MutationT @ ster 2025

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 1457853 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 90|10 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr11:61957459A>T (GRCh38)

Gene symbol

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.709A>T
g.7397A>T

AA changes

AAE:	T237S	?
Score:	58

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

not provided

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'T' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		237	A	Y	D	W	I	S	I	P	L	V	Y	T	Q	V	V	T	V	A	V	Y	S	F	F	L
mutated	all conserved	237	A	Y	D	W	I	S	I	P	L	V	Y	S	Q	V	V
Ptroglodytes	all identical	237	A	Y	D	W	I	S	I	P	L	V	Y	T	Q	V	V
Mmulatta	all identical	177	A	Y	D	W	I	S	I	P	L	V	Y	T	Q	V	V
Fcatus	all identical	237	A	Y	D	W	I	S	I	P	L	V	Y	T	Q	V	V
Mmusculus	all identical	237	A	Y	D	W	I	S	I	P	L	V	Y	T	Q	V	V
Ggallus	all identical	237	G	Y	D	W	I	S	I	P	L	V	Y	T	Q	V	V
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all identical	237	G	Y	D	W	I	S	V	P	L	V	Y	T	Q	V	V

Protein features

Start (aa)	End (aa)	Feature	Details
1	585	CHAIN		lost
83	237	TOPO_DOM	Cytoplasmic	lost
234	254	HELIX		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.716	0.998
	9.09	1
(flanking)	7.71	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

6

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

11

Strand

1

Original gDNA sequence snippet

TTAGTATCCCACTGGTGTATACACAGGTGAGGACTAGGCTG

Altered gDNA sequence snippet

TTAGTATCCCACTGGTGTATTCACAGGTGAGGACTAGGCTG

Original cDNA sequence snippet

TTAGTATCCCACTGGTGTATACACAGGTGGTGACTGTGGCG

Altered cDNA sequence snippet

TTAGTATCCCACTGGTGTATTCACAGGTGGTGACTGTGGCG

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 NARLGSFSRL LLCWRGSIYK LLYGEFLIFL LCYYIIRFIY RLALTEEQQL
MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYSQVV
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

709

cDNA position

822

gDNA position

7397

Chromosomal position

61957459

Speed

0.38 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

MutationT@ster 2025

Variant:

11:61957459A>T_2_ENST00000449131

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 1457853 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 95|5 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr11:61957459A>T (GRCh38)

Gene symbol

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

BEST1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.529A>T
g.7397A>T

AA changes

AAE:	T177S	?
Score:	58

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

not provided

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'T' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		177	A	Y	D	W	I	S	I	P	L	V	Y	T	Q	V	V	T	V	A	V	Y	S	F	F	L
mutated	all conserved	177	A	Y	D	W	I	S	I	P	L	V	Y	S	Q	V	V
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	585	CHAIN		lost
83	237	TOPO_DOM	Cytoplasmic	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.716	0.998
	9.09	1
(flanking)	7.71	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

6

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

11

Strand

1

Original gDNA sequence snippet

TTAGTATCCCACTGGTGTATACACAGGTGAGGACTAGGCTG

Altered gDNA sequence snippet

TTAGTATCCCACTGGTGTATTCACAGGTGAGGACTAGGCTG

Original cDNA sequence snippet

TTAGTATCCCACTGGTGTATACACAGGTGGTGACTGTGGCG

Altered cDNA sequence snippet

TTAGTATCCCACTGGTGTATTCACAGGTGGTGACTGTGGCG

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

MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYSQVV
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*

Position of stopcodon in wt / mu CDS

1815 / 1815

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

605 / 605

Position of stopcodon in wt / mu cDNA

1901 / 1901

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

529

cDNA position

615

gDNA position

7397

Chromosomal position

61957459

Speed

0.37 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

MutationT@ster 2025

Variant:

11:61957459A>T_1_ENST00000526988

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 1457853 (pathogenic)

Model: simple_aae
Tree vote: 97|3 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr11:61957459A>T (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.29, LOF (oe): 0.99, misssense (oe): 0.86, synonymous (oe): 0.92 ? (gnomAD)

Ensembl transcript ID

ENST00000526988.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.391A>T
g.7397A>T

AA changes

AAE:	T131S	?
Score:	58

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

not provided

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'T' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		131	A	Y	D	W	I	S	I	P	L	V	Y	T	Q	V	V	T	V	A	V	Y	S	F	F	L
mutated	all conserved	131		Y	D	W	I	S	I	P	L	V	Y	S	Q	V	V	T	V	A	V	Y	S	F	F
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.716	0.998
	9.09	1
(flanking)	7.71	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

6

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

11

Strand

1

Original gDNA sequence snippet

TTAGTATCCCACTGGTGTATACACAGGTGAGGACTAGGCTG

Altered gDNA sequence snippet

TTAGTATCCCACTGGTGTATTCACAGGTGAGGACTAGGCTG

Original cDNA sequence snippet

TTAGTATCCCACTGGTGTATACACAGGTGGTGACTGTGGCG

Altered cDNA sequence snippet

TTAGTATCCCACTGGTGTATTCACAGGTGGTGACTGTGGCG

Wildtype AA sequence

MSLVSGFVEG KDEQGRLLRR TLIRYANLGN VLILRSVSTA VYKRFPSAQH LVQAGFMTPA
EHKQLEKLSL PHNMFWVPWV WFANLSMKAW LGGRIRDPIL LQSLLNEMNT LRTQCGHLYA
YDWISIPLVY TQVVTVAVYS FFLTCLVGRQ FLNPAKAYPG HELDLVVPVF TFLQFFFYVG
WLKVGLSRAL LGWRHGQRGH GQQLPETRMQ CQERKVSRVE SSQAWWRTPV IPATREAEAG
ESLEPGRRRL WWQSSSSTPL ERMMMILRPT GLSTGICRCP CWLWMRCTRT CLGWSRTCTG
ISPSHSPPTQ LLPPSSVEPP LWAPPSTSA*

Mutated AA sequence

MSLVSGFVEG KDEQGRLLRR TLIRYANLGN VLILRSVSTA VYKRFPSAQH LVQAGFMTPA
EHKQLEKLSL PHNMFWVPWV WFANLSMKAW LGGRIRDPIL LQSLLNEMNT LRTQCGHLYA
YDWISIPLVY SQVVTVAVYS FFLTCLVGRQ FLNPAKAYPG HELDLVVPVF TFLQFFFYVG
WLKVGLSRAL LGWRHGQRGH GQQLPETRMQ CQERKVSRVE SSQAWWRTPV IPATREAEAG
ESLEPGRRRL WWQSSSSTPL ERMMMILRPT GLSTGICRCP CWLWMRCTRT CLGWSRTCTG
ISPSHSPPTQ LLPPSSVEPP LWAPPSTSA*

Position of stopcodon in wt / mu CDS

990 / 990

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

330 / 330

Position of stopcodon in wt / mu cDNA

1151 / 1151

Position of start ATG in wt / mu cDNA

162 / 162

Last intron/exon boundary

1146

Theoretical NMD boundary in CDS

934

Length of CDS

990

Coding sequence (CDS) position

391

cDNA position

552

gDNA position

7397

Chromosomal position

61957459

Speed

0.36 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

MutationT@ster 2025

Variant:

11:61957459A>T_4_ENST00000534553

Prediction:

DeleteriousPermalink

Summary:

Known disease mutation: ClinVar ID 1457853 (pathogenic)

Model: without_aae
Tree vote: 200|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr11:61957459A>T (GRCh38)

Gene symbol

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.163+1508A>T
g.7397A>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

not provided

pathogenic

Variant DBs

	Not in dbSNP
	Allele 'T' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.716	0.998
	9.09	1
(flanking)	7.71	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

TTAGTATCCCACTGGTGTATACACAGGTGAGGACTAGGCTG

Altered gDNA sequence snippet

TTAGTATCCCACTGGTGTATTCACAGGTGAGGACTAGGCTG

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

7397

Chromosomal position

61957459

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