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: ENST00000368218
Querying Taster for transcript #2: ENST00000368216
Querying Taster for transcript #3: ENST00000524343
MT speed 0.22 s - this script 2.636541 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000368218	METTL25B	Deleterious	59\|41	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000524343	METTL25B	Deleterious	66\|34	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed
ENST00000368216(MANE Select)	METTL25B	Deleterious	69\|31	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

1:156729180G>A_1_ENST00000368218

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 59|41 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:156729180G>A (GRCh38)

Gene symbol

METTL25B

Gene constraints

LOEUF: 1.15, LOF (oe): 0.81, misssense (oe): 0.89, synonymous (oe): 0.85 ? (gnomAD)

Ensembl transcript ID

ENST00000368218.8

Genbank transcript ID

NM_001142560 (by similarity)

UniProt / AlphaMissense peptide

MT25B_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.76G>A
g.739G>A

AA changes

AAE:	A26T	?
Score:	58

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs776373198
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	2	2

Protein conservation

Species	Match	AA	Alignment
Human		26	K	Q	L	A	V	N	L	T	R	V	L	A	L	Y	R	S	I	L	D	A	Y	I	I	E
mutated	not conserved	26	K	Q	L	A	V	N	L	T	R	V	L	T	L	Y	R	S	I	L	D	A	Y	I	I
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	475	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.467	0.988
	0.916	0.983
(flanking)	2.845	0.972

?

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

TTAACCTCACCCGTGTCCTGGCACTCTACCGTTCCATCTTG

Altered gDNA sequence snippet

TTAACCTCACCCGTGTCCTGACACTCTACCGTTCCATCTTG

Original cDNA sequence snippet

TTAACCTCACCCGTGTCCTGGCACTCTACCGTTCCATCTTG

Altered cDNA sequence snippet

TTAACCTCACCCGTGTCCTGACACTCTACCGTTCCATCTTG

Wildtype AA sequence

MPGISARGLS HEGRKQLAVN LTRVLALYRS ILDAYIIEFF TDNLWDTLPC SWQEALDGLK
PPQLATMLLG MPGEGEVVRY RSVWPLTLLA LKSTACALAF TRMPGFQTPS EFLENPSQSS
RLTAPFRKHV RPKKQHEIRR LGELVKKLSD FTGCTQVVDV GSGQGHLSRF MALGLGLMVK
SIEGDQRLVE RAQRLDQELL QALEKEEKRN PQICAAGATA SGARSPAATE SGCPSGPRGP
GEPCGGLLQP GSTACPTGGD AYSTGPAAVP SGTGFPC*

Mutated AA sequence

MPGISARGLS HEGRKQLAVN LTRVLTLYRS ILDAYIIEFF TDNLWDTLPC SWQEALDGLK
PPQLATMLLG MPGEGEVVRY RSVWPLTLLA LKSTACALAF TRMPGFQTPS EFLENPSQSS
RLTAPFRKHV RPKKQHEIRR LGELVKKLSD FTGCTQVVDV GSGQGHLSRF MALGLGLMVK
SIEGDQRLVE RAQRLDQELL QALEKEEKRN PQICAAGATA SGARSPAATE SGCPSGPRGP
GEPCGGLLQP GSTACPTGGD AYSTGPAAVP SGTGFPC*

Position of stopcodon in wt / mu CDS

834 / 834

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

278 / 278

Position of stopcodon in wt / mu cDNA

1497 / 1497

Position of start ATG in wt / mu cDNA

664 / 664

Last intron/exon boundary

1484

Theoretical NMD boundary in CDS

770

Length of CDS

834

Coding sequence (CDS) position

76

cDNA position

739

gDNA position

739

Chromosomal position

156729180

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

MutationT@ster 2025

Variant:

1:156729180G>A_3_ENST00000524343

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 66|34 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:156729180G>A (GRCh38)

Gene symbol

METTL25B

Gene constraints

LOEUF: 1.50, LOF (oe): 0.73, misssense (oe): 0.90, synonymous (oe): 0.85 ? (gnomAD)

Ensembl transcript ID

ENST00000524343.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.76G>A
g.739G>A

AA changes

AAE:	A26T	?
Score:	58

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs776373198
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	2	2

Protein conservation

Species	Match	AA	Alignment
Human		26	K	Q	L	A	V	N	L	T	R	V	L	A	L	Y	R	S	I	L	D	A	Y	I	I	V
mutated	not conserved	26	K	Q	L	A	V	N	L	T	R	V	L	T	L	Y	R	S	I	L	D	A	Y	I	I
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)	0.467	0.988
	0.916	0.983
(flanking)	2.845	0.972

?

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

TTAACCTCACCCGTGTCCTGGCACTCTACCGTTCCATCTTG

Altered gDNA sequence snippet

TTAACCTCACCCGTGTCCTGACACTCTACCGTTCCATCTTG

Original cDNA sequence snippet

TTAACCTCACCCGTGTCCTGGCACTCTACCGTTCCATCTTG

Altered cDNA sequence snippet

TTAACCTCACCCGTGTCCTGACACTCTACCGTTCCATCTTG

Wildtype AA sequence

MPGISARGLS HEGRKQLAVN LTRVLALYRS ILDAYIIVQV SVATHPAGPE VHGVCPGLYP
DAWLSDPLRI PGEPQPELPT NSSIPETCQA QEAA*

Mutated AA sequence

MPGISARGLS HEGRKQLAVN LTRVLTLYRS ILDAYIIVQV SVATHPAGPE VHGVCPGLYP
DAWLSDPLRI PGEPQPELPT NSSIPETCQA QEAA*

Position of stopcodon in wt / mu CDS

285 / 285

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

95 / 95

Position of stopcodon in wt / mu cDNA

430 / 430

Position of start ATG in wt / mu cDNA

146 / 146

Last intron/exon boundary

449

Theoretical NMD boundary in CDS

253

Length of CDS

285

Coding sequence (CDS) position

76

cDNA position

221

gDNA position

739

Chromosomal position

156729180

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:

1:156729180G>A_2_ENST00000368216

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 69|31 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:156729180G>A (GRCh38)

Gene symbol

METTL25B

Gene constraints

LOEUF: 1.00, LOF (oe): 0.75, misssense (oe): 0.87, synonymous (oe): 0.85 ? (gnomAD)

Ensembl transcript ID

ENST00000368216.9

Genbank transcript ID

NM_015997 (exact from MANE)

UniProt / AlphaMissense peptide

MT25B_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.76G>A
g.739G>A

AA changes

AAE:	A26T	?
Score:	58

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs776373198
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	2	2

Protein conservation

Species	Match	AA	Alignment
Human		26	K	Q	L	A	V	N	L	T	R	V	L	A	L	Y	R	S	I	L	D	A	Y	I	I	E
mutated	not conserved	26	K	Q	L	A	V	N	L	T	R	V	L	T	L	Y	R	S	I	L	D	A	Y	I	I
Ptroglodytes	all identical	26	K	Q	L	A	V	N	L	T	R	V	L	A	L	Y	R	S	I	L	D	A	Y	I	I
Mmulatta	all identical	26	R	Q	L	A	V	N	L	T	R	V	L	A	L	Y	R	S	I	L	D	A	Y	I	I
Fcatus	all identical	26	R	Q	L	A	V	N	L	T	R	V	L	A	R	Y	R	P	I	L	D	A	Y	I	I
Mmusculus	all identical	26	R	Q	L	A	V	D	L	T	R	V	L	A	H	Y	R	S	I	L	D	A	Y	I	I
Ggallus	no alignment	n/a
Trubripes	all conserved	23	K	E	L	A	E	R	I	T	R	F	L	S	L	Y	T	H	I	S	D	S	Y	I	I
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all conserved	24	K	Q	L	A	E	Y	I	A	R	V	L	S	V	Y	G	F	I	T	D	S	Y	I	I

Protein features

Start (aa)	End (aa)	Feature	Details
1	475	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.467	0.988
	0.916	0.983
(flanking)	2.845	0.972

?

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

TTAACCTCACCCGTGTCCTGGCACTCTACCGTTCCATCTTG

Altered gDNA sequence snippet

TTAACCTCACCCGTGTCCTGACACTCTACCGTTCCATCTTG

Original cDNA sequence snippet

TTAACCTCACCCGTGTCCTGGCACTCTACCGTTCCATCTTG

Altered cDNA sequence snippet

TTAACCTCACCCGTGTCCTGACACTCTACCGTTCCATCTTG

Wildtype AA sequence

MPGISARGLS HEGRKQLAVN LTRVLALYRS ILDAYIIEFF TDNLWDTLPC SWQEALDGLK
PPQLATMLLG MPGEGEVVRY RSVWPLTLLA LKSTACALAF TRMPGFQTPS EFLENPSQSS
RLTAPFRKHV RPKKQHEIRR LGELVKKLSD FTGCTQVVDV GSGQGHLSRF MALGLGLMVK
SIEGDQRLVE RAQRLDQELL QALEKEEKRN PQVVQTSPRH SPHHVVRWVD PTALCEELLL
PLENPCQGRA RLLLTGLHAC GDLSVALLRH FSCCPEVVAL ASVGCCYMKL SDPGGYPLSQ
WVAGLPGYEL PYRLREGACH ALEEYAERLQ KAGPGLRTHC YRAALETVIR RARPELRRPG
VQGIPRVHEL KIEEYVQRGL QRVGLDPQLP LNLAALQAHV AQENRVVAFF SLALLLAPLV
ETLILLDRLL YLQEQGFHAE LLPIFSPELS PRNLVLVATK MPLGQALSVL ETEDS*

Mutated AA sequence

MPGISARGLS HEGRKQLAVN LTRVLTLYRS ILDAYIIEFF TDNLWDTLPC SWQEALDGLK
PPQLATMLLG MPGEGEVVRY RSVWPLTLLA LKSTACALAF TRMPGFQTPS EFLENPSQSS
RLTAPFRKHV RPKKQHEIRR LGELVKKLSD FTGCTQVVDV GSGQGHLSRF MALGLGLMVK
SIEGDQRLVE RAQRLDQELL QALEKEEKRN PQVVQTSPRH SPHHVVRWVD PTALCEELLL
PLENPCQGRA RLLLTGLHAC GDLSVALLRH FSCCPEVVAL ASVGCCYMKL SDPGGYPLSQ
WVAGLPGYEL PYRLREGACH ALEEYAERLQ KAGPGLRTHC YRAALETVIR RARPELRRPG
VQGIPRVHEL KIEEYVQRGL QRVGLDPQLP LNLAALQAHV AQENRVVAFF SLALLLAPLV
ETLILLDRLL YLQEQGFHAE LLPIFSPELS PRNLVLVATK MPLGQALSVL ETEDS*

Position of stopcodon in wt / mu CDS

1428 / 1428

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

476 / 476

Position of stopcodon in wt / mu cDNA

2064 / 2064

Position of start ATG in wt / mu cDNA

637 / 637

Last intron/exon boundary

1942

Theoretical NMD boundary in CDS

1255

Length of CDS

1428

Coding sequence (CDS) position

76

cDNA position

712

gDNA position

739

Chromosomal position

156729180

Speed

0.09 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