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: ENST00000392701
Querying Taster for transcript #2: ENST00000409882
MT speed 0 s - this script 2.969886 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GALNT3	disease_causing_automatic	0.999999987150053	simple_aae		affected	0	T97K	single base exchange	rs137853091		show file
GALNT3	disease_causing_automatic	0.999999990131242	simple_aae		affected	0	T359K	single base exchange	rs137853091		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999987150053 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM065199)
known disease mutation: rs7796 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:166615372G>TN/A show variant in all transcripts IGV

HGNC symbol

GALNT3

Ensembl transcript ID

ENST00000409882

Genbank transcript ID

N/A

UniProt peptide

Q14435

alteration type

single base exchange

alteration region

CDS

DNA changes

c.290C>A
cDNA.303C>A
g.35821C>A

AA changes

T97K Score: 78 explain score(s)

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

frameshift

known variant

Reference ID: rs137853091
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs7796 (pathogenic for Hyperphosphatemic familial tumoral calcinosis 1) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM065199)

known disease mutation at this position, please check HGMD for details (HGMD ID CM065199)
known disease mutation at this position, please check HGMD for details (HGMD ID CM065199)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.303	0.999
	5.651	1
(flanking)	4.679	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	35818.5	sequence motif lost	-	wt: ttca\|GAAC mu: ttca.GAAA
Donor gained	35817	0.99	mu: TTTTCAGAAAACCCA	TTCA\|gaaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000012593

359

Mmulatta

all identical

ENSMMUG00000019177

359

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000026994

359

Ggallus

all identical

ENSGALG00000010960

358

Trubripes

no homologue

Drerio

all identical

ENSDARG00000063724

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000020839

351

protein features

start (aa)	end (aa)	feature	details
38	633	TOPO_DOM	Lumenal (Potential).	lost
132	132	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
184	293	REGION	Catalytic subdomain A.	might get lost (downstream of altered splice site)
297	297	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
356	418	REGION	Catalytic subdomain B.	might get lost (downstream of altered splice site)
481	481	CONFLICT	Q -> R (in Ref. 1; CAA63371).	might get lost (downstream of altered splice site)
484	484	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
504	630	DOMAIN	Ricin B-type lectin.	might get lost (downstream of altered splice site)
517	517	DISULFID	By similarity.	might get lost (downstream of altered splice site)
535	535	DISULFID	By similarity.	might get lost (downstream of altered splice site)
561	561	DISULFID	By similarity.	might get lost (downstream of altered splice site)
574	574	DISULFID	By similarity.	might get lost (downstream of altered splice site)
605	605	DISULFID	By similarity.	might get lost (downstream of altered splice site)
618	618	DISULFID	By similarity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1116 / 1116

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

372 / 372

position of stopcodon in wt / mu cDNA

1129 / 1129

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

14 / 14

chromosome

strand

-1

last intron/exon boundary

1007

theoretical NMD boundary in CDS

943

length of CDS

1116

coding sequence (CDS) position

290

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

303

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

35821

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

166615372

original gDNA sequence snippet

CAATGGATTATTTTTCAGAACACCCACTTTTGCAGGAGGAC

altered gDNA sequence snippet

CAATGGATTATTTTTCAGAAAACCCACTTTTGCAGGAGGAC

original cDNA sequence snippet

TGAAACCTACCCAATTAAAACACCCACTTTTGCAGGAGGAC

altered cDNA sequence snippet

TGAAACCTACCCAATTAAAAAACCCACTTTTGCAGGAGGAC

wildtype AA sequence

MYGYGCNIFP PSPSNLKGEC FYGWLEPLLA RIAENYTAVV SPDIASIDLN TFEFNKPSPY
GSNHNRGNFD WSLSFGWESL PDHEKQRRKD ETYPIKTPTF AGGLFSISKE YFEYIGSYDE
EMEIWGGENI EMSFRVWQCG GQLEIMPCSV VGHVFRSKSP HSFPKGTQVI ARNQVRLAEV
WMDEYKEIFY RRNTDAAKIV KQKAFGDLSK RFEIKHRLQC KNFTWYLNNI YPEVYVPDLN
PVISGYIKSV GQPLCLDVGE NNQGGKPLIM YTCHGLGGNQ YFEYSAQHEI RHNIQKELCL
HAAQGLVQLK ACTYKGHKTV VTGEQIWEIQ KDQLLYNPFL KMCLSANGEH PSLVSCNPSD
PLQKWILSQN D*

mutated AA sequence

MYGYGCNIFP PSPSNLKGEC FYGWLEPLLA RIAENYTAVV SPDIASIDLN TFEFNKPSPY
GSNHNRGNFD WSLSFGWESL PDHEKQRRKD ETYPIKKPTF AGGLFSISKE YFEYIGSYDE
EMEIWGGENI EMSFRVWQCG GQLEIMPCSV VGHVFRSKSP HSFPKGTQVI ARNQVRLAEV
WMDEYKEIFY RRNTDAAKIV KQKAFGDLSK RFEIKHRLQC KNFTWYLNNI YPEVYVPDLN
PVISGYIKSV GQPLCLDVGE NNQGGKPLIM YTCHGLGGNQ YFEYSAQHEI RHNIQKELCL
HAAQGLVQLK ACTYKGHKTV VTGEQIWEIQ KDQLLYNPFL KMCLSANGEH PSLVSCNPSD
PLQKWILSQN D*

speed

0.63 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

disease causing

Model: simple_aae, prob: 0.999999990131242 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM065199)
known disease mutation: rs7796 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:166615372G>TN/A show variant in all transcripts IGV

