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: ENST00000218867
Querying Taster for transcript #2: ENST00000682775
Querying Taster for transcript #3: ENST00000684497
Querying Taster for transcript #4: ENST00000683210
MT speed 0.06 s - this script 2.438917 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
ENST00000218867(MANE Select)	SGCG	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000682775	SACS	Benign	2\|198	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000684497	SACS	Benign	2\|198	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000683210	SACS	Benign	2\|198	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD

MutationT@ster 2025

Variant:

13:23324350T>C_1_ENST00000218867

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

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

Analysed issue

Analysis result

Variant

Chr13:23324350T>C (GRCh38)

Gene symbol

SGCG

Gene constraints

LOEUF: 1.21, LOF (oe): 0.84, misssense (oe): 0.98, synonymous (oe): 1.11 ? (gnomAD)

Ensembl transcript ID

ENST00000218867.4

Genbank transcript ID

NM_000231 (exact from MANE), NM_001378244 (by similarity), NM_001378245 (by similarity), NM_001378246 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.703-18T>C
g.143372T>C

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	rs9580603
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	595	16264	16859

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.22	0
	-0.108	0
(flanking)	0.521	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

18

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

13

Strand

1

Original gDNA sequence snippet

CTTCCTTAACTCTTCGTCTCTCATCTTCTCCCAACCAGCTT

Altered gDNA sequence snippet

CTTCCTTAACTCTTCGTCTCCCATCTTCTCCCAACCAGCTT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MVREQYTTAT EGICIERPEN QYVYKIGIYG WRKRCLYLFV LLLLIILVVN LALTIWILKV
MWFSPAGMGH LCVTKDGLRL EGESEFLFPL YAKEIHSRVD SSLLLQSTQN VTVNARNSEG
EVTGRLKVGP KMVEVQNQQF QINSNDGKPL FTVDEKEVVV GTDKLRVTGP EGALFEHSVE
TPLVRADPFQ DLRLESPTRS LSMDAPRGVH IQAHAGKIEA LSQMDILFHS SDGMLVLDAE
TVCLPKLVQG TWGPSGSSQS LYEICVCPDG KLYLSVAGVS TTCQEHNHIC L*

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

98 / 98

Last intron/exon boundary

799

Theoretical NMD boundary in CDS

651

Length of CDS

876

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

143372

Chromosomal position

23324350

Speed

0.01 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:

13:23324350T>C_2_ENST00000682775

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 2|198 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr13:23324350T>C (GRCh38)

Gene symbol

SACS

Gene constraints

LOEUF: 0.71, LOF (oe): 0.51, misssense (oe): 0.87, synonymous (oe): 1.08 ? (gnomAD)

Ensembl transcript ID

ENST00000682775.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.2186-12235A>G
g.109414A>G

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	rs9580603
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	595	16264	16859

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.22	0
	-0.108	0
(flanking)	0.521	0

?

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

13

Strand

-1

Original gDNA sequence snippet

AAGCTGGTTGGGAGAAGATGAGAGACGAAGAGTTAAGGAAG

Altered gDNA sequence snippet

AAGCTGGTTGGGAGAAGATGGGAGACGAAGAGTTAAGGAAG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

METKENRWVP VTVLPGCVGC RTVAALASWT VRDVKERIFA ETGFPVSEQR LWRGGRELSD
WIKIGDLTSK NCHLFVNLQS KGLKGGGRFG QTTPPLVDFL KDILRRYPEG GQILKELIQN
AEDAGATEVK FLYDETQYGT ETLWSKDMAP YQGPALYVYN NAVFTPEDWH GIQEIARSRK
KDDPLKVGRF GIGFNSVYHI TDVPCIFSGD QIGMLDPHQT LFGPHESGQC WNLKDDSKEI
SELSDQFAPF VGIFGSTKET FINGNFPGTF FRFPLRLQPS QLSSNLYNKQ KVLELFESFR
ADADTVLLFL KSVQDVSLYV READGTEKLV FRVTSSESKA LKHERPNSIK ILGTAISNYC
KKTPSNNITC VTYHVNIVLE EESTKDAQKT SWLVCNSVGG RGISSKLDSL ADELKFVPII
GIAMPLSSRD DEAKGATSDF SGKAFCFLPL PPGEESSTGL PVHISGFFGL TDNRRSIKWR
ELDQWRDPAA LWNEFLVMNV VPKAYATLIL DSIKRLEMEK SSDFPLSVDV IYKLWPEASK
VKVHWQPVLE PLFSELLQNA VIYSISCDWV RLEQVYFSEL DENLEYTKTV LNYLQSSGKQ
IAKVPGNVDA AVQLTAASGT TPVRKVTPAW VRQVLRKCAH LGCAEEKLHL LEFVLSDQAY
SELLGLELLP LQNGNFVPFS SSVSDQDVIY ITSAEYPRSL FPSLEGRFIL DNLKPHLVAA
LKEAAQTRGT WITWSQRRS*

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

640 / 640

Last intron/exon boundary

2824

Theoretical NMD boundary in CDS

2134

Length of CDS

2220

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

109414

Chromosomal position

23324350

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:

13:23324350T>C_3_ENST00000684497

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 2|198 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr13:23324350T>C (GRCh38)

Gene symbol

SACS

Gene constraints

LOEUF: 0.71, LOF (oe): 0.51, misssense (oe): 0.87, synonymous (oe): 1.08 ? (gnomAD)

Ensembl transcript ID

ENST00000684497.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.2186-1706A>G
g.109414A>G

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	rs9580603
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	595	16264	16859

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.22	0
	-0.108	0
(flanking)	0.521	0

?

