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: ENST00000381812
Querying Taster for transcript #2: ENST00000360779
Querying Taster for transcript #3: ENST00000381808
Querying Taster for transcript #4: ENST00000339987
MT speed 1.29 s - this script 3.753767 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000381808	SDCBP2	Deleterious	73\|27	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000381812	SDCBP2	Deleterious	78\|22	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000360779(MANE Select)	SDCBP2	Deleterious	78\|22	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000339987	SDCBP2	Deleterious	78\|22	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

20:1312653G>A_3_ENST00000381808

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 73|27 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr20:1312653G>A (GRCh38)

Gene symbol

SDCBP2

Gene constraints

LOEUF: 1.45, LOF (oe): 0.98, misssense (oe): 1.02, synonymous (oe): 1.06 ? (gnomAD)

Ensembl transcript ID

ENST00000381808.7

Genbank transcript ID

NM_015685 (by similarity)

UniProt / AlphaMissense peptide

SDCB2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.239C>T
g.16487C>T

AA changes

AAE:	S80L	?
Score:	145

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1	7	8

Protein conservation

Species	Match	AA	Alignment
Human		80	Q	I	D	G	R	D	C	A	G	W	S	S	H	K	A	H	Q	V	V	K	K	A	S	G
mutated	not conserved	80	Q	I	D	G	R	D	C	A	G	W	S	L	H	K	A	H	Q	V	V	K	K	A	S
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	292	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-6.002	0
	3.205	0.771
(flanking)	-0.101	0.672

?

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

20

Strand

-1

Original gDNA sequence snippet

TGACTGTGCTGGGTGGAGCTCGCACAAAGCCCATCAGGTGG

Altered gDNA sequence snippet

TGACTGTGCTGGGTGGAGCTTGCACAAAGCCCATCAGGTGG

Original cDNA sequence snippet

TGACTGTGCTGGGTGGAGCTCGCACAAAGCCCATCAGGTGG

Altered cDNA sequence snippet

TGACTGTGCTGGGTGGAGCTTGCACAAAGCCCATCAGGTGG

Wildtype AA sequence

MVAPVTGYSL GVRRAEIKPG VREIHLCKDE RGKTGLRLRK VDQGLFVQLV QANTPASLVG
LRFGDQLLQI DGRDCAGWSS HKAHQVVKKA SGDKIVVVVR DRPFQRTVTM HKDSMGHVGF
VIKKGKIVSL VKGSSAARNG LLTNHYVCEV DGQNVIGLKD KKIMEILATA GNVVTLTIIP
SVIYEHMVKK LPPVLLHHTM DHSIPDA*

Mutated AA sequence

MVAPVTGYSL GVRRAEIKPG VREIHLCKDE RGKTGLRLRK VDQGLFVQLV QANTPASLVG
LRFGDQLLQI DGRDCAGWSL HKAHQVVKKA SGDKIVVVVR DRPFQRTVTM HKDSMGHVGF
VIKKGKIVSL VKGSSAARNG LLTNHYVCEV DGQNVIGLKD KKIMEILATA GNVVTLTIIP
SVIYEHMVKK LPPVLLHHTM DHSIPDA*

Position of stopcodon in wt / mu CDS

624 / 624

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

208 / 208

Position of stopcodon in wt / mu cDNA

795 / 795

Position of start ATG in wt / mu cDNA

172 / 172

Last intron/exon boundary

740

Theoretical NMD boundary in CDS

518

Length of CDS

624

Coding sequence (CDS) position

239

cDNA position

410

gDNA position

16487

Chromosomal position

1312653

Speed

0.21 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:

20:1312653G>A_1_ENST00000381812

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 78|22 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr20:1312653G>A (GRCh38)

Gene symbol

SDCBP2

Gene constraints

LOEUF: 1.32, LOF (oe): 0.95, misssense (oe): 1.08, synonymous (oe): 1.09 ? (gnomAD)

