MutationT@ster 2025

NEVER press reload or F5 - unless you want to start from the very beginning.
Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000286479
Querying Taster for transcript #2: ENST00000520116
MT speed 0.18 s - this script 2.612841 s

Transcript summary:

Permalink

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
ENST00000520116	NAT2	Benign	66\|34	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Homozygous in gnomAD
ENST00000286479(MANE Select)	NAT2	Benign	69\|31	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected

MutationT@ster 2025

Variant:

8:18400593G>A_2_ENST00000520116

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD

Model: simple_aae
Tree vote: 66|34 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr8:18400593G>A (GRCh38)

Gene symbol

NAT2

Gene constraints

LOEUF: 1.94, LOF (oe): 3.39, misssense (oe): 1.19, synonymous (oe): 0.99 ? (gnomAD)

Ensembl transcript ID

ENST00000520116.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.200G>A
g.9312G>A

AA changes

AAE:	R67Q	?
Score:	43

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1799930
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		67	H	Q	K	I	Y	L	F	T	L	E	P	R	T	I	E	D	F	E	S	M	N	T	Y	L
mutated	all conserved	67						L	F	T	L	E	P	Q	T	I	E	D	F	E	S	M	N	T	Y
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

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.655	0.15
	1.089	0.13
(flanking)	-0.019	0.02

?

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

8

Strand

1

Original gDNA sequence snippet

CTTATTTACGCTTGAACCTCGAACAATTGAAGATTTTGAGT

Altered gDNA sequence snippet

CTTATTTACGCTTGAACCTCAAACAATTGAAGATTTTGAGT

Original cDNA sequence snippet

CTTATTTACGCTTGAACCTCGAACAATTGAAGATTTTGAGT

Altered cDNA sequence snippet

CTTATTTACGCTTGAACCTCAAACAATTGAAGATTTTGAGT

Wildtype AA sequence

MWQPLELISG KDQPQVPCIF CLTEERGIWY LDQIRREQYI TNKEFLNSHL LPKKKHQKIY
LFTLEPRTIE DFESMNTYLQ TSPTSSFITT SFCSLQTPEG VYCLVGFILT YRKFNYKDNT
DLVEFKTLTE EEVEEVLRNI FKISLGRNLV PKPGDGSLTI *

Mutated AA sequence

MWQPLELISG KDQPQVPCIF CLTEERGIWY LDQIRREQYI TNKEFLNSHL LPKKKHQKIY
LFTLEPQTIE DFESMNTYLQ TSPTSSFITT SFCSLQTPEG VYCLVGFILT YRKFNYKDNT
DLVEFKTLTE EEVEEVLRNI FKISLGRNLV PKPGDGSLTI *

Position of stopcodon in wt / mu CDS

483 / 483

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

161 / 161

Position of stopcodon in wt / mu cDNA

599 / 599

Position of start ATG in wt / mu cDNA

117 / 117

Last intron/exon boundary

59

Theoretical NMD boundary in CDS

cannot be calculated, distance between start ATG and last intron/exon boundary is too small

Length of CDS

483

Coding sequence (CDS) position

200

cDNA position

316

gDNA position

9312

Chromosomal position

18400593

Speed

0.10 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:

8:18400593G>A_1_ENST00000286479

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 69|31 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr8:18400593G>A (GRCh38)

Gene symbol

NAT2

Gene constraints

LOEUF: 1.94, LOF (oe): 3.39, misssense (oe): 1.22, synonymous (oe): 1.04 ? (gnomAD)

Ensembl transcript ID

ENST00000286479.4

Genbank transcript ID

NM_000015 (exact from MANE)

UniProt / AlphaMissense peptide

ARY2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.590G>A
g.9312G>A

AA changes

AAE:	R197Q	?
Score:	43

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1799930
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		197	H	Q	K	I	Y	L	F	T	L	E	P	R	T	I	E	D	F	E	S	M	N	T	Y	L
mutated	all conserved	197	H	Q	K	I	Y	L	F	T	L	E	P	Q	T	I	E	D	F	E	S	M	N	T	Y
Ptroglodytes	all identical	197	H	Q	K	I	Y	F	F	T	L	E	P	R	T	V	E	D	F	E	S	M	N	T	Y
Mmulatta	all identical	197	H	Q	K	V	Y	S	F	T	L	E	P	R	K	I	E	D	F	E	S	M	N	T	Y
Fcatus	all identical	197	Y	R	K	I	Y	S	F	T	L	E	P	R	T	I	E	D	F	E	S	V	N	T	Y
Mmusculus	all identical	487	Y	R	K	I	Y	S	F	T	L	E	P	R	T	I	E	D	F	E	S	M	N	T	Y
Ggallus	all identical	783	C	R	K	V	Y	M	F	S	L	E	P	R	T	V	E	D	F	C	F	Q	C	T	Y
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	290	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.655	0.15
	1.089	0.13
(flanking)	-0.019	0.02

?

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

8

Strand

1

Original gDNA sequence snippet

CTTATTTACGCTTGAACCTCGAACAATTGAAGATTTTGAGT

Altered gDNA sequence snippet

CTTATTTACGCTTGAACCTCAAACAATTGAAGATTTTGAGT

Original cDNA sequence snippet

CTTATTTACGCTTGAACCTCGAACAATTGAAGATTTTGAGT

Altered cDNA sequence snippet

CTTATTTACGCTTGAACCTCAAACAATTGAAGATTTTGAGT

Wildtype AA sequence

MDIEAYFERI GYKNSRNKLD LETLTDILEH QIRAVPFENL NMHCGQAMEL GLEAIFDHIV
RRNRGGWCLQ VNQLLYWALT TIGFQTTMLG GYFYIPPVNK YSTGMVHLLL QVTIDGRNYI
VDAGSGSSSQ MWQPLELISG KDQPQVPCIF CLTEERGIWY LDQIRREQYI TNKEFLNSHL
LPKKKHQKIY LFTLEPRTIE DFESMNTYLQ TSPTSSFITT SFCSLQTPEG VYCLVGFILT
YRKFNYKDNT DLVEFKTLTE EEVEEVLRNI FKISLGRNLV PKPGDGSLTI *

Mutated AA sequence

MDIEAYFERI GYKNSRNKLD LETLTDILEH QIRAVPFENL NMHCGQAMEL GLEAIFDHIV
RRNRGGWCLQ VNQLLYWALT TIGFQTTMLG GYFYIPPVNK YSTGMVHLLL QVTIDGRNYI
VDAGSGSSSQ MWQPLELISG KDQPQVPCIF CLTEERGIWY LDQIRREQYI TNKEFLNSHL
LPKKKHQKIY LFTLEPQTIE DFESMNTYLQ TSPTSSFITT SFCSLQTPEG VYCLVGFILT
YRKFNYKDNT DLVEFKTLTE EEVEEVLRNI FKISLGRNLV PKPGDGSLTI *

Position of stopcodon in wt / mu CDS

873 / 873

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

291 / 291

Position of stopcodon in wt / mu cDNA

943 / 943

Position of start ATG in wt / mu cDNA

71 / 71

Last intron/exon boundary

64

Theoretical NMD boundary in CDS

cannot be calculated, distance between start ATG and last intron/exon boundary is too small

Length of CDS

873

Coding sequence (CDS) position

590

cDNA position

660

gDNA position

9312

Chromosomal position

18400593

Speed

0.08 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