MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000404125
Querying Taster for transcript #2: ENST00000421748
MT speed 0 s - this script 4.145922 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PSME4	polymorphism_automatic	0.99976731678297	simple_aae		affected		S1371T	single base exchange	rs805408		show file
PSME4	polymorphism_automatic	0.99976731678297	simple_aae		affected		S515T	single base exchange	rs805408		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.000232683217029942 (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)

chr2:54120025A>TN/A show variant in all transcripts IGV

HGNC symbol

PSME4

Ensembl transcript ID

ENST00000404125

Genbank transcript ID

NM_014614

UniProt peptide

Q14997

alteration type

single base exchange

alteration region

CDS

DNA changes

c.4111T>A
cDNA.4167T>A
g.77953T>A

AA changes

S1371T Score: 58 explain score(s)

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

1371

frameshift

known variant

Reference ID: rs805408

database	homozygous (T/T)	heterozygous	allele carriers
1000G	354	1041	1395
ExAC	6636	19495	26131

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.327	1
	1.461	1
(flanking)	1.208	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
Donor increased	77956	wt: 0.25 / mu: 0.28	wt: ATTCACATGAAAGCA mu: ATACACATGAAAGCA	TCAC\|atga
Donor marginally increased	77957	wt: 0.9035 / mu: 0.9564 (marginal change - not scored)	wt: TTCACATGAAAGCAC mu: TACACATGAAAGCAC	CACA\|tgaa
Donor gained	77953	0.42	mu: CAGATACACATGAAA	GATA\|caca
Donor gained	77949	0.87	mu: GTTGCAGATACACAT	TGCA\|gata

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1371

mutated

all conserved

1371

Ptroglodytes

all identical

ENSPTRG00000011920

1371

Mmulatta

all identical

ENSMMUG00000008104

1249

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000040850

1371

Ggallus

all identical

ENSGALG00000008163

1293

Trubripes

all conserved

ENSTRUG00000016378

1358

Drerio

all identical

ENSDARG00000018742

1355

Dmelanogaster

no homologue

Celegans

all identical

C14C10.5

1424

Xtropicalis

all identical

ENSXETG00000015195

1356

protein features

start (aa)	end (aa)	feature	details
1354	1392	REPEAT	HEAT 4.	lost
1401	1401	CONFLICT	L -> F (in Ref. 2; AAH43602).	might get lost (downstream of altered splice site)
1636	1674	REPEAT	HEAT 5.	might get lost (downstream of altered splice site)
1680	1718	REPEAT	HEAT 6.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5532 / 5532