Ensembl transcript ID

ENST00000381812.5

Genbank transcript ID

UniProt / AlphaMissense peptide

SDCB2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.494C>T
g.16487C>T

AA changes

AAE:	S165L	?
Score:	145

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1	7	8

Protein conservation

Species	Match	AA	Alignment
Human		165	Q	I	D	G	R	D	C	A	G	W	S	S	H	K	A	H	Q	V	V	K	K	A	S	G
mutated	not conserved	165	Q	I	D	G	R	D	C	A	G	W	S	L	H	K	A	H	Q	V	V	K	K	A	S
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	292	CHAIN		lost
108	187	DOMAIN	PDZ	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-6.002	0
	3.205	0.771
(flanking)	-0.101	0.672

?

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

20

Strand

-1

Original gDNA sequence snippet

TGACTGTGCTGGGTGGAGCTCGCACAAAGCCCATCAGGTGG

Altered gDNA sequence snippet

TGACTGTGCTGGGTGGAGCTTGCACAAAGCCCATCAGGTGG

Original cDNA sequence snippet

TGACTGTGCTGGGTGGAGCTCGCACAAAGCCCATCAGGTGG

Altered cDNA sequence snippet

TGACTGTGCTGGGTGGAGCTTGCACAAAGCCCATCAGGTGG

Wildtype AA sequence

MSSLYPSLED LKVDQAIQAQ VRASPKMPAL PVQATAISPP PVLYPNLAEL ENYMGLSLSS
QEVQESLLQI PEGDSTAVSG PGPGQMVAPV TGYSLGVRRA EIKPGVREIH LCKDERGKTG
LRLRKVDQGL FVQLVQANTP ASLVGLRFGD QLLQIDGRDC AGWSSHKAHQ VVKKASGDKI
VVVVRDRPFQ RTVTMHKDSM GHVGFVIKKG KIVSLVKGSS AARNGLLTNH YVCEVDGQNV
IGLKDKKIME ILATAGNVVT LTIIPSVIYE HMVKKLPPVL LHHTMDHSIP DA*

Mutated AA sequence

MSSLYPSLED LKVDQAIQAQ VRASPKMPAL PVQATAISPP PVLYPNLAEL ENYMGLSLSS
QEVQESLLQI PEGDSTAVSG PGPGQMVAPV TGYSLGVRRA EIKPGVREIH LCKDERGKTG
LRLRKVDQGL FVQLVQANTP ASLVGLRFGD QLLQIDGRDC AGWSLHKAHQ VVKKASGDKI
VVVVRDRPFQ RTVTMHKDSM GHVGFVIKKG KIVSLVKGSS AARNGLLTNH YVCEVDGQNV
IGLKDKKIME ILATAGNVVT LTIIPSVIYE HMVKKLPPVL LHHTMDHSIP DA*

Position of stopcodon in wt / mu CDS

879 / 879

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

293 / 293

Position of stopcodon in wt / mu cDNA

1018 / 1018

Position of start ATG in wt / mu cDNA

140 / 140

Last intron/exon boundary

963

Theoretical NMD boundary in CDS

773

Length of CDS

879

Coding sequence (CDS) position

494

cDNA position

633

gDNA position

16487

Chromosomal position

1312653

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

Back to summary table

MutationT@ster 2025

Variant:

20:1312653G>A_2_ENST00000360779

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 78|22 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr20:1312653G>A (GRCh38)

Gene symbol

SDCBP2

Gene constraints

LOEUF: 1.32, LOF (oe): 0.95, misssense (oe): 1.08, synonymous (oe): 1.09 ? (gnomAD)

Ensembl transcript ID

ENST00000360779.4

Genbank transcript ID

NM_080489 (exact from MANE)

