MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000370225
Querying Taster for transcript #2: ENST00000536513
Querying Taster for transcript #3: ENST00000535881
MT speed 0 s - this script 4.392656 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ABCA4	disease_causing_automatic	0.394615753513663	simple_aae		affected	0	L1940P	single base exchange	rs61753033		show file
ABCA4	disease_causing_automatic	0.619659215837976	simple_aae		affected	0	L210P	single base exchange	rs61753033		show file
ABCA4	disease_causing_automatic	0.619659215837976	simple_aae		affected	0	L59P	single base exchange	rs61753033		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.394615753513663 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM011908)
known disease mutation: rs7911 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:94474323A>GN/A show variant in all transcripts IGV

HGNC symbol

ABCA4

Ensembl transcript ID

ENST00000370225

Genbank transcript ID

NM_000350

UniProt peptide

P78363

alteration type

single base exchange

alteration region

CDS

DNA changes

c.5819T>C
cDNA.5906T>C
g.112366T>C

AA changes

L1940P Score: 98 explain score(s)

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

1940

frameshift

known variant

Reference ID: rs61753033

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation: rs7911 (pathogenic for Stargardt disease 1|Cone-rod dystrophy 3|Stargardt disease|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM011908)

known disease mutation at this position, please check HGMD for details (HGMD ID CM011908)
known disease mutation at this position, please check HGMD for details (HGMD ID CM011908)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.066	0.096
	3.083	0.134
(flanking)	0.557	0.053

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	112357	wt: 0.9735 / mu: 0.9845 (marginal change - not scored)	wt: TGACATCTTAAGGCT mu: TGACATCTTAAGGCC	ACAT\|ctta
Donor increased	112368	wt: 0.38 / mu: 0.50	wt: GGCTACATGAACTAA mu: GGCCACATGAACTAA	CTAC\|atga
Donor increased	112363	wt: 0.83 / mu: 0.92	wt: CTTAAGGCTACATGA mu: CTTAAGGCCACATGA	TAAG\|gcta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1940

mutated

not conserved

1940

Ptroglodytes

all identical

ENSPTRG00000023377

1940

Mmulatta

not conserved

ENSMMUG00000013858

921

HPGWVPGVCVK

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000028125

1939

Ggallus

all identical

ENSGALG00000005752

1934

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000062661

2005

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000008223

2015

protein features

start (aa)	end (aa)	feature	details
1895	2273	TOPO_DOM	Cytoplasmic.	lost
1938	2170	DOMAIN	ABC transporter 2.	lost
1972	1979	NP_BIND	ATP 2 (Potential).	might get lost (downstream of altered splice site)
1975	1975	MUTAGEN	G->D: Inhibition of retinal-stimulated ATP hydrolysis.	might get lost (downstream of altered splice site)
1978	1978	MUTAGEN	K->M: Inhibition of retinal-stimulated ATP hydrolysis.	might get lost (downstream of altered splice site)
1989	1989	CONFLICT	T -> N (in Ref. 2; AAC23915).	might get lost (downstream of altered splice site)
2119	2119	CONFLICT	E -> K (in Ref. 1; AAC51144).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

