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: ENST00000568943
Querying Taster for transcript #2: ENST00000414754
Querying Taster for transcript #3: ENST00000574918
Querying Taster for transcript #4: ENST00000561820
Querying Taster for transcript #5: ENST00000566163
Querying Taster for transcript #6: ENST00000567238
Querying Taster for transcript #7: ENST00000219833
Querying Taster for transcript #8: ENST00000379906
MT speed 0.18 s - this script 2.576946 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000568943(MANE Select)	SLC6A2	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000414754	SLC6A2	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000574918	SLC6A2	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000561820	SLC6A2	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000566163	SLC6A2	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000567238	SLC6A2	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000219833	SLC6A2	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000379906	SLC6A2	Benign	0\|200	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD

MutationT@ster 2025

Variant:

16:55679176C>T_1_ENST00000568943

Back to summary table

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

Chr16:55679176C>T (GRCh38)

Gene symbol

SLC6A2

Gene constraints

LOEUF: 0.52, LOF (oe): 0.37, misssense (oe): 0.68, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000568943.6

Genbank transcript ID

NM_001172501 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.645-5967C>T
g.23189C>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	rs36020
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	1082	15091	16173

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.772	0.002
	-3.281	0
(flanking)	0.321	0.026

?

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

16

Strand

1

Original gDNA sequence snippet

CATAAAGGCACAGGAAGAAGCGGAATTAAGCATCAGATAGG

Altered gDNA sequence snippet

CATAAAGGCACAGGAAGAAGTGGAATTAAGCATCAGATAGG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MLLARMNPQV QPENNGADTG PEQPLRARKT AELLVVKERN GVQCLLAPRD GDAQPRETWG
KKIDFLLSVV GFAVDLANVW RFPYLCYKNG GGAFLIPYTL FLIIAGMPLF YMELALGQYN
REGAATVWKI CPFFKGVGYA VILIALYVGF YYNVIIAWSL YYLFSSFTLN LPWTDCGHTW
NSPNCTDPKL LNGSVLGNHT KYSKYKFTPA AEFYERGVLH LHESSGIHDI GLPQWQLLLC
LMVVVIVLYF SLWKGVKTSG KVVWITATLP YFVLFVLLVH GVTLPGASNG INAYLHIDFY
RLKEATVWID AATQIFFSLG AGFGVLIAFA SYNKFDNNCY RDALLTSSIN CITSFVSGFA
IFSILGYMAH EHKVNIEDVA TEGAGLVFIL YPEAISTLSG STFWAVVFFV MLLALGLDSS
MGGMEAVITG LADDFQVLKR HRKLFTFGVT FSTFLLALFC ITKGGIYVLT LLDTFAAGTS
ILFAVLMEAI GVSWFYGVDR FSNDIQQMMG FRPGLYWRLC WKFVSPAFLL FVVVVSIINF
KPLTYDDYIF PPWANWVGWG IALSSMVLVP IYVIYKFLST QGSLWERLAY GITPENEHHL
VAQRDIRQFQ LQHWLAI*

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

234 / 234

Last intron/exon boundary

2063

Theoretical NMD boundary in CDS

1779

Length of CDS

1854

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

23189

Chromosomal position

55679176

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

MutationT@ster 2025

Variant:

16:55679176C>T_2_ENST00000414754

Back to summary table

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

Chr16:55679176C>T (GRCh38)

Gene symbol

SLC6A2

Gene constraints

LOEUF: 0.55, LOF (oe): 0.39, misssense (oe): 0.67, synonymous (oe): 1.00 ? (gnomAD)

Ensembl transcript ID

ENST00000414754.7

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.645-5967C>T
g.23189C>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	rs36020
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	1082	15091	16173

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.772	0.002
	-3.281	0
(flanking)	0.321	0.026

?

