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: ENST00000244295
Querying Taster for transcript #2: ENST00000405312
Querying Taster for transcript #3: ENST00000433626
MT speed 0 s - this script 3.599511 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PSG4	polymorphism_automatic	1.25011112572793e-13	simple_aae		affected		S240P	single base exchange	rs3859474		show file
PSG4	polymorphism_automatic	1.25011112572793e-13	simple_aae		affected		S147P	single base exchange	rs3859474		show file
PSG4	polymorphism_automatic	5.22209459008494e-07	without_aae		affected			single base exchange	rs3859474		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999875 (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)

chr19:43699417A>GN/A show variant in all transcripts IGV

HGNC symbol

PSG4

Ensembl transcript ID

ENST00000405312

Genbank transcript ID

NM_002780

UniProt peptide

Q00888

alteration type

single base exchange

alteration region

CDS

DNA changes

c.718T>C
cDNA.956T>C
g.10510T>C

AA changes

S240P Score: 74 explain score(s)

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

240

frameshift

known variant

Reference ID: rs3859474

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1247	891	2138
ExAC	17217	-1667	15550

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.301	0.008
	-0.064	0.003
(flanking)	-0.158	0.002

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	10509	wt: 0.9085 / mu: 0.9765 (marginal change - not scored)	wt: AAGCTGTCCAAGCCC mu: AAGCTGCCCAAGCCC	GCTG\|tcca
Donor gained	10505	0.57	mu: AGCAAAGCTGCCCAA	CAAA\|gctg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

240

mutated

not conserved

240

Ptroglodytes

not conserved

ENSPTRG00000040468

240

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
237	327	DOMAIN	Ig-like C2-type 2.	lost
262	262	DISULFID	Probable.	might get lost (downstream of altered splice site)
268	268	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
299	299	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
303	303	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
310	310	DISULFID	Probable.	might get lost (downstream of altered splice site)
332	410	DOMAIN	Ig-like C2-type 3.	might get lost (downstream of altered splice site)
352	352	CONFLICT	L -> F (in Ref. 3; CAA34956).	might get lost (downstream of altered splice site)
354	354	DISULFID	Probable.	might get lost (downstream of altered splice site)
356	356	CONFLICT	A -> G (in Ref. 3; CAA34956).	might get lost (downstream of altered splice site)
394	394	DISULFID	Probable.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1260 / 1260

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

420 / 420

position of stopcodon in wt / mu cDNA

1498 / 1498

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

239 / 239

chromosome

strand

-1

last intron/exon boundary

1482

theoretical NMD boundary in CDS

1193

length of CDS

1260

coding sequence (CDS) position

718

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

956

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

10510

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

43699417

original gDNA sequence snippet

TTATCCACACAGCAAAGCTGTCCAAGCCCTACATCACAATC

altered gDNA sequence snippet

TTATCCACACAGCAAAGCTGCCCAAGCCCTACATCACAATC

original cDNA sequence snippet

TGAATCTCCTCCCAAAGCTGTCCAAGCCCTACATCACAATC

altered cDNA sequence snippet

TGAATCTCCTCCCAAAGCTGCCCAAGCCCTACATCACAATC

wildtype AA sequence

MGPLSAPPCT QRITWKGVLL TASLLNFWNP PTTAQVTIEA QPPKVSEGKD VLLLVHNLPQ
NLAGYIWYKG QMTYLYHYIT SYVVDGQRII YGPAYSGRER VYSNASLLIQ NVTQEDAGSY
TLHIIKRRDG TGGVTGHFTF TLHLETPKPS ISSSNLNPRE AMEAVILTCD PATPAASYQW
WMNGQSLPMT HRLQLSKTNR TLFIFGVTKY IAGPYECEIR NPVSASRSDP VTLNLLPKLS
KPYITINNLN PRENKDVLTF TCEPKSKNYT YIWWLNGQSL PVSPRVKRPI ENRILILPNV
TRNETGPYQC EIRDRYGGIR SDPVTLNVLY GPDLPSIYPS FTYYRSGENL YLSCFAESNP
RAQYSWTING KFQLSGQKLS IPQITTKHSG LYACSVRNSA TGKESSKSIT VKVSDWILP*

