AA sequence

MAMWNRPCQR LPQQPLVAEP TAEGEPHLPT GRELTEANRF AYAALCGISL SQLFPEPEHS
SFCTEFMAGL VQWLELSEAV LPTMTAFASG LGGEGADVFV QILLKDPILK DDPTVITQDL
LSFSLKDGHY DARARVLVCH MTSLLQVPLE ELDVLEEMFL ESLKEIKEEE SEMAEASRKK
KENRRKWKRY LLIGLATVGG GTVIGVTGGL AAPLVAAGAA TIIGSAGAAA LGSAAGIAIM
TSLFGAAGAG LTGYKMKKRV GAIEEFTFLP LTEGRQLHIT IAVTGWLASG KYRTFSAPWA
ALAHSREQYC LAWEAKYLME LGNALETILS GLANMVAQEA LKYTVLSGIV AALTWPASLL
SVANVIDNPW GVCLHRSAEV GKHLAHILLS RQQGRRPVTL IGFSLGARVI YFCLQEMAQE
KDCQGIIEDV ILLGAPVEGE AKHWEPFRKV VSGRIINGYC RGDWLLSFVY RTSSVQLRVA
GLQPVLLQDR RVENVDLTSV VSGHLDYAKQ MDAILKAVGI RTKPGWDEKG LLLAPGCLPS
EEPRQAAAAA SSGETPHQVG QTQGPISGDT SKLAMSTDPS QAQVPVGLDQ SEGASLPAAA
SPERPPICSH GMDPNPLGCP DCACKTQGPS TGLD*

mutated AA sequence

MAMWNRPCQR LPQQPLVAEP TAEGEPHLPT GRELTEANRF AYAALCGISL SQLFPEPEHS
SFCTEFMAGL VQWLELSEAV LPTMTAFASG LGGEGADVFV QILLKDPILK DDPTVITQDL
LSFSLKDGHY DARARVLVCH MTSLLQVPLE ELDVLEEMFL ESLKEIKEEE SEMAEASRKK
KENRRKWKRY LLIGLATVGG GTVIGVTGGL AAPLVAAGAA TIIGSAGAAA LGSAAGIAIM
TSLFGAAGAG LTGYKMKKRV GAIEEFTFLP LTEGRQLHIT IAVTGWLASG KYRTFSAPWA
ALAHSREQYC LAWEAKYLME LGNALETILS GLANMVAQEA LKYTVLSGIV AALTWPASLL
SVANVIDNPW GVCLHRSAEV GKHLAHILLS RQQGRRPVTL IGFSLGARVI YFCLQEMAQE
KDCQGIIEDV ILLGAPVEGE AKHWEPFRKV VSGRIINGYC RGDWLLSFVY RTSSVQLHVA
GLQPVLLQDR RVENVDLTSV VSGHLDYAKQ MDAILKAVGI RTKPGWDEKG LLLAPGCLPS
EEPRQAAAAA SSGETPHQVG QTQGPISGDT SKLAMSTDPS QAQVPVGLDQ SEGASLPAAA
SPERPPICSH GMDPNPLGCP DCACKTQGPS TGLD*

speed

0.71 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: 0.999983988054509 (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)

chr1:20020994C>TN/A show variant in all transcripts IGV

HGNC symbol

TMCO4

Ensembl transcript ID

ENST00000375127

Genbank transcript ID

N/A

UniProt peptide

Q5TGY1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1433G>A
cDNA.1704G>A
g.105445G>A

AA changes

R478H Score: 29 explain score(s)

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

478

frameshift

known variant

Reference ID: rs4515815

database	homozygous (T/T)	heterozygous	allele carriers
1000G	576	1002	1578
ExAC	21356	-9945	11411

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-3.003	0.001
	-0.639	0.002
(flanking)	1.167	0.442

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 gained	105441	0.82	mu: TGCAGCTCCATGTCG	CAGC\|tcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