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

16

Strand

1

Original gDNA sequence snippet

CATAAAGGCACAGGAAGAAGCGGAATTAAGCATCAGATAGG

Altered gDNA sequence snippet

CATAAAGGCACAGGAAGAAGTGGAATTAAGCATCAGATAGG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MLLARMNPQV QPENNGADTG PEQPLRARKT AELLVVKERN GVQCLLAPRD GDAQPRETWG
KKIDFLLSVV GFAVDLANVW RFPYLCYKNG GGAFLIPYTL FLIIAGMPLF YMELALGQYN
REGAATVWKI CPFFKGVGYA VILIALYVGF YYNVIIAWSL YYLFSSFTLN LPWTDCGHTW
NSPNCTDPKL LNGSVLGNHT KYSKYKFTPA AEFYERGVLH LHESSGIHDI GLPQWQLLLC
LMVVVIVLYF SLWKGVKTSG KVVWITATLP YFVLFVLLVH GVTLPGASNG INAYLHIDFY
RLKEATVWID AATQIFFSLG AGFGVLIAFA SYNKFDNNCY RDALLTSSIN CITSFVSGFA
IFSILGYMAH EHKVNIEDVA TEGAGLVFIL YPEAISTLSG STFWAVVFFV MLLALGLDSS
MGGMEAVITG LADDFQVLKR HRKLFTFGVT FSTFLLALFC ITKGGIYVLT LLDTFAAGTS
ILFAVLMEAI GVSWFYGVDR FSNDIQQMMG FRPGLYWRLC WKFVSPAFLL RLAYGITPEN
EHHLVAQRDI RQFQLQHWLA I*

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

112 / 112

Last intron/exon boundary

1773

Theoretical NMD boundary in CDS

1611

Length of CDS

1686

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

23189

Chromosomal position

55679176

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:

16:55679176C>T_3_ENST00000574918

Back to summary table

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

Chr16:55679176C>T (GRCh38)

Gene symbol

SLC6A2

Gene constraints

LOEUF: 0.54, LOF (oe): 0.39, misssense (oe): 0.67, synonymous (oe): 1.03 ? (gnomAD)

Ensembl transcript ID

ENST00000574918.2

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.645-5967C>T
g.23189C>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	rs36020
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	1082	15091	16173

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.772	0.002
	-3.281	0
(flanking)	0.321	0.026

?

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

16

Strand

1

Original gDNA sequence snippet

CATAAAGGCACAGGAAGAAGCGGAATTAAGCATCAGATAGG

Altered gDNA sequence snippet

CATAAAGGCACAGGAAGAAGTGGAATTAAGCATCAGATAGG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MLLARMNPQV QPENNGADTG PEQPLRARKT AELLVVKERN GVQCLLAPRD GDAQPRETWG
KKIDFLLSVV GFAVDLANVW RFPYLCYKNG GGAFLIPYTL FLIIAGMPLF YMELALGQYN
REGAATVWKI CPFFKGVGYA VILIALYVGF YYNVIIAWSL YYLFSSFTLN LPWTDCGHTW
NSPNCTDPKL LNGSVLGNHT KYSKYKFTPA AEFYERGVLH LHESSGIHDI GLPQWQLLLC
LMVVVIVLYF SLWKGVKTSG KVWIDAATQI FFSLGAGFGV LIAFASYNKF DNNCYRDALL
TSSINCITSF VSGFAIFSIL GYMAHEHKVN IEDVATEGAG LVFILYPEAI STLSGSTFWA
VVFFVMLLAL GLDSSMGGME AVITGLADDF QVLKRHRKLF TFGVTFSTFL LALFCITKGG
IYVLTLLDTF AAGTSILFAV LMEAIGVSWF YGVDRFSNDI QQMMGFRPGL YWRLCWKFVS
PAFLLFVVVV SIINFKPLTY DDYIFPPWAN WVGWGIALSS MVLVPIYVIY KFLSTQGSLW
ERLAYGITPE NEHHLVAQRD IRQFQLQHWL AI*

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

1845

Theoretical NMD boundary in CDS

1644

Length of CDS

1719

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

23189

Chromosomal position

55679176

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:

16:55679176C>T_4_ENST00000561820

Back to summary table

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

Chr16:55679176C>T (GRCh38)

Gene symbol

SLC6A2

Gene constraints

LOEUF: 0.54, LOF (oe): 0.38, misssense (oe): 0.68, synonymous (oe): 1.03 ? (gnomAD)

Ensembl transcript ID

ENST00000561820.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.645-5967C>T
g.23189C>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	rs36020
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	1082	15091	16173

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.772	0.002
	-3.281	0
(flanking)	0.321	0.026

?