UniProt / AlphaMissense peptide

SDCB2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.494C>T
g.16487C>T

AA changes

AAE:	S165L	?
Score:	145

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1	7	8

Protein conservation

Species	Match	AA	Alignment
Human		165	Q	I	D	G	R	D	C	A	G	W	S	S	H	K	A	H	Q	V	V	K	K	A	S	G
mutated	not conserved	165	Q	I	D	G	R	D	C	A	G	W	S	L	H	K	A	H	Q	V	V	K	K	A	S
Ptroglodytes	all identical	165	Q	I	D	G	R	D	C	A	G	W	S	S	H	K	A	H	Q	V	V	K	K	A	S
Mmulatta	all identical	165	Q	I	D	G	R	D	C	A	G	W	S	S	R	K	A	N	Q	V	V	K	K	A	S
Fcatus	all conserved	160	Q	I	D	G	C	D	C	A	G	W	S	T	D	R	A	H	R	V	L	K	R	A	S
Mmusculus	all conserved	165	Q	I	D	G	C	D	C	A	G	W	N	T	H	K	A	H	K	V	L	K	K	A	S
Ggallus	all identical	178												S	D	K	A	Q	R	A	L	K	K	A	S
Trubripes	all conserved	175	Q	I	N	G	Q	N	C	A	G	W	S	A	D	K	A	H	K	A
Drerio	no homologue
Dmelanogaster	not conserved	2021	A	I	N	G	L	S	L	V	G	L	P	L	S	T	C	Q	T	Y	I	K	N	T	K
Celegans	not conserved	864	N	I	N	G	I	S	L	V	G	L	P	L	S	A	A	Q	T	Q	I	KNM	K	T	A
Xtropicalis	all conserved	201	Q	V	D	G	A	S	C	A	G	W	S	T	E	R	A	H	K	A	L	K	R	A	S

Protein features

Start (aa)	End (aa)	Feature	Details
1	292	CHAIN		lost
108	187	DOMAIN	PDZ	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-6.002	0
	3.205	0.771
(flanking)	-0.101	0.672

?

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

20

Strand

-1

Original gDNA sequence snippet

TGACTGTGCTGGGTGGAGCTCGCACAAAGCCCATCAGGTGG

Altered gDNA sequence snippet

TGACTGTGCTGGGTGGAGCTTGCACAAAGCCCATCAGGTGG

Original cDNA sequence snippet

TGACTGTGCTGGGTGGAGCTCGCACAAAGCCCATCAGGTGG

Altered cDNA sequence snippet

TGACTGTGCTGGGTGGAGCTTGCACAAAGCCCATCAGGTGG

Wildtype AA sequence

MSSLYPSLED LKVDQAIQAQ VRASPKMPAL PVQATAISPP PVLYPNLAEL ENYMGLSLSS
QEVQESLLQI PEGDSTAVSG PGPGQMVAPV TGYSLGVRRA EIKPGVREIH LCKDERGKTG
LRLRKVDQGL FVQLVQANTP ASLVGLRFGD QLLQIDGRDC AGWSSHKAHQ VVKKASGDKI
VVVVRDRPFQ RTVTMHKDSM GHVGFVIKKG KIVSLVKGSS AARNGLLTNH YVCEVDGQNV
IGLKDKKIME ILATAGNVVT LTIIPSVIYE HMVKKLPPVL LHHTMDHSIP DA*

Mutated AA sequence

MSSLYPSLED LKVDQAIQAQ VRASPKMPAL PVQATAISPP PVLYPNLAEL ENYMGLSLSS
QEVQESLLQI PEGDSTAVSG PGPGQMVAPV TGYSLGVRRA EIKPGVREIH LCKDERGKTG
LRLRKVDQGL FVQLVQANTP ASLVGLRFGD QLLQIDGRDC AGWSLHKAHQ VVKKASGDKI
VVVVRDRPFQ RTVTMHKDSM GHVGFVIKKG KIVSLVKGSS AARNGLLTNH YVCEVDGQNV
IGLKDKKIME ILATAGNVVT LTIIPSVIYE HMVKKLPPVL LHHTMDHSIP DA*

Position of stopcodon in wt / mu CDS

879 / 879

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

293 / 293

Position of stopcodon in wt / mu cDNA

953 / 953

Position of start ATG in wt / mu cDNA

75 / 75

Last intron/exon boundary

898

Theoretical NMD boundary in CDS

773

Length of CDS

879

Coding sequence (CDS) position

494

cDNA position

568

gDNA position

16487

Chromosomal position

1312653

Speed

0.21 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:

20:1312653G>A_4_ENST00000339987

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 78|22 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr20:1312653G>A (GRCh38)

Gene symbol

SDCBP2

Gene constraints

LOEUF: 1.32, LOF (oe): 0.95, misssense (oe): 1.08, synonymous (oe): 1.09 ? (gnomAD)

Ensembl transcript ID

ENST00000339987.7

Genbank transcript ID

NM_001199784 (by similarity)

UniProt / AlphaMissense peptide

SDCB2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.494C>T
g.16487C>T

AA changes

AAE:	S165L	?
Score:	145

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1	7	8

Protein conservation

Species	Match	AA	Alignment
Human		165	Q	I	D	G	R	D	C	A	G	W	S	S	H	K	A	H	Q	V	V	K	K	A	S	G
mutated	not conserved	165	Q	I	D	G	R	D	C	A	G	W	S	L	H	K	A	H	Q	V	V	K	K	A	S
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	292	CHAIN		lost
108	187	DOMAIN	PDZ	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-6.002	0
	3.205	0.771
(flanking)	-0.101	0.672

?

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

20

Strand

-1

Original gDNA sequence snippet

TGACTGTGCTGGGTGGAGCTCGCACAAAGCCCATCAGGTGG

Altered gDNA sequence snippet

TGACTGTGCTGGGTGGAGCTTGCACAAAGCCCATCAGGTGG

Original cDNA sequence snippet

TGACTGTGCTGGGTGGAGCTCGCACAAAGCCCATCAGGTGG

Altered cDNA sequence snippet

TGACTGTGCTGGGTGGAGCTTGCACAAAGCCCATCAGGTGG

Wildtype AA sequence

MSSLYPSLED LKVDQAIQAQ VRASPKMPAL PVQATAISPP PVLYPNLAEL ENYMGLSLSS
QEVQESLLQI PEGDSTAVSG PGPGQMVAPV TGYSLGVRRA EIKPGVREIH LCKDERGKTG
LRLRKVDQGL FVQLVQANTP ASLVGLRFGD QLLQIDGRDC AGWSSHKAHQ VVKKASGDKI
VVVVRDRPFQ RTVTMHKDSM GHVGFVIKKG KIVSLVKGSS AARNGLLTNH YVCEVDGQNV
IGLKDKKIME ILATAGNVVT LTIIPSVIYE HMVKKLPPVL LHHTMDHSIP DA*

Mutated AA sequence

MSSLYPSLED LKVDQAIQAQ VRASPKMPAL PVQATAISPP PVLYPNLAEL ENYMGLSLSS
QEVQESLLQI PEGDSTAVSG PGPGQMVAPV TGYSLGVRRA EIKPGVREIH LCKDERGKTG
LRLRKVDQGL FVQLVQANTP ASLVGLRFGD QLLQIDGRDC AGWSLHKAHQ VVKKASGDKI
VVVVRDRPFQ RTVTMHKDSM GHVGFVIKKG KIVSLVKGSS AARNGLLTNH YVCEVDGQNV
IGLKDKKIME ILATAGNVVT LTIIPSVIYE HMVKKLPPVL LHHTMDHSIP DA*

Position of stopcodon in wt / mu CDS

879 / 879

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

293 / 293

Position of stopcodon in wt / mu cDNA

938 / 938

Position of start ATG in wt / mu cDNA

60 / 60

Last intron/exon boundary

883

Theoretical NMD boundary in CDS

773

Length of CDS

879

Coding sequence (CDS) position

494

cDNA position

553

gDNA position

16487

Chromosomal position

1312653

Speed

0.50 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