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

13

Strand

-1

Original gDNA sequence snippet

AAGCTGGTTGGGAGAAGATGAGAGACGAAGAGTTAAGGAAG

Altered gDNA sequence snippet

AAGCTGGTTGGGAGAAGATGGGAGACGAAGAGTTAAGGAAG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

METKENRWVP VTVLPGCVGC RTVAALASWT VRDVKERIFA ETGFPVSEQR LWRGGRELSD
WIKIGDLTSK NCHLFVNLQS KGLKGGGRFG QTTPPLVDFL KDILRRYPEG GQILKELIQN
AEDAGATEVK FLYDETQYGT ETLWSKDMAP YQGPALYVYN NAVFTPEDWH GIQEIARSRK
KDDPLKVGRF GIGFNSVYHI TDVPCIFSGD QIGMLDPHQT LFGPHESGQC WNLKDDSKEI
SELSDQFAPF VGIFGSTKET FINGNFPGTF FRFPLRLQPS QLSSNLYNKQ KVLELFESFR
ADADTVLLFL KSVQDVSLYV READGTEKLV FRVTSSESKA LKHERPNSIK ILGTAISNYC
KKTPSNNITC VTYHVNIVLE EESTKDAQKT SWLVCNSVGG RGISSKLDSL ADELKFVPII
GIAMPLSSRD DEAKGATSDF SGKAFCFLPL PPGEESSTGL PVHISGFFGL TDNRRSIKWR
ELDQWRDPAA LWNEFLVMNV VPKAYATLIL DSIKRLEMEK SSDFPLSVDV IYKLWPEASK
VKVHWQPVLE PLFSELLQNA VIYSISCDWV RLEQVYFSEL DENLEYTKTV LNYLQSSGKQ
IAKVPGNVDA AVQLTAASGT TPVRKVTPAW VRQVLRKCAH LGCAEEKLHL LEFVLSDQAY
SELLGLELLP LQNGNFVPFS SSVSDQDVIY ITSAEYPRSL FPSLEGRFIL DNLKPHLVAA
LKEAAQTRAH SPGVWRCT*

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

640 / 640

Last intron/exon boundary

2824

Theoretical NMD boundary in CDS

2134

Length of CDS

2217

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

109414

Chromosomal position

23324350

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:

13:23324350T>C_4_ENST00000683210

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 2|198 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr13:23324350T>C (GRCh38)

Gene symbol

SACS

Gene constraints

LOEUF: 0.71, LOF (oe): 0.51, misssense (oe): 0.87, synonymous (oe): 1.08 ? (gnomAD)

Ensembl transcript ID

ENST00000683210.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.2185+29435A>G
g.109414A>G

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	rs9580603
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	595	16264	16859

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.22	0
	-0.108	0
(flanking)	0.521	0

?

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

13

Strand

-1

Original gDNA sequence snippet

AAGCTGGTTGGGAGAAGATGAGAGACGAAGAGTTAAGGAAG

Altered gDNA sequence snippet

AAGCTGGTTGGGAGAAGATGGGAGACGAAGAGTTAAGGAAG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

METKENRWVP VTVLPGCVGC RTVAALASWT VRDVKERIFA ETGFPVSEQR LWRGGRELSD
WIKIGDLTSK NCHLFVNLQS KGLKGGGRFG QTTPPLVDFL KDILRRYPEG GQILKELIQN
AEDAGATEVK FLYDETQYGT ETLWSKDMAP YQGPALYVYN NAVFTPEDWH GIQEIARSRK
KDDPLKVGRF GIGFNSVYHI TDVPCIFSGD QIGMLDPHQT LFGPHESGQC WNLKDDSKEI
SELSDQFAPF VGIFGSTKET FINGNFPGTF FRFPLRLQPS QLSSNLYNKQ KVLELFESFR
ADADTVLLFL KSVQDVSLYV READGTEKLV FRVTSSESKA LKHERPNSIK ILGTAISNYC
KKTPSNNITC VTYHVNIVLE EESTKDAQKT SWLVCNSVGG RGISSKLDSL ADELKFVPII
GIAMPLSSRD DEAKGATSDF SGKAFCFLPL PPGEESSTGL PVHISGFFGL TDNRRSIKWR
ELDQWRDPAA LWNEFLVMNV VPKAYATLIL DSIKRLEMEK SSDFPLSVDV IYKLWPEASK
VKVHWQPVLE PLFSELLQNA VIYSISCDWV RLEQVYFSEL DENLEYTKTV LNYLQSSGKQ
IAKVPGNVDA AVQLTAASGT TPVRKVTPAW VRQVLRKCAH LGCAEEKLHL LEFVLSDQAY
SELLGLELLP LQNGNFVPFS SSVSDQDVIY ITSAEYPRSL FPSLEGRFIL DNLKPHLVAA
LKEAAQTRAE IPWTAARR*

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

640 / 640

Last intron/exon boundary

2824

Theoretical NMD boundary in CDS

2134

Length of CDS

2217

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

109414

Chromosomal position

23324350

Speed

0.01 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