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

16

Strand

1

Original gDNA sequence snippet

CATAAAGGCACAGGAAGAAGCGGAATTAAGCATCAGATAGG

Altered gDNA sequence snippet

CATAAAGGCACAGGAAGAAGTGGAATTAAGCATCAGATAGG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MLLARMNPQV QPENNGADTG PEQPLRARKT AELLVVKERN GVQCLLAPRD GDAQPRETWG
KKIDFLLSVV GFAVDLANVW RFPYLCYKNG GGAFLIPYTL FLIIAGMPLF YMELALGQYN
REGAATVWKI CPFFKGVGYA VILIALYVGF YYNVIIAWSL YYLFSSFTLN LPWTDCGHTW
NSPNCTDPKL LNGSVLGNHT KYSKYKFTPA AEFYERGVLH LHESSGIHDI GLPQWQLLLC
LMVVVIVLYF SLWKGVKTSG KVVWITATLP YFVLFVLLVH GVTLPGASNG INAYLHIDFY
RLKEATVWID AATQIFFSLG AGFGVLIAFA SYNKFDNNCY RDALLTSSIN CITSFVSGFA
IFSILGYMAH EHKVNIEDVA TEGAGLVFIL YPEAISTLSG STFWAVVFFV MLLALGLDSS
MGGMEAVITG LADDFQVLKR HRKLFTFGVT FSTFLLALFC ITKGGIYVLT LLDTFAAGTS
ILFAVLMEAI GVSWFYGVDR FSNDIQQMMG FRPGLYWRLC WKFVSPAFLL FVVVVSIINF
KPLTYDDYIF PPWANWVGWG IALSSMVLVP IYVIYKFLST QGSLWEMKTR QGRRRATNSC
QISC*

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

78 / 78

Last intron/exon boundary

1835

Theoretical NMD boundary in CDS

1707

Length of CDS

1815

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

23189

Chromosomal position

55679176

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:

16:55679176C>T_5_ENST00000566163

Back to summary table

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

Chr16:55679176C>T (GRCh38)

Gene symbol

SLC6A2

Gene constraints

LOEUF: 0.54, LOF (oe): 0.39, misssense (oe): 0.67, synonymous (oe): 1.03 ? (gnomAD)

Ensembl transcript ID

ENST00000566163.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.645-5967C>T
g.23189C>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	rs36020
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	1082	15091	16173

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.772	0.002
	-3.281	0
(flanking)	0.321	0.026

?

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

16

Strand

1

Original gDNA sequence snippet

CATAAAGGCACAGGAAGAAGCGGAATTAAGCATCAGATAGG

Altered gDNA sequence snippet

CATAAAGGCACAGGAAGAAGTGGAATTAAGCATCAGATAGG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MLLARMNPQV QPENNGADTG PEQPLRARKT AELLVVKERN GVQCLLAPRD GDAQPRETWG
KKIDFLLSVV GFAVDLANVW RFPYLCYKNG GGAFLIPYTL FLIIAGMPLF YMELALGQYN
REGAATVWKI CPFFKGVGYA VILIALYVGF YYNVIIAWSL YYLFSSFTLN LPWTDCGHTW
NSPNCTDPKL LNGSVLGNHT KYSKYKFTPA AEFYERGVLH LHESSGIHDI GLPQWQLLLC
LMVVVIVLYF SLWKGVKTSG KVWIDAATQI FFSLGAGFGV LIAFASYNKF DNNCYRDALL
TSSINCITSF VSGFAIFSIL GYMAHEHKVN IEDVATEGAG LVFILYPEAI STLSGSTFWA
VVFFVMLLAL GLDSSMGGME AVITGLADDF QVLKRHRKLF TFGVTFSTFL LALFCITKGG
IYVLTLLDTF AAGTSILFAV LMEAIGVSWF YGVDRFSNDI QQMMGFRPGL YWRLCWKFVS
PAFLLFVVVV SIINFKPLTY DDYIFPPWAN WVGWGIALSS MVLVPIYVIY KFLSTQGSLW
ERLAYGITPE NEHHLVAQRD IRQFQLQHWL AI*