6822 / 6822

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

2274 / 2274

position of stopcodon in wt / mu cDNA

6909 / 6909

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

88 / 88

chromosome

strand

-1

last intron/exon boundary

6904

theoretical NMD boundary in CDS

6766

length of CDS

6822

coding sequence (CDS) position

5819

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

5906

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

112366

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

94474323

original gDNA sequence snippet

TAAAACTGACATCTTAAGGCTACATGAACTAACCAAGGTAA

altered gDNA sequence snippet

TAAAACTGACATCTTAAGGCCACATGAACTAACCAAGGTAA

original cDNA sequence snippet

TAAAACTGACATCTTAAGGCTACATGAACTAACCAAGATTT

altered cDNA sequence snippet

TAAAACTGACATCTTAAGGCCACATGAACTAACCAAGATTT

wildtype AA sequence

MGFVRQIQLL LWKNWTLRKR QKIRFVVELV WPLSLFLVLI WLRNANPLYS HHECHFPNKA
MPSAGMLPWL QGIFCNVNNP CFQSPTPGES PGIVSNYNNS ILARVYRDFQ ELLMNAPESQ
HLGRIWTELH ILSQFMDTLR THPERIAGRG IRIRDILKDE ETLTLFLIKN IGLSDSVVYL
LINSQVRPEQ FAHGVPDLAL KDIACSEALL ERFIIFSQRR GAKTVRYALC SLSQGTLQWI
EDTLYANVDF FKLFRVLPTL LDSRSQGINL RSWGGILSDM SPRIQEFIHR PSMQDLLWVT
RPLMQNGGPE TFTKLMGILS DLLCGYPEGG GSRVLSFNWY EDNNYKAFLG IDSTRKDPIY
SYDRRTTSFC NALIQSLESN PLTKIAWRAA KPLLMGKILY TPDSPAARRI LKNANSTFEE
LEHVRKLVKA WEEVGPQIWY FFDNSTQMNM IRDTLGNPTV KDFLNRQLGE EGITAEAILN
FLYKGPRESQ ADDMANFDWR DIFNITDRTL RLVNQYLECL VLDKFESYND ETQLTQRALS
LLEENMFWAG VVFPDMYPWT SSLPPHVKYK IRMDIDVVEK TNKIKDRYWD SGPRADPVED
FRYIWGGFAY LQDMVEQGIT RSQVQAEAPV GIYLQQMPYP CFVDDSFMII LNRCFPIFMV
LAWIYSVSMT VKSIVLEKEL RLKETLKNQG VSNAVIWCTW FLDSFSIMSM SIFLLTIFIM