HGNC symbol

GALNT3

Ensembl transcript ID

ENST00000392701

Genbank transcript ID

NM_004482

UniProt peptide

Q14435

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1076C>A
cDNA.1852C>A
g.35821C>A

AA changes

T359K Score: 78 explain score(s)

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

359

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.303	0.999
	5.651	1
(flanking)	4.679	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	35818.5	sequence motif lost	-	wt: ttca\|GAAC mu: ttca.GAAA
Donor gained	35817	0.99	mu: TTTTCAGAAAACCCA	TTCA\|gaaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

359

mutated

not conserved

359

Ptroglodytes

all identical

ENSPTRG00000012593

359

Mmulatta

all identical

ENSMMUG00000019177

359

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000026994

359

Ggallus

all identical

ENSGALG00000010960

358

Trubripes

no homologue

Drerio

all identical

ENSDARG00000063724

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000020839

351

protein features

start (aa)	end (aa)	feature	details
38	633	TOPO_DOM	Lumenal (Potential).	lost
356	418	REGION	Catalytic subdomain B.	lost
481	481	CONFLICT	Q -> R (in Ref. 1; CAA63371).	might get lost (downstream of altered splice site)
484	484	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
504	630	DOMAIN	Ricin B-type lectin.	might get lost (downstream of altered splice site)
517	517	DISULFID	By similarity.	might get lost (downstream of altered splice site)
535	535	DISULFID	By similarity.	might get lost (downstream of altered splice site)
561	561	DISULFID	By similarity.	might get lost (downstream of altered splice site)
574	574	DISULFID	By similarity.	might get lost (downstream of altered splice site)
605	605	DISULFID	By similarity.	might get lost (downstream of altered splice site)
618	618	DISULFID	By similarity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1902 / 1902

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

634 / 634

position of stopcodon in wt / mu cDNA

2678 / 2678

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

777 / 777

chromosome

strand

-1

last intron/exon boundary

2556

theoretical NMD boundary in CDS

1729

length of CDS

1902

coding sequence (CDS) position

1076

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

1852

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

35821

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

166615372

original gDNA sequence snippet

CAATGGATTATTTTTCAGAACACCCACTTTTGCAGGAGGAC

altered gDNA sequence snippet

CAATGGATTATTTTTCAGAAAACCCACTTTTGCAGGAGGAC

original cDNA sequence snippet

TGAAACCTACCCAATTAAAACACCCACTTTTGCAGGAGGAC

altered cDNA sequence snippet

TGAAACCTACCCAATTAAAAAACCCACTTTTGCAGGAGGAC

wildtype AA sequence

MAHLKRLVKL HIKRHYHKKF WKLGAVIFFF IIVLVLMQRE VSVQYSKEES RMERNMKNKN
KMLDLMLEAV NNIKDAMPKM QIGAPVRQNI DAGERPCLQG YYTAAELKPV LDRPPQDSNA
PGASGKAFKT TNLSVEEQKE KERGEAKHCF NAFASDRISL HRDLGPDTRP PECIEQKFKR
CPPLPTTSVI IVFHNEAWST LLRTVHSVLY SSPAILLKEI ILVDDASVDE YLHDKLDEYV
KQFSIVKIVR QRERKGLITA RLLGATVATA ETLTFLDAHC ECFYGWLEPL LARIAENYTA
VVSPDIASID LNTFEFNKPS PYGSNHNRGN FDWSLSFGWE SLPDHEKQRR KDETYPIKTP
TFAGGLFSIS KEYFEYIGSY DEEMEIWGGE NIEMSFRVWQ CGGQLEIMPC SVVGHVFRSK
SPHSFPKGTQ VIARNQVRLA EVWMDEYKEI FYRRNTDAAK IVKQKAFGDL SKRFEIKHRL
QCKNFTWYLN NIYPEVYVPD LNPVISGYIK SVGQPLCLDV GENNQGGKPL IMYTCHGLGG
NQYFEYSAQH EIRHNIQKEL CLHAAQGLVQ LKACTYKGHK TVVTGEQIWE IQKDQLLYNP
FLKMCLSANG EHPSLVSCNP SDPLQKWILS QND*

mutated AA sequence

MAHLKRLVKL HIKRHYHKKF WKLGAVIFFF IIVLVLMQRE VSVQYSKEES RMERNMKNKN
KMLDLMLEAV NNIKDAMPKM QIGAPVRQNI DAGERPCLQG YYTAAELKPV LDRPPQDSNA
PGASGKAFKT TNLSVEEQKE KERGEAKHCF NAFASDRISL HRDLGPDTRP PECIEQKFKR
CPPLPTTSVI IVFHNEAWST LLRTVHSVLY SSPAILLKEI ILVDDASVDE YLHDKLDEYV
KQFSIVKIVR QRERKGLITA RLLGATVATA ETLTFLDAHC ECFYGWLEPL LARIAENYTA
VVSPDIASID LNTFEFNKPS PYGSNHNRGN FDWSLSFGWE SLPDHEKQRR KDETYPIKKP
TFAGGLFSIS KEYFEYIGSY DEEMEIWGGE NIEMSFRVWQ CGGQLEIMPC SVVGHVFRSK
SPHSFPKGTQ VIARNQVRLA EVWMDEYKEI FYRRNTDAAK IVKQKAFGDL SKRFEIKHRL
QCKNFTWYLN NIYPEVYVPD LNPVISGYIK SVGQPLCLDV GENNQGGKPL IMYTCHGLGG
NQYFEYSAQH EIRHNIQKEL CLHAAQGLVQ LKACTYKGHK TVVTGEQIWE IQKDQLLYNP
FLKMCLSANG EHPSLVSCNP SDPLQKWILS QND*

speed

0.34 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems