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 8 transcript(s)...
Querying Taster for transcript #1: ENST00000372756
Querying Taster for transcript #2: ENST00000372754
Querying Taster for transcript #3: ENST00000372753
Querying Taster for transcript #4: ENST00000342716
Querying Taster for transcript #5: ENST00000360607
Querying Taster for transcript #6: ENST00000353917
Querying Taster for transcript #7: ENST00000537548
Querying Taster for transcript #8: ENST00000372751
MT speed 0 s - this script 6.265055 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
MATN4	polymorphism_automatic	3.24491079561895e-08	simple_aae		affected		R164S	single base exchange	rs2072788		show file
MATN4	polymorphism_automatic	3.24491079561895e-08	simple_aae		affected		R164S	single base exchange	rs2072788		show file
MATN4	polymorphism_automatic	3.24491079561895e-08	simple_aae		affected		R164S	single base exchange	rs2072788		show file
MATN4	polymorphism_automatic	3.24491079561895e-08	simple_aae		affected		R164S	single base exchange	rs2072788		show file
MATN4	polymorphism_automatic	3.24491079561895e-08	simple_aae		affected		R164S	single base exchange	rs2072788		show file
MATN4	polymorphism_automatic	3.24491079561895e-08	simple_aae		affected		R164S	single base exchange	rs2072788		show file
MATN4	polymorphism_automatic	2.02394709519771e-05	without_aae		affected			single base exchange	rs2072788		show file
MATN4	polymorphism_automatic	2.02394709519771e-05	without_aae		affected			single base exchange	rs2072788		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999967550892 (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)

chr20:43933021G>TN/A show variant in all transcripts IGV

HGNC symbol

MATN4

Ensembl transcript ID

ENST00000372756

Genbank transcript ID

N/A

UniProt peptide

O95460

alteration type

single base exchange

alteration region

CDS

DNA changes

c.490C>A
cDNA.499C>A
g.4149C>A

AA changes

R164S Score: 110 explain score(s)

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

164

frameshift

known variant

Reference ID: rs2072788

database	homozygous (T/T)	heterozygous	allele carriers
1000G	494	994	1488
ExAC	6683	19401	26084

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.254	0.146
	0.687	0.162
(flanking)	-0.004	0.177

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	4149	0.31	mu: GCGCCAGCGGCATTG	GCCA\|gcgg

distance from splice site

154

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

164

mutated

not conserved

164

Ptroglodytes

all identical

ENSPTRG00000013541

164

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000016995

166

Ggallus

not conserved

ENSGALG00000004028

164

Trubripes

all conserved

ENSTRUG00000000492

Drerio

not conserved

ENSDARG00000015947

165

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
34	213	DOMAIN	VWFA 1.	lost
173	173	CONFLICT	V -> L (in Ref. 2; BAC11083).	might get lost (downstream of altered splice site)
215	255	DOMAIN	EGF-like 1; incomplete.	might get lost (downstream of altered splice site)
219	219	DISULFID	By similarity.	might get lost (downstream of altered splice site)
226	226	DISULFID	By similarity.	might get lost (downstream of altered splice site)
230	230	DISULFID	By similarity.	might get lost (downstream of altered splice site)
239	239	DISULFID	By similarity.	might get lost (downstream of altered splice site)
241	241	DISULFID	By similarity.	might get lost (downstream of altered splice site)
251	251	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
254	254	DISULFID	By similarity.	might get lost (downstream of altered splice site)
256	292	DOMAIN	EGF-like 2.	might get lost (downstream of altered splice site)
260	260	DISULFID	By similarity.	might get lost (downstream of altered splice site)
267	267	DISULFID	By similarity.	might get lost (downstream of altered splice site)
271	271	DISULFID	By similarity.	might get lost (downstream of altered splice site)
280	280	DISULFID	By similarity.	might get lost (downstream of altered splice site)
282	282	DISULFID	By similarity.	might get lost (downstream of altered splice site)
295	295	DISULFID	By similarity.	might get lost (downstream of altered splice site)
297	337	DOMAIN	EGF-like 3.	might get lost (downstream of altered splice site)
301	301	DISULFID	By similarity.	might get lost (downstream of altered splice site)
305	305	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
308	308	DISULFID	By similarity.	might get lost (downstream of altered splice site)
312	312	DISULFID	By similarity.	might get lost (downstream of altered splice site)
321	321	DISULFID	By similarity.	might get lost (downstream of altered splice site)
323	323	DISULFID	By similarity.	might get lost (downstream of altered splice site)
336	336	DISULFID	By similarity.	might get lost (downstream of altered splice site)
342	342	DISULFID	By similarity.	might get lost (downstream of altered splice site)
342	377	DOMAIN	EGF-like 4.	might get lost (downstream of altered splice site)
349	349	DISULFID	By similarity.	might get lost (downstream of altered splice site)
353	353	DISULFID	By similarity.	might get lost (downstream of altered splice site)
362	362	DISULFID	By similarity.	might get lost (downstream of altered splice site)
364	364	DISULFID	By similarity.	might get lost (downstream of altered splice site)
377	377	DISULFID	By similarity.	might get lost (downstream of altered splice site)
386	561	DOMAIN	VWFA 2.	might get lost (downstream of altered splice site)
563	563	CONFLICT	G -> S (in Ref. 2; BAC11083).	might get lost (downstream of altered splice site)
591	622	COILED	Potential.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1746 / 1746

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

582 / 582

position of stopcodon in wt / mu cDNA

1755 / 1755

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

10 / 10

chromosome

strand

-1

last intron/exon boundary

1697

theoretical NMD boundary in CDS

1637

length of CDS

1746

coding sequence (CDS) position

490

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

499

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

4149

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

43933021

original gDNA sequence snippet

TGGCGGCACAGGCGCGCGCCCGCGGCATTGAAATTTACGCG

altered gDNA sequence snippet

TGGCGGCACAGGCGCGCGCCAGCGGCATTGAAATTTACGCG

original cDNA sequence snippet

TGGCGGCACAGGCGCGCGCCCGCGGCATTGAAATTTACGCG

altered cDNA sequence snippet

TGGCGGCACAGGCGCGCGCCAGCGGCATTGAAATTTACGCG

wildtype AA sequence

MRGLLCWPVL LLLLQPWETQ LQLTGPRCHT GPLDLVFVID SSRSVRPFEF ETMRQFLMGL
LRGLNVGPNA TRVGVIQYSS QVQSVFPLRA FSRREDMERA IRDLVPLAQG TMTGLAIQYA
MNVAFSVAEG ARPPEERVPR VAVIVTDGRP QDRVAEVAAQ ARARGIEIYA VGVQRADVGS
LRAMASPPLD EHVFLVESFD LIQEFGLQFQ SRLCAIDLCA EGTHGCEHHC VNSPGSYFCH
CQVGFVLQQD QRSCRAIDYC SFGNHSCQHE CVSTPGGPRC HCREGHDLQP DGRSCQVRDL
CNGVDHGCEF QCVSEGLSYR CLCPEGRQLQ ADGKSCNRCR EGHVDLVLLV DGSKSVRPQN
FELVKRFVNQ IVDFLDVSPE GTRVGLVQFS SRVRTEFPLG RYGTAAEVKQ AVLAVEYMER
GTMTGLALRH MVEHSFSEAQ GARPRALNVP RVGLVFTDGR SQDDISVWAA RAKEEGIVMY
AVGVGKAVEA ELREIASEPA ELHVSYAPDF GTMTHLLENL RGSICPEEGI SAGTELRSPC
ECESLVEFQG RTLGALESLT LNLAQLTARL EDLENQLANQ K*

mutated AA sequence

MRGLLCWPVL LLLLQPWETQ LQLTGPRCHT GPLDLVFVID SSRSVRPFEF ETMRQFLMGL
LRGLNVGPNA TRVGVIQYSS QVQSVFPLRA FSRREDMERA IRDLVPLAQG TMTGLAIQYA
MNVAFSVAEG ARPPEERVPR VAVIVTDGRP QDRVAEVAAQ ARASGIEIYA VGVQRADVGS
LRAMASPPLD EHVFLVESFD LIQEFGLQFQ SRLCAIDLCA EGTHGCEHHC VNSPGSYFCH
CQVGFVLQQD QRSCRAIDYC SFGNHSCQHE CVSTPGGPRC HCREGHDLQP DGRSCQVRDL
CNGVDHGCEF QCVSEGLSYR CLCPEGRQLQ ADGKSCNRCR EGHVDLVLLV DGSKSVRPQN
FELVKRFVNQ IVDFLDVSPE GTRVGLVQFS SRVRTEFPLG RYGTAAEVKQ AVLAVEYMER
GTMTGLALRH MVEHSFSEAQ GARPRALNVP RVGLVFTDGR SQDDISVWAA RAKEEGIVMY
AVGVGKAVEA ELREIASEPA ELHVSYAPDF GTMTHLLENL RGSICPEEGI SAGTELRSPC
ECESLVEFQG RTLGALESLT LNLAQLTARL EDLENQLANQ K*

speed

0.45 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: 0.999999967550892 (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)

chr20:43933021G>TN/A show variant in all transcripts IGV

HGNC symbol

MATN4

Ensembl transcript ID

ENST00000372754

Genbank transcript ID

N/A

UniProt peptide

O95460

alteration type

single base exchange

alteration region

CDS

DNA changes

c.490C>A
cDNA.499C>A
g.4149C>A

AA changes

R164S Score: 110 explain score(s)

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

164

frameshift

known variant

Reference ID: rs2072788

database	homozygous (T/T)	heterozygous	allele carriers
1000G	494	994	1488
ExAC	6683	19401	26084

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.254	0.146
	0.687	0.162
(flanking)	-0.004	0.177

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	4149	0.31	mu: GCGCCAGCGGCATTG	GCCA\|gcgg

distance from splice site

154

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

164

mutated

not conserved

164

Ptroglodytes

all identical

ENSPTRG00000013541

164

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000016995

166

Ggallus

not conserved

ENSGALG00000004028

164

Trubripes

all conserved

ENSTRUG00000000492

Drerio

not conserved

ENSDARG00000015947

165

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
34	213	DOMAIN	VWFA 1.	lost
173	173	CONFLICT	V -> L (in Ref. 2; BAC11083).	might get lost (downstream of altered splice site)
215	255	DOMAIN	EGF-like 1; incomplete.	might get lost (downstream of altered splice site)
219	219	DISULFID	By similarity.	might get lost (downstream of altered splice site)
226	226	DISULFID	By similarity.	might get lost (downstream of altered splice site)
230	230	DISULFID	By similarity.	might get lost (downstream of altered splice site)
239	239	DISULFID	By similarity.	might get lost (downstream of altered splice site)
241	241	DISULFID	By similarity.	might get lost (downstream of altered splice site)
251	251	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
254	254	DISULFID	By similarity.	might get lost (downstream of altered splice site)
256	292	DOMAIN	EGF-like 2.	might get lost (downstream of altered splice site)
260	260	DISULFID	By similarity.	might get lost (downstream of altered splice site)
267	267	DISULFID	By similarity.	might get lost (downstream of altered splice site)
271	271	DISULFID	By similarity.	might get lost (downstream of altered splice site)
280	280	DISULFID	By similarity.	might get lost (downstream of altered splice site)
282	282	DISULFID	By similarity.	might get lost (downstream of altered splice site)
295	295	DISULFID	By similarity.	might get lost (downstream of altered splice site)
297	337	DOMAIN	EGF-like 3.	might get lost (downstream of altered splice site)
301	301	DISULFID	By similarity.	might get lost (downstream of altered splice site)
305	305	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
308	308	DISULFID	By similarity.	might get lost (downstream of altered splice site)
312	312	DISULFID	By similarity.	might get lost (downstream of altered splice site)
321	321	DISULFID	By similarity.	might get lost (downstream of altered splice site)
323	323	DISULFID	By similarity.	might get lost (downstream of altered splice site)
336	336	DISULFID	By similarity.	might get lost (downstream of altered splice site)
342	342	DISULFID	By similarity.	might get lost (downstream of altered splice site)
342	377	DOMAIN	EGF-like 4.	might get lost (downstream of altered splice site)
349	349	DISULFID	By similarity.	might get lost (downstream of altered splice site)
353	353	DISULFID	By similarity.	might get lost (downstream of altered splice site)
362	362	DISULFID	By similarity.	might get lost (downstream of altered splice site)
364	364	DISULFID	By similarity.	might get lost (downstream of altered splice site)
377	377	DISULFID	By similarity.	might get lost (downstream of altered splice site)
386	561	DOMAIN	VWFA 2.	might get lost (downstream of altered splice site)
563	563	CONFLICT	G -> S (in Ref. 2; BAC11083).	might get lost (downstream of altered splice site)
591	622	COILED	Potential.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1869 / 1869