478

mutated

not conserved

478

Ptroglodytes

all identical

ENSPTRG00000000272

478

Mmulatta

all identical

ENSMMUG00000002492

478

Fcatus

all identical

ENSFCAG00000014732

475

Mmusculus

all identical

ENSMUSG00000041143

475

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000078924

478

Dmelanogaster

no homologue

Celegans

all identical

F35D11.3

508

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
605	605	CONFLICT	P -> S (in Ref. 1; CAE45994).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1743 / 1743

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

581 / 581

position of stopcodon in wt / mu cDNA

2014 / 2014

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

272 / 272

chromosome

strand

-1

last intron/exon boundary

1929

theoretical NMD boundary in CDS

1607

length of CDS

1743

coding sequence (CDS) position

1433

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

1704

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

105445

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

20020994

original gDNA sequence snippet

CACATCCTCGGTGCAGCTCCGTGTCGCCGGCCTACAGCCCG

altered gDNA sequence snippet

CACATCCTCGGTGCAGCTCCATGTCGCCGGCCTACAGCCCG

original cDNA sequence snippet

CACATCCTCGGTGCAGCTCCGTGTCGCCGGCCTACAGCCCG

altered cDNA sequence snippet

CACATCCTCGGTGCAGCTCCATGTCGCCGGCCTACAGCCCG

wildtype AA sequence

mutated AA sequence

MAMWNRPCQR LPQQPLVAEP TAEGEPHLPT GRELTEANRF AYAALCGISL SQLFPEPEHS
SFCTEFMAGL VQWLELSEAV LPTMTAFASG LGGEGADVFV QILLKDPILK DDPTVITQDL
LSFSLKDGHY DARARVLVCH MTSLLQVPLE ELDVLEEMFL ESLKEIKEEE SEMAEASRKK
KENRRKWKRY LLIGLATVGG GTVIGVTGGL AAPLVAAGAA TIIGSAGAAA LGSAAGIAIM
TSLFGAAGAG LTGYKMKKRV GAIEEFTFLP LTEGRQLHIT IAVTGWLASG KYRTFSAPWA
ALAHSREQYC LAWEAKYLME LGNALETILS GLANMVAQEA LKYTVLSGIV AALTWPASLL
SVANVIDNPW GVCLHRSAEV GKHLAHILLS RQQGRRPVTL IGFSLGARVI YFCLQEMAQE
KDCQGIIEDV ILLGAPVEGE AKHWEPFRKV VSGRIINGYC RGDWLLSFVY RTSSVQLHVA
GLQPVLLQDR RVENVDLTSV VSGHLDYAKQ MDAILKAVGI RTKPGWDEKG LLLAPGCLPS
EEPRQAAAAA SSALESGCPS GGPEGSLGPE APTPALPWPQ *

speed

0.70 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999983988054509 (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)

chr1:20020994C>TN/A show variant in all transcripts IGV

HGNC symbol

TMCO4

Ensembl transcript ID

ENST00000375122

Genbank transcript ID

N/A

UniProt peptide

Q5TGY1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1313G>A
cDNA.1555G>A
g.105445G>A

AA changes

R438H Score: 29 explain score(s)

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

438

frameshift

known variant

Reference ID: rs4515815

database	homozygous (T/T)	heterozygous	allele carriers
1000G	576	1002	1578
ExAC	21356	-9945	11411

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-3.003	0.001
	-0.639	0.002
(flanking)	1.167	0.442

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 gained	105441	0.82	mu: TGCAGCTCCATGTCG	CAGC\|tcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

438

mutated

not conserved

438

Ptroglodytes

all identical

ENSPTRG00000000272

478

Mmulatta

all identical

ENSMMUG00000002492

478

Fcatus

all identical

ENSFCAG00000014732

475

Mmusculus

all identical

ENSMUSG00000041143

475

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000078924

478

Dmelanogaster

no homologue

Celegans

all identical

F35D11.3

508

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
605	605	CONFLICT	P -> S (in Ref. 1; CAE45994).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1785 / 1785

