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: ENST00000398158
Querying Taster for transcript #2: ENST00000398165
Querying Taster for transcript #3: ENST00000359624
Querying Taster for transcript #4: ENST00000352178
MT speed 0.08 s - this script 2.466033 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length
ENST00000398158	CBS	Benign	0\|200	without_aae	No	Single base exchange	N/A
ENST00000398165(MANE Select)	CBS	Benign	0\|200	without_aae	No	Single base exchange	N/A
ENST00000359624	CBS	Benign	0\|200	without_aae	No	Single base exchange	N/A
ENST00000352178	CBS	Benign	0\|200	without_aae	No	Single base exchange	N/A

MutationT@ster 2025

Variant:

21:43062292G>A_1_ENST00000398158

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Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 0|200 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr21:43062292G>A (GRCh38)

Gene symbol

CBS

Gene constraints

no data

Ensembl transcript ID

ENST00000398158.5

Genbank transcript ID

NM_001321072 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1039+19C>T
g.14652C>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs182908734
	Allele 'A' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.083	0
	-0.246	0
(flanking)	-5.611	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

19

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

21

Strand

-1

Original gDNA sequence snippet

CGGTGAGTGGGTGGCGGGCACGGGGGTATGGGGAAGGCAGA

Altered gDNA sequence snippet

CGGTGAGTGGGTGGCGGGCATGGGGGTATGGGGAAGGCAGA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MPSETPQAEV GPTGCPHRSG PHSAKGSLEK GSPEDKEAKE PLWIRPDAPS RCTWQLGRPA
SESPHHHTAP AKSPKILPDI LKKIGDTPMV RINKIGKKFG LKCELLAKCE FFNAGGSVKD
RISLRMIEDA ERDGTLKPGD TIIEPTSGNT GIGLALAAAV RGYRCIIVMP EKMSSEKVDV
LRALGAEIVR TPTNARFDSP ESHVGVAWRL KNEIPNSHIL DQYRNASNPL AHYDTTADEI
LQQCDGKLDM LVASVGTGGT ITGIARKLKE KCPGCRIIGV DPEGSILAEP EELNQTEQTT
YEVEGIGYDF IPTVLDRTVV DKWFKSNDEE AFTFARMLIA QEGLLCGGSA GSTVAVAVKA
AQELQEGQRC VVILPDSVRN YMTKFLSDRW MLQKGFLKEE DLTEKKPWWW HLRVQELGLS
APLTVLPTIT CGHTIEILRE KGFDQAPVVD EAGVILGMVT LGNMLSSLLA GKVQPSDQVG
KVIYKQFKQI RLTDTLGRLS HILEMDHFAL VVHEQIQYHS TGKSSQRQMV FGVVTAIDLL
NFVAAQERDQ K*

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

109 / 109

Last intron/exon boundary

1660

Theoretical NMD boundary in CDS

1501

Length of CDS

1656

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

14652

Chromosomal position

43062292

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:

21:43062292G>A_2_ENST00000398165

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 0|200 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr21:43062292G>A (GRCh38)

Gene symbol

CBS

Gene constraints

no data

Ensembl transcript ID

ENST00000398165.8

Genbank transcript ID

NM_000071 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1039+19C>T
g.14652C>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs182908734
	Allele 'A' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.083	0
	-0.246	0
(flanking)	-5.611	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

19

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

21

Strand

-1

Original gDNA sequence snippet

CGGTGAGTGGGTGGCGGGCACGGGGGTATGGGGAAGGCAGA

Altered gDNA sequence snippet

CGGTGAGTGGGTGGCGGGCATGGGGGTATGGGGAAGGCAGA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MPSETPQAEV GPTGCPHRSG PHSAKGSLEK GSPEDKEAKE PLWIRPDAPS RCTWQLGRPA
SESPHHHTAP AKSPKILPDI LKKIGDTPMV RINKIGKKFG LKCELLAKCE FFNAGGSVKD
RISLRMIEDA ERDGTLKPGD TIIEPTSGNT GIGLALAAAV RGYRCIIVMP EKMSSEKVDV
LRALGAEIVR TPTNARFDSP ESHVGVAWRL KNEIPNSHIL DQYRNASNPL AHYDTTADEI
LQQCDGKLDM LVASVGTGGT ITGIARKLKE KCPGCRIIGV DPEGSILAEP EELNQTEQTT
YEVEGIGYDF IPTVLDRTVV DKWFKSNDEE AFTFARMLIA QEGLLCGGSA GSTVAVAVKA
AQELQEGQRC VVILPDSVRN YMTKFLSDRW MLQKGFLKEE DLTEKKPWWW HLRVQELGLS
APLTVLPTIT CGHTIEILRE KGFDQAPVVD EAGVILGMVT LGNMLSSLLA GKVQPSDQVG
KVIYKQFKQI RLTDTLGRLS HILEMDHFAL VVHEQIQYHS TGKSSQRQMV FGVVTAIDLL
NFVAAQERDQ K*

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

151 / 151

Last intron/exon boundary

1702

Theoretical NMD boundary in CDS

1501

Length of CDS

1656

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

14652

Chromosomal position

43062292

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:

21:43062292G>A_3_ENST00000359624

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 0|200 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr21:43062292G>A (GRCh38)

Gene symbol

CBS

Gene constraints

no data

Ensembl transcript ID

ENST00000359624.7

Genbank transcript ID

NM_001178009 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1039+19C>T
g.14652C>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs182908734
	Allele 'A' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.083	0
	-0.246	0
(flanking)	-5.611	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

19

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

21

Strand

-1

Original gDNA sequence snippet

CGGTGAGTGGGTGGCGGGCACGGGGGTATGGGGAAGGCAGA

Altered gDNA sequence snippet

CGGTGAGTGGGTGGCGGGCATGGGGGTATGGGGAAGGCAGA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MPSETPQAEV GPTGCPHRSG PHSAKGSLEK GSPEDKEAKE PLWIRPDAPS RCTWQLGRPA
SESPHHHTAP AKSPKILPDI LKKIGDTPMV RINKIGKKFG LKCELLAKCE FFNAGGSVKD
RISLRMIEDA ERDGTLKPGD TIIEPTSGNT GIGLALAAAV RGYRCIIVMP EKMSSEKVDV
LRALGAEIVR TPTNARFDSP ESHVGVAWRL KNEIPNSHIL DQYRNASNPL AHYDTTADEI
LQQCDGKLDM LVASVGTGGT ITGIARKLKE KCPGCRIIGV DPEGSILAEP EELNQTEQTT
YEVEGIGYDF IPTVLDRTVV DKWFKSNDEE AFTFARMLIA QEGLLCGGSA GSTVAVAVKA
AQELQEGQRC VVILPDSVRN YMTKFLSDRW MLQKGFLKEE DLTEKKPWWW HLRVQELGLS
APLTVLPTIT CGHTIEILRE KGFDQAPVVD EAGVILGMVT LGNMLSSLLA GKVQPSDQVG
KVIYKQFKQI RLTDTLGRLS HILEMDHFAL VVHEQIQYHS TGKSSQRQMV FGVVTAIDLL
NFVAAQERDQ K*

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

223 / 223

Last intron/exon boundary

1896

Theoretical NMD boundary in CDS

1623

Length of CDS

1656

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

14652

Chromosomal position

43062292

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:

21:43062292G>A_4_ENST00000352178

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 0|200 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr21:43062292G>A (GRCh38)

Gene symbol

CBS

Gene constraints

no data

Ensembl transcript ID

ENST00000352178.9

Genbank transcript ID

NM_001320298 (by similarity), NM_001178008 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1039+19C>T
g.14652C>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs182908734
	Allele 'A' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.083	0
	-0.246	0
(flanking)	-5.611	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

19

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

21

Strand

-1

Original gDNA sequence snippet

CGGTGAGTGGGTGGCGGGCACGGGGGTATGGGGAAGGCAGA

Altered gDNA sequence snippet

CGGTGAGTGGGTGGCGGGCATGGGGGTATGGGGAAGGCAGA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MPSETPQAEV GPTGCPHRSG PHSAKGSLEK GSPEDKEAKE PLWIRPDAPS RCTWQLGRPA
SESPHHHTAP AKSPKILPDI LKKIGDTPMV RINKIGKKFG LKCELLAKCE FFNAGGSVKD
RISLRMIEDA ERDGTLKPGD TIIEPTSGNT GIGLALAAAV RGYRCIIVMP EKMSSEKVDV
LRALGAEIVR TPTNARFDSP ESHVGVAWRL KNEIPNSHIL DQYRNASNPL AHYDTTADEI
LQQCDGKLDM LVASVGTGGT ITGIARKLKE KCPGCRIIGV DPEGSILAEP EELNQTEQTT
YEVEGIGYDF IPTVLDRTVV DKWFKSNDEE AFTFARMLIA QEGLLCGGSA GSTVAVAVKA
AQELQEGQRC VVILPDSVRN YMTKFLSDRW MLQKGFLKEE DLTEKKPWWW HLRVQELGLS
APLTVLPTIT CGHTIEILRE KGFDQAPVVD EAGVILGMVT LGNMLSSLLA GKVQPSDQVG
KVIYKQFKQI RLTDTLGRLS HILEMDHFAL VVHEQIQYHS TGKSSQRQMV FGVVTAIDLL
NFVAAQERDQ K*

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

239 / 239

Last intron/exon boundary

1790

Theoretical NMD boundary in CDS

1501

Length of CDS

1656

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

14652

Chromosomal position

43062292

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