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

41 / 41

Last intron/exon boundary

1735

Theoretical NMD boundary in CDS

1644

Length of CDS

1719

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

23189

Chromosomal position

55679176

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:

16:55679176C>T_6_ENST00000567238

Back to summary table

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

Chr16:55679176C>T (GRCh38)

Gene symbol

SLC6A2

Gene constraints

LOEUF: 0.51, LOF (oe): 0.35, misssense (oe): 0.73, synonymous (oe): 1.00 ? (gnomAD)

Ensembl transcript ID

ENST00000567238.1

Genbank transcript ID

NM_001172502 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.330-5967C>T
g.23189C>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	rs36020
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	1082	15091	16173

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.772	0.002
	-3.281	0
(flanking)	0.321	0.026

?

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

16

Strand

1

Original gDNA sequence snippet

CATAAAGGCACAGGAAGAAGCGGAATTAAGCATCAGATAGG

Altered gDNA sequence snippet

CATAAAGGCACAGGAAGAAGTGGAATTAAGCATCAGATAGG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MGVQWWSHTQ GEVAVGLGLG DSYLTPCPCP GVGYAVILIA LYVGFYYNVI IAWSLYYLFS
SFTLNLPWTD CGHTWNSPNC TDPKLLNGSV LGNHTKYSKY KFTPAAEFYE RGVLHLHESS
GIHDIGLPQW QLLLCLMVVV IVLYFSLWKG VKTSGKVVWI TATLPYFVLF VLLVHGVTLP
GASNGINAYL HIDFYRLKEA TVWIDAATQI FFSLGAGFGV LIAFASYNKF DNNCYRDALL
TSSINCITSF VSGFAIFSIL GYMAHEHKVN IEDVATEGAG LVFILYPEAI STLSGSTFWA
VVFFVMLLAL GLDSSMGGME AVITGLADDF QVLKRHRKLF TFGVTFSTFL LALFCITKGG
IYVLTLLDTF AAGTSILFAV LMEAIGVSWF YGVDRFSNDI QQMMGFRPGL YWRLCWKFVS
PAFLLFVVVV SIINFKPLTY DDYIFPPWAN WVGWGIALSS MVLVPIYVIY KFLSTQGSLW
ERLAYGITPE NEHHLVAQRD IRQFQLQHWL AI*

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

177 / 177

Last intron/exon boundary

1691

Theoretical NMD boundary in CDS

1464

Length of CDS

1539

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

23189

Chromosomal position

55679176

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:

16:55679176C>T_7_ENST00000219833

Back to summary table

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

Chr16:55679176C>T (GRCh38)

Gene symbol

SLC6A2

Gene constraints

LOEUF: 0.53, LOF (oe): 0.38, misssense (oe): 0.69, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000219833.13

Genbank transcript ID

NM_001172504 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.645-5967C>T
g.23189C>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	rs36020
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	1082	15091	16173

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.772	0.002
	-3.281	0
(flanking)	0.321	0.026

?