HGRILHYSDP FILFLFLLAF STATIMLCFL LSTFFSKASL AAACSGVIYF TLYLPHILCF
AWQDRMTAEL KKAVSLLSPV AFGFGTEYLV RFEEQGLGLQ WSNIGNSPTE GDEFSFLLSM
QMMLLDAAVY GLLAWYLDQV FPGDYGTPLP WYFLLQESYW LGGEGCSTRE ERALEKTEPL
TEETEDPEHP EGIHDSFFER EHPGWVPGVC VKNLVKIFEP CGRPAVDRLN ITFYENQITA
FLGHNGAGKT TTLSILTGLL PPTSGTVLVG GRDIETSLDA VRQSLGMCPQ HNILFHHLTV
AEHMLFYAQL KGKSQEEAQL EMEAMLEDTG LHHKRNEEAQ DLSGGMQRKL SVAIAFVGDA
KVVILDEPTS GVDPYSRRSI WDLLLKYRSG RTIIMSTHHM DEADLLGDRI AIIAQGRLYC
SGTPLFLKNC FGTGLYLTLV RKMKNIQSQR KGSEGTCSCS SKGFSTTCPA HVDDLTPEQV
LDGDVNELMD VVLHHVPEAK LVECIGQELI FLLPNKNFKH RAYASLFREL EETLADLGLS
SFGISDTPLE EIFLKVTEDS DSGPLFAGGA QQKRENVNPR HPCLGPREKA GQTPQDSNVC
SPGAPAAHPE GQPPPEPECP GPQLNTGTQL VLQHVQALLV KRFQHTIRSH KDFLAQIVLP
ATFVFLALML SIVIPPFGEY PALTLHPWIY GQQYTFFSMD EPGSEQFTVL ADVLLNKPGF
GNRCLKEGWL PEYPCGNSTP WKTPSVSPNI TQLFQKQKWT QVNPSPSCRC STREKLTMLP
ECPEGAGGLP PPQRTQRSTE ILQDLTDRNI SDFLVKTYPA LIRSSLKSKF WVNEQRYGGI
SIGGKLPVVP ITGEALVGFL SDLGRIMNVS GGPITREASK EIPDFLKHLE TEDNIKVWFN
NKGWHALVSF LNVAHNAILR ASLPKDRSPE EYGITVISQP LNLTKEQLSE ITVLTTSVDA
VVAICVIFSM SFVPASFVLY LIQERVNKSK HLQFISGVSP TTYWVTNFLW DIMNYSVSAG
LVVGIFIGFQ KKAYTSPENL PALVALLLLY GWAVIPMMYP ASFLFDVPST AYVALSCANL
FIGINSSAIT FILELFENNR TLLRFNAVLR KLLIVFPHFC LGRGLIDLAL SQAVTDVYAR
FGEEHSANPF HWDLIGKNLF AMVVEGVVYF LLTLLVQRHF FLSQWIAEPT KEPIVDEDDD
VAEERQRIIT GGNKTDILRL HELTKIYPGT SSPAVDRLCV GVRPGECFGL LGVNGAGKTT
TFKMLTGDTT VTSGDATVAG KSILTNISEV HQNMGYCPQF DAIDELLTGR EHLYLYARLR
GVPAEEIEKV ANWSIKSLGL TVYADCLAGT YSGGNKRKLS TAIALIGCPP LVLLDEPTTG
MDPQARRMLW NVIVSIIREG RAVVLTSHSM EECEALCTRL AIMVKGAFRC MGTIQHLKSK
FGDGYIVTMK IKSPKDDLLP DLNPVEQFFQ GNFPGSVQRE RHYNMLQFQV SSSSLARIFQ
LLLSHKDSLL IEEYSVTQTT LDQVFVNFAK QQTESHDLPL HPRAAGASRQ AQD*

mutated AA sequence

MGFVRQIQLL LWKNWTLRKR QKIRFVVELV WPLSLFLVLI WLRNANPLYS HHECHFPNKA
MPSAGMLPWL QGIFCNVNNP CFQSPTPGES PGIVSNYNNS ILARVYRDFQ ELLMNAPESQ
HLGRIWTELH ILSQFMDTLR THPERIAGRG IRIRDILKDE ETLTLFLIKN IGLSDSVVYL
LINSQVRPEQ FAHGVPDLAL KDIACSEALL ERFIIFSQRR GAKTVRYALC SLSQGTLQWI
EDTLYANVDF FKLFRVLPTL LDSRSQGINL RSWGGILSDM SPRIQEFIHR PSMQDLLWVT
RPLMQNGGPE TFTKLMGILS DLLCGYPEGG GSRVLSFNWY EDNNYKAFLG IDSTRKDPIY
SYDRRTTSFC NALIQSLESN PLTKIAWRAA KPLLMGKILY TPDSPAARRI LKNANSTFEE
LEHVRKLVKA WEEVGPQIWY FFDNSTQMNM IRDTLGNPTV KDFLNRQLGE EGITAEAILN
FLYKGPRESQ ADDMANFDWR DIFNITDRTL RLVNQYLECL VLDKFESYND ETQLTQRALS
LLEENMFWAG VVFPDMYPWT SSLPPHVKYK IRMDIDVVEK TNKIKDRYWD SGPRADPVED
FRYIWGGFAY LQDMVEQGIT RSQVQAEAPV GIYLQQMPYP CFVDDSFMII LNRCFPIFMV
LAWIYSVSMT VKSIVLEKEL RLKETLKNQG VSNAVIWCTW FLDSFSIMSM SIFLLTIFIM
HGRILHYSDP FILFLFLLAF STATIMLCFL LSTFFSKASL AAACSGVIYF TLYLPHILCF
AWQDRMTAEL KKAVSLLSPV AFGFGTEYLV RFEEQGLGLQ WSNIGNSPTE GDEFSFLLSM
QMMLLDAAVY GLLAWYLDQV FPGDYGTPLP WYFLLQESYW LGGEGCSTRE ERALEKTEPL
TEETEDPEHP EGIHDSFFER EHPGWVPGVC VKNLVKIFEP CGRPAVDRLN ITFYENQITA
FLGHNGAGKT TTLSILTGLL PPTSGTVLVG GRDIETSLDA VRQSLGMCPQ HNILFHHLTV
AEHMLFYAQL KGKSQEEAQL EMEAMLEDTG LHHKRNEEAQ DLSGGMQRKL SVAIAFVGDA
KVVILDEPTS GVDPYSRRSI WDLLLKYRSG RTIIMSTHHM DEADLLGDRI AIIAQGRLYC
SGTPLFLKNC FGTGLYLTLV RKMKNIQSQR KGSEGTCSCS SKGFSTTCPA HVDDLTPEQV
LDGDVNELMD VVLHHVPEAK LVECIGQELI FLLPNKNFKH RAYASLFREL EETLADLGLS
SFGISDTPLE EIFLKVTEDS DSGPLFAGGA QQKRENVNPR HPCLGPREKA GQTPQDSNVC
SPGAPAAHPE GQPPPEPECP GPQLNTGTQL VLQHVQALLV KRFQHTIRSH KDFLAQIVLP
ATFVFLALML SIVIPPFGEY PALTLHPWIY GQQYTFFSMD EPGSEQFTVL ADVLLNKPGF
GNRCLKEGWL PEYPCGNSTP WKTPSVSPNI TQLFQKQKWT QVNPSPSCRC STREKLTMLP
ECPEGAGGLP PPQRTQRSTE ILQDLTDRNI SDFLVKTYPA LIRSSLKSKF WVNEQRYGGI
SIGGKLPVVP ITGEALVGFL SDLGRIMNVS GGPITREASK EIPDFLKHLE TEDNIKVWFN
NKGWHALVSF LNVAHNAILR ASLPKDRSPE EYGITVISQP LNLTKEQLSE ITVLTTSVDA
VVAICVIFSM SFVPASFVLY LIQERVNKSK HLQFISGVSP TTYWVTNFLW DIMNYSVSAG
LVVGIFIGFQ KKAYTSPENL PALVALLLLY GWAVIPMMYP ASFLFDVPST AYVALSCANL
FIGINSSAIT FILELFENNR TLLRFNAVLR KLLIVFPHFC LGRGLIDLAL SQAVTDVYAR
FGEEHSANPF HWDLIGKNLF AMVVEGVVYF LLTLLVQRHF FLSQWIAEPT KEPIVDEDDD
VAEERQRIIT GGNKTDILRP HELTKIYPGT SSPAVDRLCV GVRPGECFGL LGVNGAGKTT
TFKMLTGDTT VTSGDATVAG KSILTNISEV HQNMGYCPQF DAIDELLTGR EHLYLYARLR
GVPAEEIEKV ANWSIKSLGL TVYADCLAGT YSGGNKRKLS TAIALIGCPP LVLLDEPTTG
MDPQARRMLW NVIVSIIREG RAVVLTSHSM EECEALCTRL AIMVKGAFRC MGTIQHLKSK
FGDGYIVTMK IKSPKDDLLP DLNPVEQFFQ GNFPGSVQRE RHYNMLQFQV SSSSLARIFQ
LLLSHKDSLL IEEYSVTQTT LDQVFVNFAK QQTESHDLPL HPRAAGASRQ AQD*

speed

1.34 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: 0.619659215837976 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM011908)
known disease mutation: rs7911 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:94474323A>GN/A show variant in all transcripts IGV

HGNC symbol

ABCA4

Ensembl transcript ID

ENST00000536513

Genbank transcript ID

N/A

UniProt peptide

P78363

alteration type

single base exchange

alteration region

CDS

DNA changes

c.629T>C
cDNA.722T>C
g.112366T>C

AA changes

L210P Score: 98 explain score(s)

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

210

frameshift

known variant

Reference ID: rs61753033

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.066	0.096
	3.083	0.134
(flanking)	0.557	0.053

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	112357	wt: 0.9735 / mu: 0.9845 (marginal change - not scored)	wt: TGACATCTTAAGGCT mu: TGACATCTTAAGGCC	ACAT\|ctta
Donor increased	112368	wt: 0.38 / mu: 0.50	wt: GGCTACATGAACTAA mu: GGCCACATGAACTAA	CTAC\|atga
Donor increased	112363	wt: 0.83 / mu: 0.92	wt: CTTAAGGCTACATGA mu: CTTAAGGCCACATGA	TAAG\|gcta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

210

mutated

not conserved

210

Ptroglodytes

all identical

ENSPTRG00000023377

1940

Mmulatta

no alignment

ENSMMUG00000013858

n/a

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000028125

1939

Ggallus

all identical

ENSGALG00000005752

1934

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000062661

2005

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000008223

2015

protein features

start (aa)	end (aa)	feature	details
43	646	TOPO_DOM	Extracellular.	lost
324	324	DISULFID	By similarity.	might get lost (downstream of altered splice site)
415	415	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
444	444	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
504	504	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
647	667	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
700	720	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
722	722	CONFLICT	G -> V (in Ref. 2; AAC23915).	might get lost (downstream of altered splice site)
731	751	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
760	780	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
836	856	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
849	849	CONFLICT	V -> C (in Ref. 1; AAC51144).	might get lost (downstream of altered splice site)
857	1376	TOPO_DOM	Cytoplasmic.	might get lost (downstream of altered splice site)
882	882	CONFLICT	G -> S (in Ref. 1; AAC51144 and 3; CAA75729).	might get lost (downstream of altered splice site)
929	1160	DOMAIN	ABC transporter 1.	might get lost (downstream of altered splice site)
941	941	CONFLICT	C -> S (in Ref. 2; AAC23915).	might get lost (downstream of altered splice site)
963	970	NP_BIND	ATP 1 (Potential).	might get lost (downstream of altered splice site)
966	966	MUTAGEN	G->D: Abolishes basal and retinal- stimulated ATP hydrolysis.	might get lost (downstream of altered splice site)
969	969	MUTAGEN	K->M: Abolishes basal and retinal- stimulated ATP hydrolysis.	might get lost (downstream of altered splice site)
1116	1116	CONFLICT	S -> P (in Ref. 1; AAC51144).	might get lost (downstream of altered splice site)
1125	1126	CONFLICT	LL -> HQ (in Ref. 1; AAC51144).	might get lost (downstream of altered splice site)
1377	1397	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1395	1395	CONFLICT	P -> L (in Ref. 1; AAC51144 and 3; CAA75729).	might get lost (downstream of altered splice site)
1398	1727	TOPO_DOM	Extracellular.	might get lost (downstream of altered splice site)
1465	1465	CONFLICT	S -> C (in Ref. 4; AAC05632).	might get lost (downstream of altered splice site)
1469	1469	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
1488	1488	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1502	1502	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1518	1518	CONFLICT	S -> T (in Ref. 4; AAC05632).	might get lost (downstream of altered splice site)
1529	1529	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
1588	1588	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
1662	1662	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
1728	1748	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1733	1733	CONFLICT	M -> V (in Ref. 2; AAC23915).	might get lost (downstream of altered splice site)
1760	1780	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1793	1813	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1832	1852	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1874	1894	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1895	2273	TOPO_DOM	Cytoplasmic.	might get lost (downstream of altered splice site)
1938	2170	DOMAIN	ABC transporter 2.	might get lost (downstream of altered splice site)
1972	1979	NP_BIND	ATP 2 (Potential).	might get lost (downstream of altered splice site)
1975	1975	MUTAGEN	G->D: Inhibition of retinal-stimulated ATP hydrolysis.	might get lost (downstream of altered splice site)
1978	1978	MUTAGEN	K->M: Inhibition of retinal-stimulated ATP hydrolysis.	might get lost (downstream of altered splice site)
1989	1989	CONFLICT	T -> N (in Ref. 2; AAC23915).	might get lost (downstream of altered splice site)
2119	2119	CONFLICT	E -> K (in Ref. 1; AAC51144).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1632 / 1632

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

544 / 544

position of stopcodon in wt / mu cDNA

1725 / 1725

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

94 / 94

chromosome

strand

-1

last intron/exon boundary

1720

theoretical NMD boundary in CDS

1576

length of CDS

1632

coding sequence (CDS) position

629

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

722

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

112366

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

94474323

original gDNA sequence snippet

TAAAACTGACATCTTAAGGCTACATGAACTAACCAAGGTAA

altered gDNA sequence snippet

TAAAACTGACATCTTAAGGCCACATGAACTAACCAAGGTAA

original cDNA sequence snippet

TAAAACTGACATCTTAAGGCTACATGAACTAACCAAGATTT

altered cDNA sequence snippet

TAAAACTGACATCTTAAGGCCACATGAACTAACCAAGATTT

wildtype AA sequence

MMMNYSVSAG LVVGIFIGFQ KKAYTSPENL PALVALLLLY GWAVIPMMYP ASFLFDVPST
AYVALSCANL FIGINSSAIT FILELFENNR TLLRFNAVLR KLLIVFPHFC LGRGLIDLAL
SQAVTDVYAR FGEEHSANPF HWDLIGKNLF AMVVEGVVYF LLTLLVQRHF FLSQWIAEPT
KEPIVDEDDD VAEERQRIIT GGNKTDILRL HELTKIYPGT SSPAVDRLCV GVRPGECFGL
LGVNGAGKTT TFKMLTGDTT VTSGDATVAG KSILTNISEV HQNMGYCPQF DAIDELLTGR
EHLYLYARLR GVPAEEIEKV ANWSIKSLGL TVYADCLAGT YSGGNKRKLS TAIALIGCPP
LVLLDEPTTG MDPQARRMLW NVIVSIIREG RAVVLTSHSM EECEALCTRL AIMVKGAFRC
MGTIQHLKSK FGDGYIVTMK IKSPKDDLLP DLNPVEQFFQ GNFPGSVQRE RHYNMLQFQV
SSSSLARIFQ LLLSHKDSLL IEEYSVTQTT LDQVFVNFAK QQTESHDLPL HPRAAGASRQ
AQD*

mutated AA sequence

MMMNYSVSAG LVVGIFIGFQ KKAYTSPENL PALVALLLLY GWAVIPMMYP ASFLFDVPST
AYVALSCANL FIGINSSAIT FILELFENNR TLLRFNAVLR KLLIVFPHFC LGRGLIDLAL
SQAVTDVYAR FGEEHSANPF HWDLIGKNLF AMVVEGVVYF LLTLLVQRHF FLSQWIAEPT
KEPIVDEDDD VAEERQRIIT GGNKTDILRP HELTKIYPGT SSPAVDRLCV GVRPGECFGL
LGVNGAGKTT TFKMLTGDTT VTSGDATVAG KSILTNISEV HQNMGYCPQF DAIDELLTGR
EHLYLYARLR GVPAEEIEKV ANWSIKSLGL TVYADCLAGT YSGGNKRKLS TAIALIGCPP
LVLLDEPTTG MDPQARRMLW NVIVSIIREG RAVVLTSHSM EECEALCTRL AIMVKGAFRC
MGTIQHLKSK FGDGYIVTMK IKSPKDDLLP DLNPVEQFFQ GNFPGSVQRE RHYNMLQFQV
SSSSLARIFQ LLLSHKDSLL IEEYSVTQTT LDQVFVNFAK QQTESHDLPL HPRAAGASRQ
AQD*

speed

0.93 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.619659215837976 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM011908)
known disease mutation: rs7911 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:94474323A>GN/A show variant in all transcripts IGV

HGNC symbol

ABCA4

Ensembl transcript ID

ENST00000535881

Genbank transcript ID

N/A

UniProt peptide

P78363

alteration type

single base exchange

alteration region

CDS

DNA changes

c.176T>C
cDNA.401T>C
g.112366T>C

AA changes

L59P Score: 98 explain score(s)

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

frameshift

known variant

Reference ID: rs61753033

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.066	0.096
	3.083	0.134
(flanking)	0.557	0.053

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	112357	wt: 0.9735 / mu: 0.9845 (marginal change - not scored)	wt: TGACATCTTAAGGCT mu: TGACATCTTAAGGCC	ACAT\|ctta
Donor increased	112368	wt: 0.38 / mu: 0.50	wt: GGCTACATGAACTAA mu: GGCCACATGAACTAA	CTAC\|atga
Donor increased	112363	wt: 0.83 / mu: 0.92	wt: CTTAAGGCTACATGA mu: CTTAAGGCCACATGA	TAAG\|gcta

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

ENSPTRG00000023377

1940

Mmulatta

no alignment

ENSMMUG00000013858

n/a

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000028125

1939

Ggallus

all identical

ENSGALG00000005752

1934

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000062661

2005

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000008223

2015

protein features

start (aa)	end (aa)	feature	details
43	646	TOPO_DOM	Extracellular.	lost
75	75	DISULFID	By similarity.	might get lost (downstream of altered splice site)
98	98	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
324	324	DISULFID	By similarity.	might get lost (downstream of altered splice site)
415	415	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
444	444	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
504	504	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
647	667	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
700	720	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
722	722	CONFLICT	G -> V (in Ref. 2; AAC23915).	might get lost (downstream of altered splice site)
731	751	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
760	780	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
836	856	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
849	849	CONFLICT	V -> C (in Ref. 1; AAC51144).	might get lost (downstream of altered splice site)
857	1376	TOPO_DOM	Cytoplasmic.	might get lost (downstream of altered splice site)
882	882	CONFLICT	G -> S (in Ref. 1; AAC51144 and 3; CAA75729).	might get lost (downstream of altered splice site)
929	1160	DOMAIN	ABC transporter 1.	might get lost (downstream of altered splice site)
941	941	CONFLICT	C -> S (in Ref. 2; AAC23915).	might get lost (downstream of altered splice site)
963	970	NP_BIND	ATP 1 (Potential).	might get lost (downstream of altered splice site)
966	966	MUTAGEN	G->D: Abolishes basal and retinal- stimulated ATP hydrolysis.	might get lost (downstream of altered splice site)
969	969	MUTAGEN	K->M: Abolishes basal and retinal- stimulated ATP hydrolysis.	might get lost (downstream of altered splice site)
1116	1116	CONFLICT	S -> P (in Ref. 1; AAC51144).	might get lost (downstream of altered splice site)
1125	1126	CONFLICT	LL -> HQ (in Ref. 1; AAC51144).	might get lost (downstream of altered splice site)
1377	1397	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1395	1395	CONFLICT	P -> L (in Ref. 1; AAC51144 and 3; CAA75729).	might get lost (downstream of altered splice site)
1398	1727	TOPO_DOM	Extracellular.	might get lost (downstream of altered splice site)
1465	1465	CONFLICT	S -> C (in Ref. 4; AAC05632).	might get lost (downstream of altered splice site)
1469	1469	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
1488	1488	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1502	1502	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1518	1518	CONFLICT	S -> T (in Ref. 4; AAC05632).	might get lost (downstream of altered splice site)
1529	1529	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
1588	1588	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
1662	1662	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
1728	1748	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1733	1733	CONFLICT	M -> V (in Ref. 2; AAC23915).	might get lost (downstream of altered splice site)
1760	1780	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1793	1813	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1832	1852	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1874	1894	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1895	2273	TOPO_DOM	Cytoplasmic.	might get lost (downstream of altered splice site)
1938	2170	DOMAIN	ABC transporter 2.	might get lost (downstream of altered splice site)
1972	1979	NP_BIND	ATP 2 (Potential).	might get lost (downstream of altered splice site)
1975	1975	MUTAGEN	G->D: Inhibition of retinal-stimulated ATP hydrolysis.	might get lost (downstream of altered splice site)
1978	1978	MUTAGEN	K->M: Inhibition of retinal-stimulated ATP hydrolysis.	might get lost (downstream of altered splice site)
1989	1989	CONFLICT	T -> N (in Ref. 2; AAC23915).	might get lost (downstream of altered splice site)
2119	2119	CONFLICT	E -> K (in Ref. 1; AAC51144).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1179 / 1179

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

393 / 393

position of stopcodon in wt / mu cDNA

1404 / 1404

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

226 / 226

chromosome

strand

-1

last intron/exon boundary

1399

theoretical NMD boundary in CDS

1123

length of CDS

1179

coding sequence (CDS) position

176

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

401

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

112366

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

94474323

original gDNA sequence snippet

TAAAACTGACATCTTAAGGCTACATGAACTAACCAAGGTAA

altered gDNA sequence snippet

TAAAACTGACATCTTAAGGCCACATGAACTAACCAAGGTAA

original cDNA sequence snippet

TAAAACTGACATCTTAAGGCTACATGAACTAACCAAGATTT

altered cDNA sequence snippet

TAAAACTGACATCTTAAGGCCACATGAACTAACCAAGATTT

wildtype AA sequence

MVVEGVVYFL LTLLVQRHFF LSQWIAEPTK EPIVDEDDDV AEERQRIITG GNKTDILRLH
ELTKIYPGTS SPAVDRLCVG VRPGECFGLL GVNGAGKTTT FKMLTGDTTV TSGDATVAGK
SILTNISEVH QNMGYCPQFD AIDELLTGRE HLYLYARLRG VPAEEIEKVA NWSIKSLGLT
VYADCLAGTY SGGNKRKLST AIALIGCPPL VLLDEPTTGM DPQARRMLWN VIVSIIREGR
AVVLTSHSME ECEALCTRLA IMVKGAFRCM GTIQHLKSKF GDGYIVTMKI KSPKDDLLPD
LNPVEQFFQG NFPGSVQRER HYNMLQFQVS SSSLARIFQL LLSHKDSLLI EEYSVTQTTL
DQVFVNFAKQ QTESHDLPLH PRAAGASRQA QD*

mutated AA sequence

MVVEGVVYFL LTLLVQRHFF LSQWIAEPTK EPIVDEDDDV AEERQRIITG GNKTDILRPH
ELTKIYPGTS SPAVDRLCVG VRPGECFGLL GVNGAGKTTT FKMLTGDTTV TSGDATVAGK
SILTNISEVH QNMGYCPQFD AIDELLTGRE HLYLYARLRG VPAEEIEKVA NWSIKSLGLT
VYADCLAGTY SGGNKRKLST AIALIGCPPL VLLDEPTTGM DPQARRMLWN VIVSIIREGR
AVVLTSHSME ECEALCTRLA IMVKGAFRCM GTIQHLKSKF GDGYIVTMKI KSPKDDLLPD
LNPVEQFFQG NFPGSVQRER HYNMLQFQVS SSSLARIFQL LLSHKDSLLI EEYSVTQTTL
DQVFVNFAKQ QTESHDLPLH PRAAGASRQA QD*

speed

0.93 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems