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: ENST00000374135
Querying Taster for transcript #2: ENST00000431781
MT speed 0.28 s - this script 2.662618 s

Transcript summary:

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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
ENST00000374135(MANE Select)	GPN2	Deleterious	53\|47	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000431781	GPN2	Benign	18\|182	without_aae		No				Single base exchange		N/A

MutationT@ster 2025

Variant:

1:26889808C>A_1_ENST00000374135

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 53|47 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:26889808C>A (GRCh38)

Gene symbol

GPN2

Gene constraints

LOEUF: 1.22, LOF (oe): 0.84, misssense (oe): 1.00, synonymous (oe): 1.20 ? (gnomAD)

Ensembl transcript ID

ENST00000374135.9

Genbank transcript ID

NM_018066 (exact from MANE)

UniProt / AlphaMissense peptide

GPN2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.289G>T
g.476G>T

AA changes

AAE:	A97S	?
Score:	99

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs770046718
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	7	7

Protein conservation

Species	Match	AA	Alignment
Human		97	E	Y	L	E	A	N	L	D	W	L	R	A	K	L	D	P	L	R	G	H	Y	F	L	F
mutated	all conserved	97	E	Y	L	E	A	N	L	D	W	L	R	S	K	L	D	P	L	R	G	H	Y	F	L
Ptroglodytes	all identical	97	E	Y	L	E	A	N	L	D	W	L	R	A	K	L	D	P	L	R	G	H	Y	F	L
Mmulatta	all identical	97	E	Y	L	E	A	N	L	D	W	L	R	A	K	L	D	P	L	R	G	H	Y	F	L
Fcatus	all identical	97	E	Y	L	E	A	N	L	D	W	L	R	A	K	L	D	P	L	R	G	H	Y	F	L
Mmusculus	all identical	97	E	Y	L	E	A	N	L	D	W	L	R	A	K	L	E	P	L	R	G	H	Y	F	L
Ggallus	not conserved	100	E	Y	L	E	A	N	F	D	W	L	Q	E	K	L	A	A	F	R	G	H	Y	Y	L
Trubripes	not conserved	101	E	Y	V	E	A	N	L	D	W	L	E	N	K	L	K	Q	H	K	D	C	Y	F	L
Drerio	no homologue
Dmelanogaster	not conserved	103	E	Y	L	A	D	H	LE	D	W	L	L	P	A	L	R	K	L	S	ATY	N	Y	F	L
Celegans	not conserved	89	E	T	L	G	A	N	C	N	W	L	L	Q	K	I	E	A	N	H	K	K	Y	L	I
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
2	310	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.561	0.786
	1.666	0.677
(flanking)	-1.947	0

?

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

1

Strand

-1

Original gDNA sequence snippet

CCAACCTGGACTGGCTGCGTGCCAAGCTCGACCCCCTCCGC

Altered gDNA sequence snippet

CCAACCTGGACTGGCTGCGTTCCAAGCTCGACCCCCTCCGC

Original cDNA sequence snippet

CCAACCTGGACTGGCTGCGTGCCAAGCTCGACCCCCTCCGC

Altered cDNA sequence snippet

CCAACCTGGACTGGCTGCGTTCCAAGCTCGACCCCCTCCGC

Wildtype AA sequence

MAGAAPTTAF GQAVIGPPGS GKTTYCLGMS EFLRALGRRV AVVNLDPANE GLPYECAVDV
GELVGLGDVM DALRLGPNGG LLYCMEYLEA NLDWLRAKLD PLRGHYFLFD CPGQVELCTH
HGALRSIFSQ MAQWDLRLTA VHLVDSHYCT DPAKFISVLC TSLATMLHVE LPHINLLSKM
DLIEHYGKLA FNLDYYTEVL DLSYLLDHLA SDPFFRHYRQ LNEKLVQLIE DYSLVSFIPL
NIQDKESIQR VLQAVDKANG YCFRAQEQRS LEAMMSAAMG ADFHFSSTLG IQEKYLAPSN
QSVEQEAMQL *

Mutated AA sequence

MAGAAPTTAF GQAVIGPPGS GKTTYCLGMS EFLRALGRRV AVVNLDPANE GLPYECAVDV
GELVGLGDVM DALRLGPNGG LLYCMEYLEA NLDWLRSKLD PLRGHYFLFD CPGQVELCTH
HGALRSIFSQ MAQWDLRLTA VHLVDSHYCT DPAKFISVLC TSLATMLHVE LPHINLLSKM
DLIEHYGKLA FNLDYYTEVL DLSYLLDHLA SDPFFRHYRQ LNEKLVQLIE DYSLVSFIPL
NIQDKESIQR VLQAVDKANG YCFRAQEQRS LEAMMSAAMG ADFHFSSTLG IQEKYLAPSN
QSVEQEAMQL *

Position of stopcodon in wt / mu CDS

933 / 933

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

311 / 311

Position of stopcodon in wt / mu cDNA

1120 / 1120

Position of start ATG in wt / mu cDNA

188 / 188

Last intron/exon boundary

1047

Theoretical NMD boundary in CDS

809

Length of CDS

933

Coding sequence (CDS) position

289

cDNA position

476

gDNA position

476

Chromosomal position

26889808

Speed

0.24 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:

1:26889808C>A_2_ENST00000431781

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Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 18|182 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:26889808C>A (GRCh38)

Gene symbol

GPN2

Gene constraints

LOEUF: 1.66, LOF (oe): 1.00, misssense (oe): 1.12, synonymous (oe): 1.23 ? (gnomAD)

Ensembl transcript ID

ENST00000431781.2

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.153-76G>T
g.476G>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	rs770046718
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	7	7

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.561	0.786
	1.666	0.677
(flanking)	-1.947	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

1

Strand

-1

Original gDNA sequence snippet

CCAACCTGGACTGGCTGCGTGCCAAGCTCGACCCCCTCCGC

Altered gDNA sequence snippet

CCAACCTGGACTGGCTGCGTTCCAAGCTCGACCCCCTCCGC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAGAAPTTAF GQAVIGPPGS GKTTYCLGMS EFLRALGRRV AVVNLDPANE GRLAQHLLPN
GAVGPQADCR PPRGFSLLHR PCQVHFSTVY LPGHHAARGT APHQPPFQDG PH*

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

165 / 165

Last intron/exon boundary

681

Theoretical NMD boundary in CDS

466

Length of CDS

339

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

476

Chromosomal position

26889808

Speed

0.04 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