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

623 / 623

position of stopcodon in wt / mu cDNA

1878 / 1878

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

10 / 10

chromosome

strand

-1

last intron/exon boundary

1820

theoretical NMD boundary in CDS

1760

length of CDS

1869

coding sequence (CDS) position

490

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

499

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

4149

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

43933021

original gDNA sequence snippet

TGGCGGCACAGGCGCGCGCCCGCGGCATTGAAATTTACGCG

altered gDNA sequence snippet

TGGCGGCACAGGCGCGCGCCAGCGGCATTGAAATTTACGCG

original cDNA sequence snippet

TGGCGGCACAGGCGCGCGCCCGCGGCATTGAAATTTACGCG

altered cDNA sequence snippet

TGGCGGCACAGGCGCGCGCCAGCGGCATTGAAATTTACGCG

wildtype AA sequence

MRGLLCWPVL LLLLQPWETQ LQLTGPRCHT GPLDLVFVID SSRSVRPFEF ETMRQFLMGL
LRGLNVGPNA TRVGVIQYSS QVQSVFPLRA FSRREDMERA IRDLVPLAQG TMTGLAIQYA
MNVAFSVAEG ARPPEERVPR VAVIVTDGRP QDRVAEVAAQ ARARGIEIYA VGVQRADVGS
LRAMASPPLD EHVFLVESFD LIQEFGLQFQ SRLCGKDQCA EGGHGCQHQC VNAWAMFHCT
CNPGYKLAAD NKSCLAIDLC AEGTHGCEHH CVNSPGSYFC HCQVGFVLQQ DQRSCRAIDY
CSFGNHSCQH ECVSTPGGPR CHCREGHDLQ PDGRSCQVRD LCNGVDHGCE FQCVSEGLSY
RCLCPEGRQL QADGKSCNRC REGHVDLVLL VDGSKSVRPQ NFELVKRFVN QIVDFLDVSP
EGTRVGLVQF SSRVRTEFPL GRYGTAAEVK QAVLAVEYME RGTMTGLALR HMVEHSFSEA
QGARPRALNV PRVGLVFTDG RSQDDISVWA ARAKEEGIVM YAVGVGKAVE AELREIASEP
AELHVSYAPD FGTMTHLLEN LRGSICPEEG ISAGTELRSP CECESLVEFQ GRTLGALESL
TLNLAQLTAR LEDLENQLAN QK*

mutated AA sequence

MRGLLCWPVL LLLLQPWETQ LQLTGPRCHT GPLDLVFVID SSRSVRPFEF ETMRQFLMGL
LRGLNVGPNA TRVGVIQYSS QVQSVFPLRA FSRREDMERA IRDLVPLAQG TMTGLAIQYA
MNVAFSVAEG ARPPEERVPR VAVIVTDGRP QDRVAEVAAQ ARASGIEIYA VGVQRADVGS
LRAMASPPLD EHVFLVESFD LIQEFGLQFQ SRLCGKDQCA EGGHGCQHQC VNAWAMFHCT
CNPGYKLAAD NKSCLAIDLC AEGTHGCEHH CVNSPGSYFC HCQVGFVLQQ DQRSCRAIDY
CSFGNHSCQH ECVSTPGGPR CHCREGHDLQ PDGRSCQVRD LCNGVDHGCE FQCVSEGLSY
RCLCPEGRQL QADGKSCNRC REGHVDLVLL VDGSKSVRPQ NFELVKRFVN QIVDFLDVSP
EGTRVGLVQF SSRVRTEFPL GRYGTAAEVK QAVLAVEYME RGTMTGLALR HMVEHSFSEA
QGARPRALNV PRVGLVFTDG RSQDDISVWA ARAKEEGIVM YAVGVGKAVE AELREIASEP
AELHVSYAPD FGTMTHLLEN LRGSICPEEG ISAGTELRSP CECESLVEFQ GRTLGALESL
TLNLAQLTAR LEDLENQLAN QK*

speed

1.15 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999967550892 (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)

chr20:43933021G>TN/A show variant in all transcripts IGV

HGNC symbol

MATN4

Ensembl transcript ID

ENST00000342716

Genbank transcript ID

NM_003833

UniProt peptide

O95460

alteration type

single base exchange

alteration region

CDS

DNA changes

c.490C>A
cDNA.677C>A
g.4149C>A

AA changes

R164S Score: 110 explain score(s)

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

164

frameshift

known variant

Reference ID: rs2072788

database	homozygous (T/T)	heterozygous	allele carriers
1000G	494	994	1488
ExAC	6683	19401	26084

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.254	0.146
	0.687	0.162
(flanking)	-0.004	0.177

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	4149	0.31	mu: GCGCCAGCGGCATTG	GCCA\|gcgg

distance from splice site

154

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

164

mutated

not conserved

164

Ptroglodytes

all identical

ENSPTRG00000013541

164

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000016995

166

Ggallus

not conserved

ENSGALG00000004028

164

Trubripes

all conserved

ENSTRUG00000000492

Drerio

not conserved

ENSDARG00000015947

165

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
34	213	DOMAIN	VWFA 1.	lost
173	173	CONFLICT	V -> L (in Ref. 2; BAC11083).	might get lost (downstream of altered splice site)
215	255	DOMAIN	EGF-like 1; incomplete.	might get lost (downstream of altered splice site)
219	219	DISULFID	By similarity.	might get lost (downstream of altered splice site)
226	226	DISULFID	By similarity.	might get lost (downstream of altered splice site)
230	230	DISULFID	By similarity.	might get lost (downstream of altered splice site)
239	239	DISULFID	By similarity.	might get lost (downstream of altered splice site)
241	241	DISULFID	By similarity.	might get lost (downstream of altered splice site)
251	251	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
254	254	DISULFID	By similarity.	might get lost (downstream of altered splice site)
256	292	DOMAIN	EGF-like 2.	might get lost (downstream of altered splice site)
260	260	DISULFID	By similarity.	might get lost (downstream of altered splice site)
267	267	DISULFID	By similarity.	might get lost (downstream of altered splice site)
271	271	DISULFID	By similarity.	might get lost (downstream of altered splice site)
280	280	DISULFID	By similarity.	might get lost (downstream of altered splice site)
282	282	DISULFID	By similarity.	might get lost (downstream of altered splice site)
295	295	DISULFID	By similarity.	might get lost (downstream of altered splice site)
297	337	DOMAIN	EGF-like 3.	might get lost (downstream of altered splice site)
301	301	DISULFID	By similarity.	might get lost (downstream of altered splice site)
305	305	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
308	308	DISULFID	By similarity.	might get lost (downstream of altered splice site)
312	312	DISULFID	By similarity.	might get lost (downstream of altered splice site)
321	321	DISULFID	By similarity.	might get lost (downstream of altered splice site)
323	323	DISULFID	By similarity.	might get lost (downstream of altered splice site)
336	336	DISULFID	By similarity.	might get lost (downstream of altered splice site)
342	342	DISULFID	By similarity.	might get lost (downstream of altered splice site)
342	377	DOMAIN	EGF-like 4.	might get lost (downstream of altered splice site)
349	349	DISULFID	By similarity.	might get lost (downstream of altered splice site)
353	353	DISULFID	By similarity.	might get lost (downstream of altered splice site)
362	362	DISULFID	By similarity.	might get lost (downstream of altered splice site)
364	364	DISULFID	By similarity.	might get lost (downstream of altered splice site)
377	377	DISULFID	By similarity.	might get lost (downstream of altered splice site)
386	561	DOMAIN	VWFA 2.	might get lost (downstream of altered splice site)
563	563	CONFLICT	G -> S (in Ref. 2; BAC11083).	might get lost (downstream of altered splice site)
591	622	COILED	Potential.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1746 / 1746