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

1844 / 1844

position of stopcodon in wt / mu cDNA

5588 / 5588

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

57 / 57

chromosome

strand

-1

last intron/exon boundary

5593

theoretical NMD boundary in CDS

5486

length of CDS

5532

coding sequence (CDS) position

4111

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

4167

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

77953

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

54120025

original gDNA sequence snippet

TAGAACATTTGGTTGCAGATTCACATGAAAGCACCCAGCGA

altered gDNA sequence snippet

TAGAACATTTGGTTGCAGATACACATGAAAGCACCCAGCGA

original cDNA sequence snippet

TAGAACATTTGGTTGCAGATTCACATGAAAGCACCCAGCGA

altered cDNA sequence snippet

TAGAACATTTGGTTGCAGATACACATGAAAGCACCCAGCGA

wildtype AA sequence

MEPAERAGVG EPPEPGGRPE PGPRGFVPQK EIVYNKLLPY AERLDAESDL QLAQIKCNLG
RAVQLQELWP GGLFWTRKLS TYIRLYGRKF SKEDHVLFIK LLYELVSIPK LEISMMQGFA
RLLINLLKKK ELLSRADLEL PWRPLYDMVE RILYSKTEHL GLNWFPNSVE NILKTLVKSC
RPYFPADATA EMLEEWRPLM CPFDVTMQKA ITYFEIFLPT SLPPELHHKG FKLWFDELIG
LWVSVQNLPQ WEGQLVNLFA RLATDNIGYI DWDPYVPKIF TRILRSLNLP VGSSQVLVPR
FLTNAYDIGH AVIWITAMMG GPSKLVQKHL AGLFNSITSF YHPSNNGRWL NKLMKLLQRL
PNSVVRRLHR ERYKKPSWLT PVPDSHKLTD QDVTDFVQCI IQPVLLAMFS KTGSLEAAQA
LQNLALMRPE LVIPPVLERT YPALETLTEP HQLTATLSCV IGVARSLVSG GRWFPEGPTH
MLPLLMRALP GVDPNDFSKC MITFQFIATF STLVPLVDCS SVLQERNDLT EVERELCSAT
AEFEDFVLQF MDRCFGLIES STLEQTREET ETEKMTHLES LVELGLSSTF STILTQCSKE
IFMVALQKVF NFSTSHIFET RVAGRMVADM CRAAVKCCPE ESLKLFVPHC CSVITQLTMN
DDVLNDEELD KELLWNLQLL SEITRVDGRK LLLYREQLVK ILQRTLHLTC KQGYTLSCNL
LHHLLRSTTL IYPTEYCSVP GGFDKPPSEY FPIKDWGKPG DLWNLGIQWH VPSSEEVSFA
FYLLDSFLQP ELVKLQHCGD GKLEMSRDDI LQSLTIVHNC LIGSGNLLPP LKGEPVTNLV
PSMVSLEETK LYTGLEYDLS RENHREVIAT VIRKLLNHIL DNSEDDTKSL FLIIKIIGDL
LQFQGSHKHE FDSRWKSFNL VKKSMENRLH GKKQHIRALL IDRVMLQHEL RTLTVEGCEY
KKIHQDMIRD LLRLSTSSYS QVRNKAQQTF FAALGAYNFC CRDIIPLVLE FLRPDRQGVT
QQQFKGALYC LLGNHSGVCL ANLHDWDCIV QTWPAIVSSG LSQAMSLEKP SIVRLFDDLA
EKIHRQYETI GLDFTIPKSC VEIAELLQQS KNPSINQILL SPEKIKEGIK RQQEKNADAL
RNYENLVDTL LDGVEQRNLP WKFEHIGIGL LSLLLRDDRV LPLRAIRFFV ENLNHDAIVV
RKMAISAVAG ILKQLKRTHK KLTINPCEIS GCPKPTQIIA GDRPDNHWLH YDSKTIPRTK
KEWESSCFVE KTHWGYYTWP KNMVVYAGVE EQPKLGRSRE DMTEAEQIIF DHFSDPKFVE
QLITFLSLED RKGKDKFNPR RFCLFKGIFR NFDDAFLPVL KPHLEHLVAD SHESTQRCVA
EIIAGLIRGS KHWTFEKVEK LWELLCPLLR TALSNITVET YNDWGACIAT SCESRDPRKL
HWLFELLLES PLSGEGGSFV DACRLYVLQG GLAQQEWRVP ELLHRLLKYL EPKLTQVYKN
VRERIGSVLT YIFMIDVSLP NTTPTISPHV PEFTARILEK LKPLMDVDEE IQNHVMEENG
IGEEDERTQG IKLLKTILKW LMASAGRSFS TAVTEQLQLL PLFFKIAPVE NDNSYDELKR
DAKLCLSLMS QGLLYPHQVP LVLQVLKQTA RSSSWHARYT VLTYLQTMVF YNLFIFLNNE
DAVKDIRWLV ISLLEDEQLE VREMAATTLS GLLQCNFLTM DSPMQIHFEQ LCKTKLPKKR
KRDPGSVGDT IPSAELVKRH AGVLGLGACV LSSPYDVPTW MPQLLMNLSA HLNDPQPIEM
TVKKTLSNFR RTHHDNWQEH KQQFTDDQLL VLTDLLVSPC YYA*