mutated AA sequence

MGPLSAPPCT QRITWKGVLL TASLLNFWNP PTTAQVTIEA QPPKVSEGKD VLLLVHNLPQ
NLAGYIWYKG QMTYLYHYIT SYVVDGQRII YGPAYSGRER VYSNASLLIQ NVTQEDAGSY
TLHIIKRRDG TGGVTGHFTF TLHLETPKPS ISSSNLNPRE AMEAVILTCD PATPAASYQW
WMNGQSLPMT HRLQLSKTNR TLFIFGVTKY IAGPYECEIR NPVSASRSDP VTLNLLPKLP
KPYITINNLN PRENKDVLTF TCEPKSKNYT YIWWLNGQSL PVSPRVKRPI ENRILILPNV
TRNETGPYQC EIRDRYGGIR SDPVTLNVLY GPDLPSIYPS FTYYRSGENL YLSCFAESNP
RAQYSWTING KFQLSGQKLS IPQITTKHSG LYACSVRNSA TGKESSKSIT VKVSDWILP*

speed

1.13 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: 0.999999999999875 (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)

chr19:43699417A>GN/A show variant in all transcripts IGV

HGNC symbol

PSG4

Ensembl transcript ID

ENST00000433626

Genbank transcript ID

N/A

UniProt peptide

Q00888

alteration type

single base exchange

alteration region

CDS

DNA changes

c.439T>C
cDNA.571T>C
g.10510T>C

AA changes

S147P Score: 74 explain score(s)

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

147

frameshift

known variant

Reference ID: rs3859474

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1247	891	2138
ExAC	17217	-1667	15550

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.301	0.008
	-0.064	0.003
(flanking)	-0.158	0.002

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	10509	wt: 0.9085 / mu: 0.9765 (marginal change - not scored)	wt: AAGCTGTCCAAGCCC mu: AAGCTGCCCAAGCCC	GCTG\|tcca
Donor gained	10505	0.57	mu: AGCAAAGCTGCCCAA	CAAA\|gctg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

147

mutated

not conserved

147

Ptroglodytes

not conserved

ENSPTRG00000040468

147

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
147	234	DOMAIN	Ig-like C2-type 1.	lost
169	169	DISULFID	Probable.	might get lost (downstream of altered splice site)
175	175	CONFLICT	A -> P (in Ref. 1; M32624).	might get lost (downstream of altered splice site)
199	199	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
217	217	DISULFID	Probable.	might get lost (downstream of altered splice site)
237	327	DOMAIN	Ig-like C2-type 2.	might get lost (downstream of altered splice site)
262	262	DISULFID	Probable.	might get lost (downstream of altered splice site)
268	268	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
299	299	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
303	303	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
310	310	DISULFID	Probable.	might get lost (downstream of altered splice site)
332	410	DOMAIN	Ig-like C2-type 3.	might get lost (downstream of altered splice site)
352	352	CONFLICT	L -> F (in Ref. 3; CAA34956).	might get lost (downstream of altered splice site)
354	354	DISULFID	Probable.	might get lost (downstream of altered splice site)
356	356	CONFLICT	A -> G (in Ref. 3; CAA34956).	might get lost (downstream of altered splice site)
394	394	DISULFID	Probable.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

981 / 981

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

327 / 327

position of stopcodon in wt / mu cDNA

1113 / 1113

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

133 / 133

chromosome

strand

-1

last intron/exon boundary

1097

theoretical NMD boundary in CDS

914

length of CDS

981

coding sequence (CDS) position

439

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

571

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

10510

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

43699417

original gDNA sequence snippet

TTATCCACACAGCAAAGCTGTCCAAGCCCTACATCACAATC

altered gDNA sequence snippet

TTATCCACACAGCAAAGCTGCCCAAGCCCTACATCACAATC

original cDNA sequence snippet

TCACCTTACACCCAAAGCTGTCCAAGCCCTACATCACAATC

altered cDNA sequence snippet

TCACCTTACACCCAAAGCTGCCCAAGCCCTACATCACAATC

wildtype AA sequence

MGPLSAPPCT QRITWKGVLL TASLLNFWNP PTTAQVTIEA QPPKVSEGKD VLLLVHNLPQ
NLAGYIWYKG QMTYLYHYIT SYVVDGQRII YGPAYSGRER VYSNASLLIQ NVTQEDAGSY
TLHIIKRRDG TGGVTGHFTF TLHPKLSKPY ITINNLNPRE NKDVLTFTCE PKSKNYTYIW
WLNGQSLPVS PRVKRPIENR ILILPNVTRN ETGPYQCEIR DRYGGIRSDP VTLNVLYGPD
LPSIYPSFTY YRSGENLYLS CFAESNPRAQ YSWTINGKFQ LSGQKLSIPQ ITTKHSGLYA
CSVRNSATGK ESSKSITVKV SDWILP*