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

582 / 582

position of stopcodon in wt / mu cDNA

1933 / 1933

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

188 / 188

chromosome

strand

-1

last intron/exon boundary

1875

theoretical NMD boundary in CDS

1637

length of CDS

1746

coding sequence (CDS) position

490

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

677

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

4149

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

43933021

original gDNA sequence snippet

TGGCGGCACAGGCGCGCGCCCGCGGCATTGAAATTTACGCG

altered gDNA sequence snippet

TGGCGGCACAGGCGCGCGCCAGCGGCATTGAAATTTACGCG

original cDNA sequence snippet

TGGCGGCACAGGCGCGCGCCCGCGGCATTGAAATTTACGCG

altered cDNA sequence snippet

TGGCGGCACAGGCGCGCGCCAGCGGCATTGAAATTTACGCG

wildtype AA sequence

mutated AA sequence

MRGLLCWPVL LLLLQPWETQ LQLTGPRCHT GPLDLVFVID SSRSVRPFEF ETMRQFLMGL
LRGLNVGPNA TRVGVIQYSS QVQSVFPLRA FSRREDMERA IRDLVPLAQG TMTGLAIQYA
MNVAFSVAEG ARPPEERVPR VAVIVTDGRP QDRVAEVAAQ ARASGIEIYA VGVQRADVGS
LRAMASPPLD EHVFLVESFD LIQEFGLQFQ SRLCAIDLCA EGTHGCEHHC VNSPGSYFCH
CQVGFVLQQD QRSCRAIDYC SFGNHSCQHE CVSTPGGPRC HCREGHDLQP DGRSCQVRDL
CNGVDHGCEF QCVSEGLSYR CLCPEGRQLQ ADGKSCNRCR EGHVDLVLLV DGSKSVRPQN
FELVKRFVNQ IVDFLDVSPE GTRVGLVQFS SRVRTEFPLG RYGTAAEVKQ AVLAVEYMER
GTMTGLALRH MVEHSFSEAQ GARPRALNVP RVGLVFTDGR SQDDISVWAA RAKEEGIVMY
AVGVGKAVEA ELREIASEPA ELHVSYAPDF GTMTHLLENL RGSICPEEGI SAGTELRSPC
ECESLVEFQG RTLGALESLT LNLAQLTARL EDLENQLANQ K*

speed

0.42 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999967550892 (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)

chr20:43933021G>TN/A show variant in all transcripts IGV

HGNC symbol

MATN4

Ensembl transcript ID

ENST00000360607

Genbank transcript ID

NM_030590

UniProt peptide

O95460

alteration type

single base exchange

alteration region

CDS

DNA changes

c.490C>A
cDNA.677C>A
g.4149C>A

AA changes

R164S Score: 110 explain score(s)

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

164

frameshift

known variant

Reference ID: rs2072788

database	homozygous (T/T)	heterozygous	allele carriers
1000G	494	994	1488
ExAC	6683	19401	26084

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.254	0.146
	0.687	0.162
(flanking)	-0.004	0.177

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	4149	0.31	mu: GCGCCAGCGGCATTG	GCCA\|gcgg

distance from splice site

154

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

164

mutated

not conserved

164

Ptroglodytes

all identical

ENSPTRG00000013541

164

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000016995

166

Ggallus

not conserved

ENSGALG00000004028

164

Trubripes

all conserved

ENSTRUG00000000492

Drerio

not conserved

ENSDARG00000015947

165

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
34	213	DOMAIN	VWFA 1.	lost
173	173	CONFLICT	V -> L (in Ref. 2; BAC11083).	might get lost (downstream of altered splice site)
215	255	DOMAIN	EGF-like 1; incomplete.	might get lost (downstream of altered splice site)
219	219	DISULFID	By similarity.	might get lost (downstream of altered splice site)
226	226	DISULFID	By similarity.	might get lost (downstream of altered splice site)
230	230	DISULFID	By similarity.	might get lost (downstream of altered splice site)
239	239	DISULFID	By similarity.	might get lost (downstream of altered splice site)
241	241	DISULFID	By similarity.	might get lost (downstream of altered splice site)
251	251	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
254	254	DISULFID	By similarity.	might get lost (downstream of altered splice site)
256	292	DOMAIN	EGF-like 2.	might get lost (downstream of altered splice site)
260	260	DISULFID	By similarity.	might get lost (downstream of altered splice site)
267	267	DISULFID	By similarity.	might get lost (downstream of altered splice site)
271	271	DISULFID	By similarity.	might get lost (downstream of altered splice site)
280	280	DISULFID	By similarity.	might get lost (downstream of altered splice site)
282	282	DISULFID	By similarity.	might get lost (downstream of altered splice site)
295	295	DISULFID	By similarity.	might get lost (downstream of altered splice site)
297	337	DOMAIN	EGF-like 3.	might get lost (downstream of altered splice site)
301	301	DISULFID	By similarity.	might get lost (downstream of altered splice site)
305	305	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
308	308	DISULFID	By similarity.	might get lost (downstream of altered splice site)
312	312	DISULFID	By similarity.	might get lost (downstream of altered splice site)
321	321	DISULFID	By similarity.	might get lost (downstream of altered splice site)
323	323	DISULFID	By similarity.	might get lost (downstream of altered splice site)
336	336	DISULFID	By similarity.	might get lost (downstream of altered splice site)
342	342	DISULFID	By similarity.	might get lost (downstream of altered splice site)
342	377	DOMAIN	EGF-like 4.	might get lost (downstream of altered splice site)
349	349	DISULFID	By similarity.	might get lost (downstream of altered splice site)
353	353	DISULFID	By similarity.	might get lost (downstream of altered splice site)
362	362	DISULFID	By similarity.	might get lost (downstream of altered splice site)
364	364	DISULFID	By similarity.	might get lost (downstream of altered splice site)
377	377	DISULFID	By similarity.	might get lost (downstream of altered splice site)
386	561	DOMAIN	VWFA 2.	might get lost (downstream of altered splice site)
563	563	CONFLICT	G -> S (in Ref. 2; BAC11083).	might get lost (downstream of altered splice site)
591	622	COILED	Potential.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1623 / 1623