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

595 / 595

position of stopcodon in wt / mu cDNA

2027 / 2027

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

243 / 243

chromosome

strand

-1

last intron/exon boundary

1623

theoretical NMD boundary in CDS

1330

length of CDS

1785

coding sequence (CDS) position

1313

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

1555

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

105445

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

20020994

original gDNA sequence snippet

CACATCCTCGGTGCAGCTCCGTGTCGCCGGCCTACAGCCCG

altered gDNA sequence snippet

CACATCCTCGGTGCAGCTCCATGTCGCCGGCCTACAGCCCG

original cDNA sequence snippet

CACATCCTCGGTGCAGCTCCGTGTCGCCGGCCTACAGCCCG

altered cDNA sequence snippet

CACATCCTCGGTGCAGCTCCATGTCGCCGGCCTACAGCCCG

wildtype AA sequence

MAMWNRPCQR LPQQPLVAEP TAEGEPHLPT GRELTEANRF AYAALCGISL SQLFPEPEHS
SFCTEFMAGL VQWLELSEAV LPTMTAFASG LGGEGADVFV QILLKDPILK DDPTVITQDL
LSFSLKDGHY DARARVLVCH MTSLLQVPLE ELDVLEEMFL ESLKEIKEEE SEMAEASRKK
KENRRKWKRY LLIGLATVGG GTVIGVTGGL AAPLVAAGAA TIIGSAGAAA LGSAAGIAIM
TSLFGAAGAG LTGTFSAPWA ALAHSREQYC LAWEAKYLME LGNALETILS GLANMVAQEA
LKYTVLSGIV AALTWPASLL SVANVIDNPW GVCLHRSAEV GKHLAHILLS RQQGRRPVTL
IGFSLGARVI YFCLQEMAQE KDCQGIIEDV ILLGAPVEGE AKHWEPFRKV VSGRIINGYC
RGDWLLSFVY RTSSVQLRVA GLQPVLLQDR RVENVDLTSV VSGHLDYAKQ MDAILKAVGI
RTKPGWDEKG LLLAPGCLPS EEPRQAAAAA SSGETPHQVG QTQGPISGDT SKLAMSTDPS
QAQVPVGLDQ SEGASLPAAA SPERPPICSH GMDPNPLGCP DCACKTQGPS TGLD*

mutated AA sequence

MAMWNRPCQR LPQQPLVAEP TAEGEPHLPT GRELTEANRF AYAALCGISL SQLFPEPEHS
SFCTEFMAGL VQWLELSEAV LPTMTAFASG LGGEGADVFV QILLKDPILK DDPTVITQDL
LSFSLKDGHY DARARVLVCH MTSLLQVPLE ELDVLEEMFL ESLKEIKEEE SEMAEASRKK
KENRRKWKRY LLIGLATVGG GTVIGVTGGL AAPLVAAGAA TIIGSAGAAA LGSAAGIAIM
TSLFGAAGAG LTGTFSAPWA ALAHSREQYC LAWEAKYLME LGNALETILS GLANMVAQEA
LKYTVLSGIV AALTWPASLL SVANVIDNPW GVCLHRSAEV GKHLAHILLS RQQGRRPVTL
IGFSLGARVI YFCLQEMAQE KDCQGIIEDV ILLGAPVEGE AKHWEPFRKV VSGRIINGYC
RGDWLLSFVY RTSSVQLHVA GLQPVLLQDR RVENVDLTSV VSGHLDYAKQ MDAILKAVGI
RTKPGWDEKG LLLAPGCLPS EEPRQAAAAA SSGETPHQVG QTQGPISGDT SKLAMSTDPS
QAQVPVGLDQ SEGASLPAAA SPERPPICSH GMDPNPLGCP DCACKTQGPS TGLD*

speed

0.81 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