mutated AA sequence

MEPAERAGVG EPPEPGGRPE PGPRGFVPQK EIVYNKLLPY AERLDAESDL QLAQIKCNLG
RAVQLQELWP GGLFWTRKLS TYIRLYGRKF SKEDHVLFIK LLYELVSIPK LEISMMQGFA
RLLINLLKKK ELLSRADLEL PWRPLYDMVE RILYSKTEHL GLNWFPNSVE NILKTLVKSC
RPYFPADATA EMLEEWRPLM CPFDVTMQKA ITYFEIFLPT SLPPELHHKG FKLWFDELIG
LWVSVQNLPQ WEGQLVNLFA RLATDNIGYI DWDPYVPKIF TRILRSLNLP VGSSQVLVPR
FLTNAYDIGH AVIWITAMMG GPSKLVQKHL AGLFNSITSF YHPSNNGRWL NKLMKLLQRL
PNSVVRRLHR ERYKKPSWLT PVPDSHKLTD QDVTDFVQCI IQPVLLAMFS KTGSLEAAQA
LQNLALMRPE LVIPPVLERT YPALETLTEP HQLTATLSCV IGVARSLVSG GRWFPEGPTH
MLPLLMRALP GVDPNDFSKC MITFQFIATF STLVPLVDCS SVLQERNDLT EVERELCSAT
AEFEDFVLQF MDRCFGLIES STLEQTREET ETEKMTHLES LVELGLSSTF STILTQCSKE
IFMVALQKVF NFSTSHIFET RVAGRMVADM CRAAVKCCPE ESLKLFVPHC CSVITQLTMN
DDVLNDEELD KELLWNLQLL SEITRVDGRK LLLYREQLVK ILQRTLHLTC KQGYTLSCNL
LHHLLRSTTL IYPTEYCSVP GGFDKPPSEY FPIKDWGKPG DLWNLGIQWH VPSSEEVSFA
FYLLDSFLQP ELVKLQHCGD GKLEMSRDDI LQSLTIVHNC LIGSGNLLPP LKGEPVTNLV
PSMVSLEETK LYTGLEYDLS RENHREVIAT VIRKLLNHIL DNSEDDTKSL FLIIKIIGDL
LQFQGSHKHE FDSRWKSFNL VKKSMENRLH GKKQHIRALL IDRVMLQHEL RTLTVEGCEY
KKIHQDMIRD LLRLSTSSYS QVRNKAQQTF FAALGAYNFC CRDIIPLVLE FLRPDRQGVT
QQQFKGALYC LLGNHSGVCL ANLHDWDCIV QTWPAIVSSG LSQAMSLEKP SIVRLFDDLA
EKIHRQYETI GLDFTIPKSC VEIAELLQQS KNPSINQILL SPEKIKEGIK RQQEKNADAL
RNYENLVDTL LDGVEQRNLP WKFEHIGIGL LSLLLRDDRV LPLRAIRFFV ENLNHDAIVV
RKMAISAVAG ILKQLKRTHK KLTINPCEIS GCPKPTQIIA GDRPDNHWLH YDSKTIPRTK
KEWESSCFVE KTHWGYYTWP KNMVVYAGVE EQPKLGRSRE DMTEAEQIIF DHFSDPKFVE
QLITFLSLED RKGKDKFNPR RFCLFKGIFR NFDDAFLPVL KPHLEHLVAD THESTQRCVA
EIIAGLIRGS KHWTFEKVEK LWELLCPLLR TALSNITVET YNDWGACIAT SCESRDPRKL
HWLFELLLES PLSGEGGSFV DACRLYVLQG GLAQQEWRVP ELLHRLLKYL EPKLTQVYKN
VRERIGSVLT YIFMIDVSLP NTTPTISPHV PEFTARILEK LKPLMDVDEE IQNHVMEENG
IGEEDERTQG IKLLKTILKW LMASAGRSFS TAVTEQLQLL PLFFKIAPVE NDNSYDELKR
DAKLCLSLMS QGLLYPHQVP LVLQVLKQTA RSSSWHARYT VLTYLQTMVF YNLFIFLNNE
DAVKDIRWLV ISLLEDEQLE VREMAATTLS GLLQCNFLTM DSPMQIHFEQ LCKTKLPKKR
KRDPGSVGDT IPSAELVKRH AGVLGLGACV LSSPYDVPTW MPQLLMNLSA HLNDPQPIEM
TVKKTLSNFR RTHHDNWQEH KQQFTDDQLL VLTDLLVSPC YYA*

speed

1.11 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: 0.000232683217029942 (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)

chr2:54120025A>TN/A show variant in all transcripts IGV

HGNC symbol

PSME4

Ensembl transcript ID

ENST00000421748

Genbank transcript ID

N/A

UniProt peptide

Q14997

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1543T>A
cDNA.1543T>A
g.77953T>A

