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: ENST00000274353
Querying Taster for transcript #2: ENST00000524080
MT speed 0.19 s - this script 2.621548 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
ENST00000274353(MANE Select)	BHMT	Deleterious	96\|4	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000524080	BHMT	Deleterious	97\|3	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed

MutationT@ster 2025

Variant:

5:79115893G>A_1_ENST00000274353

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 96|4 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr5:79115893G>A (GRCh38)

Gene symbol

BHMT

Gene constraints

LOEUF: 0.88, LOF (oe): 0.66, misssense (oe): 0.82, synonymous (oe): 0.91 ? (gnomAD)

Ensembl transcript ID

ENST00000274353.10

Genbank transcript ID

NM_001713 (exact from MANE)

UniProt / AlphaMissense peptide

BHMT1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.160G>A
g.4085G>A

AA changes

AAE:	E54K	?
Score:	56

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1756379987
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		54	P	W	T	P	E	A	A	V	E	H	P	E	A	V	R	Q	L	H	R	E	F	L	R	A
mutated	all conserved	54	P	W	T	P	E	A	A	V	E	H	P	K	A	V	R	Q	L	H
Ptroglodytes	all identical	118	P	W	T	P	E	A	A	V	E	H	P	E	A	V	R	Q	L	H
Mmulatta	all identical	118	P	W	T	P	E	A	A	V	E	H	P	E	A	V	R	Q	L	H
Fcatus	all identical	54	P	W	T	P	E	A	A	V	E	H	P	E	A	V	R	Q	L	H
Mmusculus	all identical	54	P	W	T	P	E	A	A	V	E	H	P	E	A	V	R	Q	L	H
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	406	CHAIN		lost
11	314	DOMAIN	Hcy-binding	lost
53	66	HELIX		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0	0.821
	9.602	1
(flanking)	8.947	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

7

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

5

Strand

1

Original gDNA sequence snippet

AAGCTGCTGTGGAGCACCCAGAAGCAGGTTGGTGCAGAGCT

Altered gDNA sequence snippet

AAGCTGCTGTGGAGCACCCAAAAGCAGGTTGGTGCAGAGCT

Original cDNA sequence snippet

AAGCTGCTGTGGAGCACCCAGAAGCAGTTCGCCAGCTTCAT

Altered cDNA sequence snippet

AAGCTGCTGTGGAGCACCCAAAAGCAGTTCGCCAGCTTCAT

Wildtype AA sequence

MPPVGGKKAK KGILERLNAG EIVIGDGGFV FALEKRGYVK AGPWTPEAAV EHPEAVRQLH
REFLRAGSNV MQTFTFYASE DKLENRGNYV LEKISGQEVN EAACDIARQV ADEGDALVAG
GVSQTPSYLS CKSETEVKKV FLQQLEVFMK KNVDFLIAEY FEHVEEAVWA VETLIASGKP
VAATMCIGPE GDLHGVPPGE CAVRLVKAGA SIIGVNCHFD PTISLKTVKL MKEGLEAARL
KAHLMSQPLA YHTPDCNKQG FIDLPEFPFG LEPRVATRWD IQKYAREAYN LGVRYIGGCC
GFEPYHIRAI AEELAPERGF LPPASEKHGS WGSGLDMHTK PWVRARARKE YWENLRIASG
RPYNPSMSKP DGWGVTKGTA ELMQQKEATT EQQLKELFEK QKFKSQ*

Mutated AA sequence

MPPVGGKKAK KGILERLNAG EIVIGDGGFV FALEKRGYVK AGPWTPEAAV EHPKAVRQLH
REFLRAGSNV MQTFTFYASE DKLENRGNYV LEKISGQEVN EAACDIARQV ADEGDALVAG
GVSQTPSYLS CKSETEVKKV FLQQLEVFMK KNVDFLIAEY FEHVEEAVWA VETLIASGKP
VAATMCIGPE GDLHGVPPGE CAVRLVKAGA SIIGVNCHFD PTISLKTVKL MKEGLEAARL
KAHLMSQPLA YHTPDCNKQG FIDLPEFPFG LEPRVATRWD IQKYAREAYN LGVRYIGGCC
GFEPYHIRAI AEELAPERGF LPPASEKHGS WGSGLDMHTK PWVRARARKE YWENLRIASG
RPYNPSMSKP DGWGVTKGTA ELMQQKEATT EQQLKELFEK QKFKSQ*