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

16

Strand

1

Original gDNA sequence snippet

CATAAAGGCACAGGAAGAAGCGGAATTAAGCATCAGATAGG

Altered gDNA sequence snippet

CATAAAGGCACAGGAAGAAGTGGAATTAAGCATCAGATAGG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MLLARMNPQV QPENNGADTG PEQPLRARKT AELLVVKERN GVQCLLAPRD GDAQPRETWG
KKIDFLLSVV GFAVDLANVW RFPYLCYKNG GGAFLIPYTL FLIIAGMPLF YMELALGQYN
REGAATVWKI CPFFKGVGYA VILIALYVGF YYNVIIAWSL YYLFSSFTLN LPWTDCGHTW
NSPNCTDPKL LNGSVLGNHT KYSKYKFTPA AEFYERGVLH LHESSGIHDI GLPQWQLLLC
LMVVVIVLYF SLWKGVKTSG KVVWITATLP YFVLFVLLVH GVTLPGASNG INAYLHIDFY
RLKEATVWID AATQIFFSLG AGFGVLIAFA SYNKFDNNCY RDALLTSSIN CITSFVSGFA
IFSILGYMAH EHKVNIEDVA TEGAGLVFIL YPEAISTLSG STFWAVVFFV MLLALGLDSS
MGGMEAVITG LADDFQVLKR HRKLFTFGVT FSTFLLALFC ITKGGIYVLT LLDTFAAGTS
ILFAVLMEAI GVSWFYGVDR FSNDIQQMMG FRPGLYWRLC WKFVSPAFLL FVVVVSIINF
KPLTYDDYIF PPWANWVGWG IALSSMVLVP IYVIYKFLST QGSLWERLAY GITPENEHHL
VAQRDIRQFQ MKTRQGRRRA TNSCQISC*

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

442 / 442

Last intron/exon boundary

2271

Theoretical NMD boundary in CDS

1779

Length of CDS

1887

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

23189

Chromosomal position

55679176

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

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MutationT@ster 2025

Variant:

16:55679176C>T_8_ENST00000379906

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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

Chr16:55679176C>T (GRCh38)

Gene symbol

SLC6A2

Gene constraints

LOEUF: 0.52, LOF (oe): 0.37, misssense (oe): 0.68, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000379906.6

Genbank transcript ID

NM_001043 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.645-5967C>T
g.23189C>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	rs36020
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	1082	15091	16173

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.772	0.002
	-3.281	0
(flanking)	0.321	0.026

?

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

16

Strand

1

Original gDNA sequence snippet

CATAAAGGCACAGGAAGAAGCGGAATTAAGCATCAGATAGG

Altered gDNA sequence snippet

CATAAAGGCACAGGAAGAAGTGGAATTAAGCATCAGATAGG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MLLARMNPQV QPENNGADTG PEQPLRARKT AELLVVKERN GVQCLLAPRD GDAQPRETWG
KKIDFLLSVV GFAVDLANVW RFPYLCYKNG GGAFLIPYTL FLIIAGMPLF YMELALGQYN
REGAATVWKI CPFFKGVGYA VILIALYVGF YYNVIIAWSL YYLFSSFTLN LPWTDCGHTW
NSPNCTDPKL LNGSVLGNHT KYSKYKFTPA AEFYERGVLH LHESSGIHDI GLPQWQLLLC
LMVVVIVLYF SLWKGVKTSG KVVWITATLP YFVLFVLLVH GVTLPGASNG INAYLHIDFY
RLKEATVWID AATQIFFSLG AGFGVLIAFA SYNKFDNNCY RDALLTSSIN CITSFVSGFA
IFSILGYMAH EHKVNIEDVA TEGAGLVFIL YPEAISTLSG STFWAVVFFV MLLALGLDSS
MGGMEAVITG LADDFQVLKR HRKLFTFGVT FSTFLLALFC ITKGGIYVLT LLDTFAAGTS
ILFAVLMEAI GVSWFYGVDR FSNDIQQMMG FRPGLYWRLC WKFVSPAFLL FVVVVSIINF
KPLTYDDYIF PPWANWVGWG IALSSMVLVP IYVIYKFLST QGSLWERLAY GITPENEHHL
VAQRDIRQFQ LQHWLAI*

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

256 / 256

Last intron/exon boundary

2085

Theoretical NMD boundary in CDS

1779

Length of CDS

1854

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

23189

Chromosomal position

55679176

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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