AA changes

S515T Score: 58 explain score(s)

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

515

frameshift

known variant

Reference ID: rs805408

database	homozygous (T/T)	heterozygous	allele carriers
1000G	354	1041	1395
ExAC	6636	19495	26131

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.327	1
	1.461	1
(flanking)	1.208	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
Donor increased	77956	wt: 0.25 / mu: 0.28	wt: ATTCACATGAAAGCA mu: ATACACATGAAAGCA	TCAC\|atga
Donor marginally increased	77957	wt: 0.9035 / mu: 0.9564 (marginal change - not scored)	wt: TTCACATGAAAGCAC mu: TACACATGAAAGCAC	CACA\|tgaa
Donor gained	77953	0.42	mu: CAGATACACATGAAA	GATA\|caca
Donor gained	77949	0.87	mu: GTTGCAGATACACAT	TGCA\|gata

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

515

mutated

all conserved

515

Ptroglodytes

all identical

ENSPTRG00000011920

1371

Mmulatta

all identical

ENSMMUG00000008104

1249

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000040850

1371

Ggallus

all identical

ENSGALG00000008163

1293

Trubripes

all conserved

ENSTRUG00000016378

1358

Drerio

all identical

ENSDARG00000018742

1355

Dmelanogaster

no homologue

Celegans

all identical

C14C10.5

1424

Xtropicalis

all identical

ENSXETG00000015195

1356

protein features

start (aa)	end (aa)	feature	details
475	519	REPEAT	HEAT 1.	lost
710	710	CONFLICT	C -> R (in Ref. 1; AAX83871).	might get lost (downstream of altered splice site)
984	984	CONFLICT	N -> S (in Ref. 1; AAX83871).	might get lost (downstream of altered splice site)
998	1037	REPEAT	HEAT 2.	might get lost (downstream of altered splice site)
1121	1121	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1179	1217	REPEAT	HEAT 3.	might get lost (downstream of altered splice site)
1354	1392	REPEAT	HEAT 4.	might get lost (downstream of altered splice site)
1401	1401	CONFLICT	L -> F (in Ref. 2; AAH43602).	might get lost (downstream of altered splice site)
1636	1674	REPEAT	HEAT 5.	might get lost (downstream of altered splice site)
1680	1718	REPEAT	HEAT 6.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2964 / 2964