Position of stopcodon in wt / mu CDS

1221 / 1221

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

407 / 407

Position of stopcodon in wt / mu cDNA

1298 / 1298

Position of start ATG in wt / mu cDNA

78 / 78

Last intron/exon boundary

1114

Theoretical NMD boundary in CDS

986

Length of CDS

1221

Coding sequence (CDS) position

160

cDNA position

237

gDNA position

4085

Chromosomal position

79115893

Speed

0.13 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:

5:79115893G>A_2_ENST00000524080

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 97|3 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr5:79115893G>A (GRCh38)

Gene symbol

BHMT

Gene constraints

LOEUF: 0.98, LOF (oe): 0.68, misssense (oe): 0.81, synonymous (oe): 0.94 ? (gnomAD)

Ensembl transcript ID

ENST00000524080.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.160G>A
g.4085G>A

AA changes

AAE:	E54K	?
Score:	56

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1756379987
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		54	P	W	T	P	E	A	A	V	E	H	P	E	A	G	A	S	I	I	G	V	N	C	H	F
mutated	all conserved	54	P	W	T	P	E	A	A	V	E	H	P	K	A	G	A	S	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	0.821
	9.602	1
(flanking)	8.947	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

7

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

5

Strand

1

Original gDNA sequence snippet

AAGCTGCTGTGGAGCACCCAGAAGCAGGTTGGTGCAGAGCT

Altered gDNA sequence snippet

AAGCTGCTGTGGAGCACCCAAAAGCAGGTTGGTGCAGAGCT

Original cDNA sequence snippet

AAGCTGCTGTGGAGCACCCAGAAGCAGGAGCATCCATCATT

Altered cDNA sequence snippet

AAGCTGCTGTGGAGCACCCAAAAGCAGGAGCATCCATCATT

Wildtype AA sequence

MPPVGGKKAK KGILERLNAG EIVIGDGGFV FALEKRGYVK AGPWTPEAAV EHPEAGASII
GVNCHFDPTI SLKTVKLMKE GLEAARLKAH LMSQPLAYHT PDCNKQGFID LPEFPFGLEP
RVATRWDIQK YAREAYNLGV RYIGGCCGFE PYHIRAIAEE LAPERGFLPP ASEKHGSWGS
GLDMHTKPWV RARARKEYWE NLRIASGRPY NPSMSKPDGW GVTKGTAELM QQKEATTEQQ
LKELFEKQKF KSQ*

Mutated AA sequence

MPPVGGKKAK KGILERLNAG EIVIGDGGFV FALEKRGYVK AGPWTPEAAV EHPKAGASII
GVNCHFDPTI SLKTVKLMKE GLEAARLKAH LMSQPLAYHT PDCNKQGFID LPEFPFGLEP
RVATRWDIQK YAREAYNLGV RYIGGCCGFE PYHIRAIAEE LAPERGFLPP ASEKHGSWGS
GLDMHTKPWV RARARKEYWE NLRIASGRPY NPSMSKPDGW GVTKGTAELM QQKEATTEQQ
LKELFEKQKF KSQ*

Position of stopcodon in wt / mu CDS

762 / 762

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

254 / 254

Position of stopcodon in wt / mu cDNA

839 / 839

Position of start ATG in wt / mu cDNA

78 / 78

Last intron/exon boundary

655

Theoretical NMD boundary in CDS

527

Length of CDS

762

Coding sequence (CDS) position

160

cDNA position

237

gDNA position

4085

Chromosomal position

79115893

Speed

0.06 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