mutated AA sequence

MGPLSAPPCT QRITWKGVLL TASLLNFWNP PTTAQVTIEA QPPKVSEGKD VLLLVHNLPQ
NLAGYIWYKG QMTYLYHYIT SYVVDGQRII YGPAYSGRER VYSNASLLIQ NVTQEDAGSY
TLHIIKRRDG TGGVTGHFTF TLHPKLPKPY ITINNLNPRE NKDVLTFTCE PKSKNYTYIW
WLNGQSLPVS PRVKRPIENR ILILPNVTRN ETGPYQCEIR DRYGGIRSDP VTLNVLYGPD
LPSIYPSFTY YRSGENLYLS CFAESNPRAQ YSWTINGKFQ LSGQKLSIPQ ITTKHSGLYA
CSVRNSATGK ESSKSITVKV SDWILP*

speed

0.44 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.999999477790541 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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)

chr19:43699417A>GN/A show variant in all transcripts IGV

HGNC symbol

PSG4

Ensembl transcript ID

ENST00000244295

Genbank transcript ID

NM_213633

UniProt peptide

Q00888

alteration type

single base exchange

alteration region

intron

DNA changes

g.10510T>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs3859474

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1247	891	2138
ExAC	17217	-1667	15550

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.301	0.008
	-0.064	0.003
(flanking)	-0.158	0.002

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	10509	wt: 0.9085 / mu: 0.9765 (marginal change - not scored)	wt: AAGCTGTCCAAGCCC mu: AAGCTGCCCAAGCCC	GCTG\|tcca
Donor gained	10505	0.57	mu: AGCAAAGCTGCCCAA	CAAA\|gctg

distance from splice site

671

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
237	327	DOMAIN	Ig-like C2-type 2.	might get lost (downstream of altered splice site)
262	262	DISULFID	Probable.	might get lost (downstream of altered splice site)
268	268	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
299	299	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
303	303	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
310	310	DISULFID	Probable.	might get lost (downstream of altered splice site)
332	410	DOMAIN	Ig-like C2-type 3.	might get lost (downstream of altered splice site)
352	352	CONFLICT	L -> F (in Ref. 3; CAA34956).	might get lost (downstream of altered splice site)
354	354	DISULFID	Probable.	might get lost (downstream of altered splice site)
356	356	CONFLICT	A -> G (in Ref. 3; CAA34956).	might get lost (downstream of altered splice site)
394	394	DISULFID	Probable.	might get lost (downstream of altered splice site)

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

28 / 28

chromosome

strand

-1

last intron/exon boundary

992

theoretical NMD boundary in CDS

914

length of CDS

981

coding sequence (CDS) position

N/A

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

N/A

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

10510

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

43699417

original gDNA sequence snippet

TTATCCACACAGCAAAGCTGTCCAAGCCCTACATCACAATC

altered gDNA sequence snippet

TTATCCACACAGCAAAGCTGCCCAAGCCCTACATCACAATC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MGPLSAPPCT QRITWKGVLL TASLLNFWNP PTTAQVTIEA QPPKVSEGKD VLLLVHNLPQ
NLAGYIWYKG QMTYLYHYIT SYVVDGQRII YGPAYSGRER VYSNASLLIQ NVTQEDAGSY
TLHIIKRRDG TGGVTGHFTF TLHLETPKPS ISSSNLNPRE AMEAVILTCD PATPAASYQW
WMNGQSLPMT HRLQLSKTNR TLFIFGVTKY IAGPYECEIR NPVSASRSDP VTLNLLHGPD
LPSIYPSFTY YRSGENLYLS CFAESNPRAQ YSWTINGKFQ LSGQKLSIPQ ITTKHSGLYA
CSVRNSATGK ESSKSITVKV SDWILP*

mutated AA sequence

N/A

speed

0.87 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