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

988 / 988

position of stopcodon in wt / mu cDNA

2964 / 2964

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

1 / 1

chromosome

strand

-1

last intron/exon boundary

2969

theoretical NMD boundary in CDS

2918

length of CDS

2964

coding sequence (CDS) position

1543

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

1543

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

77953

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

54120025

original gDNA sequence snippet

TAGAACATTTGGTTGCAGATTCACATGAAAGCACCCAGCGA

altered gDNA sequence snippet

TAGAACATTTGGTTGCAGATACACATGAAAGCACCCAGCGA

original cDNA sequence snippet

TAGAACATTTGGTTGCAGATTCACATGAAAGCACCCAGCGA

altered cDNA sequence snippet

TAGAACATTTGGTTGCAGATACACATGAAAGCACCCAGCGA

wildtype AA sequence

MGENLAKKIM FFLLTIKLIL NHILDNSEDD TKSLFLIIKI IGDLLQFQGS HKHEFDSRWK
SFNLVKKSME NRLHGKKQHI RALLIDRVML QHELRTLTVE GCEYKKIHQD MIRDLLRLST
SSYSQVRNKA QQTFFAALGA YNFCCRDIIP LVLEFLRPDR QGVTQQQFKG ALYCLLGNHS
GVCLANLHDW DCIVQTWPAI VSSGLSQAMS LEKPSIVRLF DDLAEKIHRQ YETIGLDFTI
PKSCVEIAEL LQQSKNPSIN QILLSPEKIK EGIKRQQEKN ADALRNYENL VDTLLDGVEQ
RNLPWKFEHI GIGLLSLLLR DDRVLPLRAI RFFVENLNHD AIVVRKMAIS AVAGILKQLK
RTHKKLTINP CEISGCPKPT QIIAGDRPDN HWLHYDSKTI PRTKKEWESS CFVEKTHWGY
YTWPKNMVVY AGVEEQPKLG RSREDMTEAE QIIFDHFSDP KFVEQLITFL SLEDRKGKDK
FNPRRFCLFK GIFRNFDDAF LPVLKPHLEH LVADSHESTQ RCVAEIIAGL IRGSKHWTFE
KVEKLWELLC PLLRTALSNI TVETYNDWGA CIATSCESRD PRKLHWLFEL LLESPLSGEG
GSFVDACRLY VLQGGLAQQE WRVPELLHRL LKYLEPKLTQ VYKNVRERIG SVLTYIFMID
VSLPNTTPTI SPHVPEFTAR ILEKLKPLMD VDEEIQNHVM EENGIGEEDE RTQGIKLLKT
ILKWLMASAG RSFSTAVTEQ LQLLPLFFKI APVENDNSYD ELKRDAKLCL SLMSQGLLYP
HQVPLVLQVL KQTARSSSWH ARYTVLTYLQ TMVFYNLFIF LNNEDAVKDI RWLVISLLED
EQLEVREMAA TTLSGLLQCN FLTMDSPMQI HFEQLCKTKL PKKRKRDPGS VGDTIPSAEL
VKRHAGVLGL GACVLSSPYD VPTWMPQLLM NLSAHLNDPQ PIEMTVKKTL SNFRRTHHDN
WQEHKQQFTD DQLLVLTDLL VSPCYYA*

mutated AA sequence

MGENLAKKIM FFLLTIKLIL NHILDNSEDD TKSLFLIIKI IGDLLQFQGS HKHEFDSRWK
SFNLVKKSME NRLHGKKQHI RALLIDRVML QHELRTLTVE GCEYKKIHQD MIRDLLRLST
SSYSQVRNKA QQTFFAALGA YNFCCRDIIP LVLEFLRPDR QGVTQQQFKG ALYCLLGNHS
GVCLANLHDW DCIVQTWPAI VSSGLSQAMS LEKPSIVRLF DDLAEKIHRQ YETIGLDFTI
PKSCVEIAEL LQQSKNPSIN QILLSPEKIK EGIKRQQEKN ADALRNYENL VDTLLDGVEQ
RNLPWKFEHI GIGLLSLLLR DDRVLPLRAI RFFVENLNHD AIVVRKMAIS AVAGILKQLK
RTHKKLTINP CEISGCPKPT QIIAGDRPDN HWLHYDSKTI PRTKKEWESS CFVEKTHWGY
YTWPKNMVVY AGVEEQPKLG RSREDMTEAE QIIFDHFSDP KFVEQLITFL SLEDRKGKDK
FNPRRFCLFK GIFRNFDDAF LPVLKPHLEH LVADTHESTQ RCVAEIIAGL IRGSKHWTFE
KVEKLWELLC PLLRTALSNI TVETYNDWGA CIATSCESRD PRKLHWLFEL LLESPLSGEG
GSFVDACRLY VLQGGLAQQE WRVPELLHRL LKYLEPKLTQ VYKNVRERIG SVLTYIFMID
VSLPNTTPTI SPHVPEFTAR ILEKLKPLMD VDEEIQNHVM EENGIGEEDE RTQGIKLLKT
ILKWLMASAG RSFSTAVTEQ LQLLPLFFKI APVENDNSYD ELKRDAKLCL SLMSQGLLYP
HQVPLVLQVL KQTARSSSWH ARYTVLTYLQ TMVFYNLFIF LNNEDAVKDI RWLVISLLED
EQLEVREMAA TTLSGLLQCN FLTMDSPMQI HFEQLCKTKL PKKRKRDPGS VGDTIPSAEL
VKRHAGVLGL GACVLSSPYD VPTWMPQLLM NLSAHLNDPQ PIEMTVKKTL SNFRRTHHDN
WQEHKQQFTD DQLLVLTDLL VSPCYYA*

speed

1.05 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems