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: ENST00000536005
Querying Taster for transcript #2: ENST00000299694
MT speed 0.12 s - this script 2.503188 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Prediction problem	Splice site change	Known ClinVar disease mutation	Potential ClinVar disease mutation	Amino acid changes	Variant type	dbSNP ID	Protein length	Features at a glance
ENST00000299694	BEAN1	Benign	36\|64	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000536005(MANE Select)	BEAN1	Benign	39\|61	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

16:66480711G>C_2_ENST00000299694

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Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 36|64 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr16:66480711G>C (GRCh38)

Gene symbol

BEAN1

Gene constraints

LOEUF: 1.11, LOF (oe): 0.24, misssense (oe): 1.04, synonymous (oe): 1.00 ? (gnomAD)

Ensembl transcript ID

ENST00000299694.12

Genbank transcript ID

NM_001136106 (by similarity)

UniProt / AlphaMissense peptide

BEAN1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.239G>C
g.53417G>C

AA changes

AAE:	S80T	?
Score:	58

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1388849213
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	3	3

Protein conservation

Species	Match	AA	Alignment
Human		80	L	D	G	T	S	D	S	G	S	G	H	S	P	G	R	H	Q	Q	E	Q	R	T	P	A
mutated	all conserved	80	L	D	G	T	S	D	S	G	S	G	H	T	P	G	R	H	Q	Q	E	Q	R	T	P
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	259	CHAIN		lost
71	91	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.788	0.002
	0.27	0.005
(flanking)	1.368	0.008

?

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

16

Strand

1

Original gDNA sequence snippet

CGACTCAGGCAGCGGCCACAGCCCTGGCCGACACCAGCAGG

Altered gDNA sequence snippet

CGACTCAGGCAGCGGCCACACCCCTGGCCGACACCAGCAGG

Original cDNA sequence snippet

CGACTCAGGCAGCGGCCACAGCCCTGGCCGACACCAGCAGG

Altered cDNA sequence snippet

CGACTCAGGCAGCGGCCACACCCCTGGCCGACACCAGCAGG

Wildtype AA sequence

MRYACSSSED WPPPLDISSD GDVDATVLRE LYPDSPPGYE ECVGPGATQL YVPTDAPPPY
SLTDSCPTLD GTSDSGSGHS PGRHQQEQRT PAQGGLHTVS MDTLPPYEAV CGAGPPSGLL
PLPGPDPGPR GSQGSPTPTR APASGPERIV *

Mutated AA sequence

MRYACSSSED WPPPLDISSD GDVDATVLRE LYPDSPPGYE ECVGPGATQL YVPTDAPPPY
SLTDSCPTLD GTSDSGSGHT PGRHQQEQRT PAQGGLHTVS MDTLPPYEAV CGAGPPSGLL
PLPGPDPGPR GSQGSPTPTR APASGPERIV *

Position of stopcodon in wt / mu CDS

453 / 453

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

151 / 151

Position of stopcodon in wt / mu cDNA

816 / 816

Position of start ATG in wt / mu cDNA

364 / 364

Last intron/exon boundary

476

Theoretical NMD boundary in CDS

62

Length of CDS

453

Coding sequence (CDS) position

239

cDNA position

602

gDNA position

53417

Chromosomal position

66480711

Speed

0.07 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

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MutationT@ster 2025

Variant:

16:66480711G>C_1_ENST00000536005

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 39|61 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr16:66480711G>C (GRCh38)

Gene symbol

BEAN1

Gene constraints

LOEUF: 1.45, LOF (oe): 0.97, misssense (oe): 0.99, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000536005.7

Genbank transcript ID

NM_001178020 (exact from MANE)

UniProt / AlphaMissense peptide

BEAN1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.566G>C
g.53417G>C

AA changes

AAE:	S189T	?
Score:	58

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1388849213
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	3	3

Protein conservation

Species	Match	AA	Alignment
Human		189	L	D	G	T	S	D	S	G	S	G	H	S	P	G	R	H	Q	Q	E	Q	R	T	P	A
mutated	all conserved	189				T	S	D	S	G	S	G	H	T	P	G	R	H	Q	Q	E	Q	R	T	P
Ptroglodytes	all identical	189				T	S	D	S	G	S	G	H	S	P	G	R	H	Q	Q	E	Q	R	T	P
Mmulatta	all identical	189				T	S	N	S	G	S	S	H	S	P	G	R	H	Q	Q	E	Q	R	T	P
Fcatus	not conserved	187				I	I	D	V	G	G	-	-	-	-	G	R	H	Q	Q	A	Q	R	I	L
Mmusculus	all identical	256	L	N	G	A	L	D	S	D	S	G	Q	S	R	S	H	R	Q	Q	E	Q	R	T	Q
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	259	CHAIN		lost
152	259	REGION		lost
174	206	COMPBIAS	Polar residues	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.788	0.002
	0.27	0.005
(flanking)	1.368	0.008

?

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

16

Strand

1

Original gDNA sequence snippet

CGACTCAGGCAGCGGCCACAGCCCTGGCCGACACCAGCAGG

Altered gDNA sequence snippet

CGACTCAGGCAGCGGCCACACCCCTGGCCGACACCAGCAGG

Original cDNA sequence snippet

CGACTCAGGCAGCGGCCACAGCCCTGGCCGACACCAGCAGG

Altered cDNA sequence snippet

CGACTCAGGCAGCGGCCACACCCCTGGCCGACACCAGCAGG

Wildtype AA sequence

MSFKRPCPLA RYNRTSYFYP TFSESSEHSH LLVSPVLVAS AVIGVVIILS CITIIVGSIR
RDRQARLQRH RHRHHRHHHH HHHHRRRRHR EYEHGYVSDE HTYSRSSRRM RYACSSSEDW
PPPLDISSDG DVDATVLREL YPDSPPGYEE CVGPGATQLY VPTDAPPPYS LTDSCPTLDG
TSDSGSGHSP GRHQQEQRTP AQGGLHTVSM DTLPPYEAVC GAGPPSGLLP LPGPDPGPRG
SQGSPTPTRA PASGPERIV*

Mutated AA sequence

MSFKRPCPLA RYNRTSYFYP TFSESSEHSH LLVSPVLVAS AVIGVVIILS CITIIVGSIR
RDRQARLQRH RHRHHRHHHH HHHHRRRRHR EYEHGYVSDE HTYSRSSRRM RYACSSSEDW
PPPLDISSDG DVDATVLREL YPDSPPGYEE CVGPGATQLY VPTDAPPPYS LTDSCPTLDG
TSDSGSGHTP GRHQQEQRTP AQGGLHTVSM DTLPPYEAVC GAGPPSGLLP LPGPDPGPRG
SQGSPTPTRA PASGPERIV*

Position of stopcodon in wt / mu CDS

780 / 780

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

260 / 260

Position of stopcodon in wt / mu cDNA

999 / 999

Position of start ATG in wt / mu cDNA

220 / 220

Last intron/exon boundary

659

Theoretical NMD boundary in CDS

389

Length of CDS

780

Coding sequence (CDS) position

566

cDNA position

785

gDNA position

53417

Chromosomal position

66480711

Speed

0.05 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