MutationT@ster 2025

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Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000449131
Querying Taster for transcript #2: ENST00000378043
Querying Taster for transcript #3: ENST00000534553
MT speed 0.55 s - this script 2.904332 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Known ClinVar disease mutation	Variant type	Protein length	Features at a glance
ENST00000378043(MANE Select)	BEST1	Deleterious	86\|14	simple_aae	No	Yes	Single base exchange	Normal	Amino acid sequence changed Known disease mutation: ClinVar ID 279701 (pathogenic) Protein features (might be) affected
ENST00000449131	BEST1	Deleterious	191\|9	without_aae	No	Yes	Single base exchange	N/A	Known disease mutation: ClinVar ID 279701 (pathogenic)
ENST00000534553	BEST1	Deleterious	193\|7	without_aae	No	Yes	Single base exchange	N/A	Known disease mutation: ClinVar ID 279701 (pathogenic)

MutationT@ster 2025

Variant:

11:61951843C>T_2_ENST00000378043

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 279701 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 86|14 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr11:61951843C>T (GRCh38)

Gene symbol

BEST1

Gene constraints

LOEUF: 1.28, LOF (oe): 1.02, misssense (oe): 0.90, synonymous (oe): 0.95 ? (gnomAD)

Ensembl transcript ID

ENST00000378043.9

Genbank transcript ID

NM_004183 (exact from MANE), NM_001300787 (by similarity), NM_001300786 (by similarity)

UniProt / AlphaMissense peptide

BEST1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.37C>T
g.1781C>T

AA changes

AAE:	R13C	?
Score:	180

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Vitelliform macular dystrophy 2
Macular dystrophy
Retinal dystrophy

pathogenic

ClinVar OMIM

Variant DBs

dbSNP ID	rs886041141
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	13	13

Protein conservation

Species	Match	AA	Alignment
Human		13	T	I	T	Y	T	S	Q	V	A	N	A	R	L	G	S	F	S	R	L	L	L	C	W	R
mutated	not conserved	13	T	I	T	Y	T	S	Q	V	A	N	A	C	L	G	S	F	S	R	L	L	L	C	W
Ptroglodytes	all identical	13	T	I	T	Y	T	S	Q	V	A	N	A	R	L	G	S	F	S	R	L	L	L	C	W
Mmulatta	no alignment	n/a
Fcatus	all identical	13	T	V	T	Y	S	S	Q	V	A	N	A	R	L	G	S	F	S	R	L	L	L	C	W
Mmusculus	all identical	13	T	I	T	Y	T	N	K	V	A	N	A	R	L	G	S	F	S	S	L	L	L	C	W
Ggallus	all identical	13	T	V	T	Y	T	N	R	V	A	D	A	R	L	G	T	F	S	Q	L	L	L	Q	W
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all identical	13	T	V	T	Y	S	N	R	V	A	D	A	R	L	G	T	F	S	R	L	L	L	R	W

Protein features

Start (aa)	End (aa)	Feature	Details
1	31	TOPO_DOM	Cytoplasmic	lost
1	585	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.117	0.644
	6.226	1
(flanking)	4.636	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

11

Strand

1

Original gDNA sequence snippet

CAAGCCAAGTGGCTAATGCCCGCTTAGGCTCCTTCTCCCGC

Altered gDNA sequence snippet

CAAGCCAAGTGGCTAATGCCTGCTTAGGCTCCTTCTCCCGC

Original cDNA sequence snippet

CAAGCCAAGTGGCTAATGCCCGCTTAGGCTCCTTCTCCCGC

Altered cDNA sequence snippet

CAAGCCAAGTGGCTAATGCCTGCTTAGGCTCCTTCTCCCGC

Wildtype AA sequence

MTITYTSQVA NARLGSFSRL LLCWRGSIYK LLYGEFLIFL LCYYIIRFIY RLALTEEQQL
MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYTQVV
TVAVYSFFLT CLVGRQFLNP AKAYPGHELD LVVPVFTFLQ FFFYVGWLKV AEQLINPFGE
DDDDFETNWI VDRNLQVSLL AVDEMHQDLP RMEPDMYWNK PEPQPPYTAA SAQFRRASFM
GSTFNISLNK EEMEFQPNQE DEEDAHAGII GRFLGLQSHD HHPPRANSRT KLLWPKRESL
LHEGLPKNHK AAKQNVRGQE DNKAWKLKAV DAFKSAPLYQ RPGYYSAPQT PLSPTPMFFP
LEPSAPSKLH SVTGIDTKDK SLKTVSSGAK KSFELLSESD GALMEHPEVS QVRRKTVEFN
LTDMPEIPEN HLKEPLEQSP TNIHTTLKDH MDPYWALENR DEAHS*

Mutated AA sequence

MTITYTSQVA NACLGSFSRL LLCWRGSIYK LLYGEFLIFL LCYYIIRFIY RLALTEEQQL
MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYTQVV
TVAVYSFFLT CLVGRQFLNP AKAYPGHELD LVVPVFTFLQ FFFYVGWLKV AEQLINPFGE
DDDDFETNWI VDRNLQVSLL AVDEMHQDLP RMEPDMYWNK PEPQPPYTAA SAQFRRASFM
GSTFNISLNK EEMEFQPNQE DEEDAHAGII GRFLGLQSHD HHPPRANSRT KLLWPKRESL
LHEGLPKNHK AAKQNVRGQE DNKAWKLKAV DAFKSAPLYQ RPGYYSAPQT PLSPTPMFFP
LEPSAPSKLH SVTGIDTKDK SLKTVSSGAK KSFELLSESD GALMEHPEVS QVRRKTVEFN
LTDMPEIPEN HLKEPLEQSP TNIHTTLKDH MDPYWALENR DEAHS*

Position of stopcodon in wt / mu CDS

1758 / 1758

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

586 / 586

Position of stopcodon in wt / mu cDNA

1871 / 1871

Position of start ATG in wt / mu cDNA

114 / 114

Last intron/exon boundary

1852

Theoretical NMD boundary in CDS

1688

Length of CDS

1758

Coding sequence (CDS) position

37

cDNA position

150

gDNA position

1781

Chromosomal position

61951843

Speed

0.51 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

11:61951843C>T_1_ENST00000449131

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Known disease mutation: ClinVar ID 279701 (pathogenic)

Model: without_aae
Tree vote: 191|9 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr11:61951843C>T (GRCh38)

Gene symbol

BEST1

Gene constraints

LOEUF: 1.22, LOF (oe): 0.92, misssense (oe): 0.92, synonymous (oe): 0.95 ? (gnomAD)

Ensembl transcript ID

ENST00000449131.6

Genbank transcript ID

NM_001139443 (by similarity), NM_001363593 (by similarity), NM_001363591 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-29+1416C>T
g.1781C>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Vitelliform macular dystrophy 2
Macular dystrophy
Retinal dystrophy

pathogenic

ClinVar OMIM

Variant DBs

dbSNP ID	rs886041141
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	13	13

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.117	0.644
	6.226	1
(flanking)	4.636	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

11

Strand

1

Original gDNA sequence snippet

CAAGCCAAGTGGCTAATGCCCGCTTAGGCTCCTTCTCCCGC

Altered gDNA sequence snippet

CAAGCCAAGTGGCTAATGCCTGCTTAGGCTCCTTCTCCCGC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYTQVV
TVAVYSFFLT CLVGRQFLNP AKAYPGHELD LVVPVFTFLQ FFFYVGWLKV AEQLINPFGE
DDDDFETNWI VDRNLQVSLL AVDEMHQDLP RMEPDMYWNK PEPQPPYTAA SAQFRRASFM
GSTFNISLNK EEMEFQPNQE DEEDAHAGII GRFLGLQSHD HHPPRANSRT KLLWPKRESL
LHEGLPKNHK AAKQNVRGQE DNKAWKLKAV DAFKSAPLYQ RPGYYSAPQT PLSPTPMFFP
LEPSAPSKLH SVTGIDTKDK SLKTVSSGAK KSFELLSESD GALMEHPEVS QVRRKTVEFN
LTDMPEIPEN HLKEPLEQSP TNIHTTLKDH MDPYWALENR SVLHLNQGHC IALCPTPASL
ALSLPFLHNF LGFHHCQSTL DLRPALAWGI YLATFTGILG KCSGPFLTSP WYHPEDFLGP
GEGR*

Mutated AA sequence

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

Position of start ATG in wt / mu cDNA

87 / 87

Last intron/exon boundary

1006

Theoretical NMD boundary in CDS

869

Length of CDS

1815

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

1781

Chromosomal position

61951843

Speed

0.02 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

11:61951843C>T_3_ENST00000534553

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Known disease mutation: ClinVar ID 279701 (pathogenic)

Model: without_aae
Tree vote: 193|7 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr11:61951843C>T (GRCh38)

Gene symbol

BEST1

Gene constraints

LOEUF: 1.94, LOF (oe): 1.57, misssense (oe): 1.20, synonymous (oe): 1.20 ? (gnomAD)

Ensembl transcript ID

ENST00000534553.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-212+1416C>T
g.1781C>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Vitelliform macular dystrophy 2
Macular dystrophy
Retinal dystrophy

pathogenic

ClinVar OMIM

Variant DBs

dbSNP ID	rs886041141
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	13	13

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.117	0.644
	6.226	1
(flanking)	4.636	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

11

Strand

1

Original gDNA sequence snippet

CAAGCCAAGTGGCTAATGCCCGCTTAGGCTCCTTCTCCCGC

Altered gDNA sequence snippet

CAAGCCAAGTGGCTAATGCCTGCTTAGGCTCCTTCTCCCGC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MSLVSGFVEG KDEQGRLLRR TLIRYANLGN VLILRSVSTA VYKRFPSAQH LVQAA*

Mutated AA sequence

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

Position of start ATG in wt / mu cDNA

577 / 577

Last intron/exon boundary

739

Theoretical NMD boundary in CDS

112

Length of CDS

168

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

1781

Chromosomal position

61951843

Speed

0.02 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table