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

541 / 541

position of stopcodon in wt / mu cDNA

1810 / 1810

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

188 / 188

chromosome

strand

-1

last intron/exon boundary

1752

theoretical NMD boundary in CDS

1514

length of CDS

1623

coding sequence (CDS) position

490

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

677

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

4149

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

43933021

original gDNA sequence snippet

TGGCGGCACAGGCGCGCGCCCGCGGCATTGAAATTTACGCG

altered gDNA sequence snippet

TGGCGGCACAGGCGCGCGCCAGCGGCATTGAAATTTACGCG

original cDNA sequence snippet

TGGCGGCACAGGCGCGCGCCCGCGGCATTGAAATTTACGCG

altered cDNA sequence snippet

TGGCGGCACAGGCGCGCGCCAGCGGCATTGAAATTTACGCG

wildtype AA sequence

MRGLLCWPVL LLLLQPWETQ LQLTGPRCHT GPLDLVFVID SSRSVRPFEF ETMRQFLMGL
LRGLNVGPNA TRVGVIQYSS QVQSVFPLRA FSRREDMERA IRDLVPLAQG TMTGLAIQYA
MNVAFSVAEG ARPPEERVPR VAVIVTDGRP QDRVAEVAAQ ARARGIEIYA VGVQRADVGS
LRAMASPPLD EHVFLVESFD LIQEFGLQFQ SRLCAIDYCS FGNHSCQHEC VSTPGGPRCH
CREGHDLQPD GRSCQVRDLC NGVDHGCEFQ CVSEGLSYRC LCPEGRQLQA DGKSCNRCRE
GHVDLVLLVD GSKSVRPQNF ELVKRFVNQI VDFLDVSPEG TRVGLVQFSS RVRTEFPLGR
YGTAAEVKQA VLAVEYMERG TMTGLALRHM VEHSFSEAQG ARPRALNVPR VGLVFTDGRS
QDDISVWAAR AKEEGIVMYA VGVGKAVEAE LREIASEPAE LHVSYAPDFG TMTHLLENLR
GSICPEEGIS AGTELRSPCE CESLVEFQGR TLGALESLTL NLAQLTARLE DLENQLANQK
*

mutated AA sequence

MRGLLCWPVL LLLLQPWETQ LQLTGPRCHT GPLDLVFVID SSRSVRPFEF ETMRQFLMGL
LRGLNVGPNA TRVGVIQYSS QVQSVFPLRA FSRREDMERA IRDLVPLAQG TMTGLAIQYA
MNVAFSVAEG ARPPEERVPR VAVIVTDGRP QDRVAEVAAQ ARASGIEIYA VGVQRADVGS
LRAMASPPLD EHVFLVESFD LIQEFGLQFQ SRLCAIDYCS FGNHSCQHEC VSTPGGPRCH
CREGHDLQPD GRSCQVRDLC NGVDHGCEFQ CVSEGLSYRC LCPEGRQLQA DGKSCNRCRE
GHVDLVLLVD GSKSVRPQNF ELVKRFVNQI VDFLDVSPEG TRVGLVQFSS RVRTEFPLGR
YGTAAEVKQA VLAVEYMERG TMTGLALRHM VEHSFSEAQG ARPRALNVPR VGLVFTDGRS
QDDISVWAAR AKEEGIVMYA VGVGKAVEAE LREIASEPAE LHVSYAPDFG TMTHLLENLR
GSICPEEGIS AGTELRSPCE CESLVEFQGR TLGALESLTL NLAQLTARLE DLENQLANQK
*

speed

0.46 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999967550892 (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)

chr20:43933021G>TN/A show variant in all transcripts IGV

HGNC symbol

MATN4

Ensembl transcript ID

ENST00000353917

Genbank transcript ID

NM_030592

UniProt peptide

O95460

alteration type

single base exchange

alteration region

CDS

DNA changes

c.490C>A
cDNA.677C>A
g.4149C>A

AA changes

R164S Score: 110 explain score(s)

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

164

frameshift

known variant

Reference ID: rs2072788

database	homozygous (T/T)	heterozygous	allele carriers
1000G	494	994	1488
ExAC	6683	19401	26084

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.254	0.146
	0.687	0.162
(flanking)	-0.004	0.177

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	4149	0.31	mu: GCGCCAGCGGCATTG	GCCA\|gcgg

distance from splice site

154

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

164

mutated

not conserved

164

Ptroglodytes

all identical

ENSPTRG00000013541

164

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000016995

166

Ggallus

not conserved

ENSGALG00000004028

164

Trubripes

all conserved

ENSTRUG00000000492

Drerio

not conserved

ENSDARG00000015947

165

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
34	213	DOMAIN	VWFA 1.	lost
173	173	CONFLICT	V -> L (in Ref. 2; BAC11083).	might get lost (downstream of altered splice site)
215	255	DOMAIN	EGF-like 1; incomplete.	might get lost (downstream of altered splice site)
219	219	DISULFID	By similarity.	might get lost (downstream of altered splice site)
226	226	DISULFID	By similarity.	might get lost (downstream of altered splice site)
230	230	DISULFID	By similarity.	might get lost (downstream of altered splice site)
239	239	DISULFID	By similarity.	might get lost (downstream of altered splice site)
241	241	DISULFID	By similarity.	might get lost (downstream of altered splice site)
251	251	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
254	254	DISULFID	By similarity.	might get lost (downstream of altered splice site)
256	292	DOMAIN	EGF-like 2.	might get lost (downstream of altered splice site)
260	260	DISULFID	By similarity.	might get lost (downstream of altered splice site)
267	267	DISULFID	By similarity.	might get lost (downstream of altered splice site)
271	271	DISULFID	By similarity.	might get lost (downstream of altered splice site)
280	280	DISULFID	By similarity.	might get lost (downstream of altered splice site)
282	282	DISULFID	By similarity.	might get lost (downstream of altered splice site)
295	295	DISULFID	By similarity.	might get lost (downstream of altered splice site)
297	337	DOMAIN	EGF-like 3.	might get lost (downstream of altered splice site)
301	301	DISULFID	By similarity.	might get lost (downstream of altered splice site)
305	305	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
308	308	DISULFID	By similarity.	might get lost (downstream of altered splice site)
312	312	DISULFID	By similarity.	might get lost (downstream of altered splice site)
321	321	DISULFID	By similarity.	might get lost (downstream of altered splice site)
323	323	DISULFID	By similarity.	might get lost (downstream of altered splice site)
336	336	DISULFID	By similarity.	might get lost (downstream of altered splice site)
342	342	DISULFID	By similarity.	might get lost (downstream of altered splice site)
342	377	DOMAIN	EGF-like 4.	might get lost (downstream of altered splice site)
349	349	DISULFID	By similarity.	might get lost (downstream of altered splice site)
353	353	DISULFID	By similarity.	might get lost (downstream of altered splice site)
362	362	DISULFID	By similarity.	might get lost (downstream of altered splice site)
364	364	DISULFID	By similarity.	might get lost (downstream of altered splice site)
377	377	DISULFID	By similarity.	might get lost (downstream of altered splice site)
386	561	DOMAIN	VWFA 2.	might get lost (downstream of altered splice site)
563	563	CONFLICT	G -> S (in Ref. 2; BAC11083).	might get lost (downstream of altered splice site)
591	622	COILED	Potential.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1500 / 1500

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

500 / 500

position of stopcodon in wt / mu cDNA

1687 / 1687

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

188 / 188

chromosome

strand

-1

last intron/exon boundary

1629

theoretical NMD boundary in CDS

1391

length of CDS

1500

coding sequence (CDS) position

490

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

677

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

4149

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

43933021

original gDNA sequence snippet

TGGCGGCACAGGCGCGCGCCCGCGGCATTGAAATTTACGCG

altered gDNA sequence snippet

TGGCGGCACAGGCGCGCGCCAGCGGCATTGAAATTTACGCG

original cDNA sequence snippet

TGGCGGCACAGGCGCGCGCCCGCGGCATTGAAATTTACGCG

altered cDNA sequence snippet

TGGCGGCACAGGCGCGCGCCAGCGGCATTGAAATTTACGCG

wildtype AA sequence

MRGLLCWPVL LLLLQPWETQ LQLTGPRCHT GPLDLVFVID SSRSVRPFEF ETMRQFLMGL
LRGLNVGPNA TRVGVIQYSS QVQSVFPLRA FSRREDMERA IRDLVPLAQG TMTGLAIQYA
MNVAFSVAEG ARPPEERVPR VAVIVTDGRP QDRVAEVAAQ ARARGIEIYA VGVQRADVGS
LRAMASPPLD EHVFLVESFD LIQEFGLQFQ SRLCVRDLCN GVDHGCEFQC VSEGLSYRCL
CPEGRQLQAD GKSCNRCREG HVDLVLLVDG SKSVRPQNFE LVKRFVNQIV DFLDVSPEGT
RVGLVQFSSR VRTEFPLGRY GTAAEVKQAV LAVEYMERGT MTGLALRHMV EHSFSEAQGA
RPRALNVPRV GLVFTDGRSQ DDISVWAARA KEEGIVMYAV GVGKAVEAEL REIASEPAEL
HVSYAPDFGT MTHLLENLRG SICPEEGISA GTELRSPCEC ESLVEFQGRT LGALESLTLN
LAQLTARLED LENQLANQK*

mutated AA sequence

MRGLLCWPVL LLLLQPWETQ LQLTGPRCHT GPLDLVFVID SSRSVRPFEF ETMRQFLMGL
LRGLNVGPNA TRVGVIQYSS QVQSVFPLRA FSRREDMERA IRDLVPLAQG TMTGLAIQYA
MNVAFSVAEG ARPPEERVPR VAVIVTDGRP QDRVAEVAAQ ARASGIEIYA VGVQRADVGS
LRAMASPPLD EHVFLVESFD LIQEFGLQFQ SRLCVRDLCN GVDHGCEFQC VSEGLSYRCL
CPEGRQLQAD GKSCNRCREG HVDLVLLVDG SKSVRPQNFE LVKRFVNQIV DFLDVSPEGT
RVGLVQFSSR VRTEFPLGRY GTAAEVKQAV LAVEYMERGT MTGLALRHMV EHSFSEAQGA
RPRALNVPRV GLVFTDGRSQ DDISVWAARA KEEGIVMYAV GVGKAVEAEL REIASEPAEL
HVSYAPDFGT MTHLLENLRG SICPEEGISA GTELRSPCEC ESLVEFQGRT LGALESLTLN
LAQLTARLED LENQLANQK*

speed

1.16 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999967550892 (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)

chr20:43933021G>TN/A show variant in all transcripts IGV

HGNC symbol

MATN4

Ensembl transcript ID

ENST00000537548

Genbank transcript ID

N/A

UniProt peptide

O95460

alteration type

single base exchange

alteration region

CDS

DNA changes

c.490C>A
cDNA.735C>A
g.4149C>A

AA changes

R164S Score: 110 explain score(s)

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

164

frameshift

known variant

Reference ID: rs2072788

database	homozygous (T/T)	heterozygous	allele carriers
1000G	494	994	1488
ExAC	6683	19401	26084

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.254	0.146
	0.687	0.162
(flanking)	-0.004	0.177

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	4149	0.31	mu: GCGCCAGCGGCATTG	GCCA\|gcgg

distance from splice site

154

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

164

mutated

not conserved

164

Ptroglodytes

all identical

ENSPTRG00000013541

164

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000016995

166

Ggallus

not conserved

ENSGALG00000004028

164

Trubripes

all conserved

ENSTRUG00000000492

Drerio

not conserved

ENSDARG00000015947

165

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
34	213	DOMAIN	VWFA 1.	lost
173	173	CONFLICT	V -> L (in Ref. 2; BAC11083).	might get lost (downstream of altered splice site)
215	255	DOMAIN	EGF-like 1; incomplete.	might get lost (downstream of altered splice site)
219	219	DISULFID	By similarity.	might get lost (downstream of altered splice site)
226	226	DISULFID	By similarity.	might get lost (downstream of altered splice site)
230	230	DISULFID	By similarity.	might get lost (downstream of altered splice site)
239	239	DISULFID	By similarity.	might get lost (downstream of altered splice site)
241	241	DISULFID	By similarity.	might get lost (downstream of altered splice site)
251	251	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
254	254	DISULFID	By similarity.	might get lost (downstream of altered splice site)
256	292	DOMAIN	EGF-like 2.	might get lost (downstream of altered splice site)
260	260	DISULFID	By similarity.	might get lost (downstream of altered splice site)
267	267	DISULFID	By similarity.	might get lost (downstream of altered splice site)
271	271	DISULFID	By similarity.	might get lost (downstream of altered splice site)
280	280	DISULFID	By similarity.	might get lost (downstream of altered splice site)
282	282	DISULFID	By similarity.	might get lost (downstream of altered splice site)
295	295	DISULFID	By similarity.	might get lost (downstream of altered splice site)
297	337	DOMAIN	EGF-like 3.	might get lost (downstream of altered splice site)
301	301	DISULFID	By similarity.	might get lost (downstream of altered splice site)
305	305	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
308	308	DISULFID	By similarity.	might get lost (downstream of altered splice site)
312	312	DISULFID	By similarity.	might get lost (downstream of altered splice site)
321	321	DISULFID	By similarity.	might get lost (downstream of altered splice site)
323	323	DISULFID	By similarity.	might get lost (downstream of altered splice site)
336	336	DISULFID	By similarity.	might get lost (downstream of altered splice site)
342	342	DISULFID	By similarity.	might get lost (downstream of altered splice site)
342	377	DOMAIN	EGF-like 4.	might get lost (downstream of altered splice site)
349	349	DISULFID	By similarity.	might get lost (downstream of altered splice site)
353	353	DISULFID	By similarity.	might get lost (downstream of altered splice site)
362	362	DISULFID	By similarity.	might get lost (downstream of altered splice site)
364	364	DISULFID	By similarity.	might get lost (downstream of altered splice site)
377	377	DISULFID	By similarity.	might get lost (downstream of altered splice site)
386	561	DOMAIN	VWFA 2.	might get lost (downstream of altered splice site)
563	563	CONFLICT	G -> S (in Ref. 2; BAC11083).	might get lost (downstream of altered splice site)
591	622	COILED	Potential.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1746 / 1746

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

582 / 582

position of stopcodon in wt / mu cDNA

1991 / 1991

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

246 / 246

chromosome

strand

-1

last intron/exon boundary

1933

theoretical NMD boundary in CDS

1637

length of CDS

1746

coding sequence (CDS) position

490

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

735

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

4149

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

43933021

original gDNA sequence snippet

TGGCGGCACAGGCGCGCGCCCGCGGCATTGAAATTTACGCG

altered gDNA sequence snippet

TGGCGGCACAGGCGCGCGCCAGCGGCATTGAAATTTACGCG

original cDNA sequence snippet

TGGCGGCACAGGCGCGCGCCCGCGGCATTGAAATTTACGCG

altered cDNA sequence snippet

TGGCGGCACAGGCGCGCGCCAGCGGCATTGAAATTTACGCG

wildtype AA sequence

mutated AA sequence

MRGLLCWPVL LLLLQPWETQ LQLTGPRCHT GPLDLVFVID SSRSVRPFEF ETMRQFLMGL
LRGLNVGPNA TRVGVIQYSS QVQSVFPLRA FSRREDMERA IRDLVPLAQG TMTGLAIQYA
MNVAFSVAEG ARPPEERVPR VAVIVTDGRP QDRVAEVAAQ ARASGIEIYA VGVQRADVGS
LRAMASPPLD EHVFLVESFD LIQEFGLQFQ SRLCAIDLCA EGTHGCEHHC VNSPGSYFCH
CQVGFVLQQD QRSCRAIDYC SFGNHSCQHE CVSTPGGPRC HCREGHDLQP DGRSCQVRDL
CNGVDHGCEF QCVSEGLSYR CLCPEGRQLQ ADGKSCNRCR EGHVDLVLLV DGSKSVRPQN
FELVKRFVNQ IVDFLDVSPE GTRVGLVQFS SRVRTEFPLG RYGTAAEVKQ AVLAVEYMER
GTMTGLALRH MVEHSFSEAQ GARPRALNVP RVGLVFTDGR SQDDISVWAA RAKEEGIVMY
AVGVGKAVEA ELREIASEPA ELHVSYAPDF GTMTHLLENL RGSICPEEGI SAGTELRSPC
ECESLVEFQG RTLGALESLT LNLAQLTARL EDLENQLANQ K*

speed

0.39 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.999979760529048 (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)

chr20:43933021G>TN/A show variant in all transcripts IGV

HGNC symbol

MATN4

Ensembl transcript ID

ENST00000372753

Genbank transcript ID

N/A

UniProt peptide

O95460

alteration type

single base exchange

alteration region

intron

DNA changes

g.4149C>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs2072788

database	homozygous (T/T)	heterozygous	allele carriers
1000G	494	994	1488
ExAC	6683	19401	26084

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.254	0.146
	0.687	0.162
(flanking)	-0.004	0.177

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	4149	0.31	mu: GCGCCAGCGGCATTG	GCCA\|gcgg

distance from splice site

870

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
34	213	DOMAIN	VWFA 1.	might get lost (downstream of altered splice site)
69	69	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
173	173	CONFLICT	V -> L (in Ref. 2; BAC11083).	might get lost (downstream of altered splice site)
215	255	DOMAIN	EGF-like 1; incomplete.	might get lost (downstream of altered splice site)
219	219	DISULFID	By similarity.	might get lost (downstream of altered splice site)
226	226	DISULFID	By similarity.	might get lost (downstream of altered splice site)
230	230	DISULFID	By similarity.	might get lost (downstream of altered splice site)
239	239	DISULFID	By similarity.	might get lost (downstream of altered splice site)
241	241	DISULFID	By similarity.	might get lost (downstream of altered splice site)
251	251	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
254	254	DISULFID	By similarity.	might get lost (downstream of altered splice site)
256	292	DOMAIN	EGF-like 2.	might get lost (downstream of altered splice site)
260	260	DISULFID	By similarity.	might get lost (downstream of altered splice site)
267	267	DISULFID	By similarity.	might get lost (downstream of altered splice site)
271	271	DISULFID	By similarity.	might get lost (downstream of altered splice site)
280	280	DISULFID	By similarity.	might get lost (downstream of altered splice site)
282	282	DISULFID	By similarity.	might get lost (downstream of altered splice site)
295	295	DISULFID	By similarity.	might get lost (downstream of altered splice site)
297	337	DOMAIN	EGF-like 3.	might get lost (downstream of altered splice site)
301	301	DISULFID	By similarity.	might get lost (downstream of altered splice site)
305	305	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
308	308	DISULFID	By similarity.	might get lost (downstream of altered splice site)
312	312	DISULFID	By similarity.	might get lost (downstream of altered splice site)
321	321	DISULFID	By similarity.	might get lost (downstream of altered splice site)
323	323	DISULFID	By similarity.	might get lost (downstream of altered splice site)
336	336	DISULFID	By similarity.	might get lost (downstream of altered splice site)
342	342	DISULFID	By similarity.	might get lost (downstream of altered splice site)
342	377	DOMAIN	EGF-like 4.	might get lost (downstream of altered splice site)
349	349	DISULFID	By similarity.	might get lost (downstream of altered splice site)
353	353	DISULFID	By similarity.	might get lost (downstream of altered splice site)
362	362	DISULFID	By similarity.	might get lost (downstream of altered splice site)
364	364	DISULFID	By similarity.	might get lost (downstream of altered splice site)
377	377	DISULFID	By similarity.	might get lost (downstream of altered splice site)
386	561	DOMAIN	VWFA 2.	might get lost (downstream of altered splice site)
563	563	CONFLICT	G -> S (in Ref. 2; BAC11083).	might get lost (downstream of altered splice site)
591	622	COILED	Potential.	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

10 / 10

chromosome

strand

-1

last intron/exon boundary

1250

theoretical NMD boundary in CDS

1190

length of CDS

1299

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)

4149

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

43933021

original gDNA sequence snippet

TGGCGGCACAGGCGCGCGCCCGCGGCATTGAAATTTACGCG

altered gDNA sequence snippet

TGGCGGCACAGGCGCGCGCCAGCGGCATTGAAATTTACGCG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MRGLLCWPVL LLLLQPWETQ LQLTGKDQCA EGGHGCQHQC VNAWAMFHCT CNPGYKLAAD
NKSCLAIDLC AEGTHGCEHH CVNSPGSYFC HCQVGFVLQQ DQRSCRAIDY CSFGNHSCQH
ECVSTPGGPR CHCREGHDLQ PDGRSCQVRD LCNGVDHGCE FQCVSEGLSY RCLCPEGRQL
QADGKSCNRC REGHVDLVLL VDGSKSVRPQ NFELVKRFVN QIVDFLDVSP EGTRVGLVQF
SSRVRTEFPL GRYGTAAEVK QAVLAVEYME RGTMTGLALR HMVEHSFSEA QGARPRALNV
PRVGLVFTDG RSQDDISVWA ARAKEEGIVM YAVGVGKAVE AELREIASEP AELHVSYAPD
FGTMTHLLEN LRGSICPEEG ISAGTELRSP CECESLVEFQ GRTLGALESL TLNLAQLTAR
LEDLENQLAN QK*

mutated AA sequence

N/A

speed

0.85 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.999979760529048 (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)

chr20:43933021G>TN/A show variant in all transcripts IGV

HGNC symbol

MATN4

Ensembl transcript ID

ENST00000372751

Genbank transcript ID

N/A

UniProt peptide

O95460

alteration type

single base exchange

alteration region

intron

DNA changes

g.4149C>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs2072788

database	homozygous (T/T)	heterozygous	allele carriers
1000G	494	994	1488
ExAC	6683	19401	26084

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.254	0.146
	0.687	0.162
(flanking)	-0.004	0.177

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	4149	0.31	mu: GCGCCAGCGGCATTG	GCCA\|gcgg

distance from splice site

870

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
34	213	DOMAIN	VWFA 1.	might get lost (downstream of altered splice site)
69	69	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
173	173	CONFLICT	V -> L (in Ref. 2; BAC11083).	might get lost (downstream of altered splice site)
215	255	DOMAIN	EGF-like 1; incomplete.	might get lost (downstream of altered splice site)
219	219	DISULFID	By similarity.	might get lost (downstream of altered splice site)
226	226	DISULFID	By similarity.	might get lost (downstream of altered splice site)
230	230	DISULFID	By similarity.	might get lost (downstream of altered splice site)
239	239	DISULFID	By similarity.	might get lost (downstream of altered splice site)
241	241	DISULFID	By similarity.	might get lost (downstream of altered splice site)
251	251	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
254	254	DISULFID	By similarity.	might get lost (downstream of altered splice site)
256	292	DOMAIN	EGF-like 2.	might get lost (downstream of altered splice site)
260	260	DISULFID	By similarity.	might get lost (downstream of altered splice site)
267	267	DISULFID	By similarity.	might get lost (downstream of altered splice site)
271	271	DISULFID	By similarity.	might get lost (downstream of altered splice site)
280	280	DISULFID	By similarity.	might get lost (downstream of altered splice site)
282	282	DISULFID	By similarity.	might get lost (downstream of altered splice site)
295	295	DISULFID	By similarity.	might get lost (downstream of altered splice site)
297	337	DOMAIN	EGF-like 3.	might get lost (downstream of altered splice site)
301	301	DISULFID	By similarity.	might get lost (downstream of altered splice site)
305	305	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
308	308	DISULFID	By similarity.	might get lost (downstream of altered splice site)
312	312	DISULFID	By similarity.	might get lost (downstream of altered splice site)
321	321	DISULFID	By similarity.	might get lost (downstream of altered splice site)
323	323	DISULFID	By similarity.	might get lost (downstream of altered splice site)
336	336	DISULFID	By similarity.	might get lost (downstream of altered splice site)
342	342	DISULFID	By similarity.	might get lost (downstream of altered splice site)
342	377	DOMAIN	EGF-like 4.	might get lost (downstream of altered splice site)
349	349	DISULFID	By similarity.	might get lost (downstream of altered splice site)
353	353	DISULFID	By similarity.	might get lost (downstream of altered splice site)
362	362	DISULFID	By similarity.	might get lost (downstream of altered splice site)
364	364	DISULFID	By similarity.	might get lost (downstream of altered splice site)
377	377	DISULFID	By similarity.	might get lost (downstream of altered splice site)
386	561	DOMAIN	VWFA 2.	might get lost (downstream of altered splice site)
563	563	CONFLICT	G -> S (in Ref. 2; BAC11083).	might get lost (downstream of altered splice site)
591	622	COILED	Potential.	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

188 / 188

chromosome

strand

-1

last intron/exon boundary

1427

theoretical NMD boundary in CDS

1189

length of CDS

1299

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)

4149

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

43933021

original gDNA sequence snippet

TGGCGGCACAGGCGCGCGCCCGCGGCATTGAAATTTACGCG

altered gDNA sequence snippet

TGGCGGCACAGGCGCGCGCCAGCGGCATTGAAATTTACGCG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

mutated AA sequence

N/A

speed

0.94 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems