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: ENST00000645361
Querying Taster for transcript #2: ENST00000359033
MT speed 0.02 s - this script 2.402873 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
ENST00000645361(MANE Select)	CYP2D6	Deleterious	199\|1	without_aae		No				Single base exchange		N/A	Splice site lost
ENST00000359033	CYP2D6	Deleterious	200\|0	without_aae		No				Single base exchange		N/A	Splice site lost

MutationT@ster 2025

Variant:

22:42128945C>A_1_ENST00000645361

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Prediction:

DeleteriousPermalink

Summary:

Splice site lost

Model: without_aae
Tree vote: 199|1 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr22:42128945C>A (GRCh38)

Gene symbol

CYP2D6

Gene constraints

LOEUF: 1.71, LOF (oe): 1.36, misssense (oe): 1.15, synonymous (oe): 1.32 ? (gnomAD)

Ensembl transcript ID

ENST00000645361.2

Genbank transcript ID

NM_000106 (exact from MANE)

UniProt / AlphaMissense peptide

CP2D6_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.506-1G>T
g.1921G>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	rs3892097
	Allele 'A' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.912	1
	5.88	1
(flanking)	5.983	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor lost	1921	wt: 0.00 / mu: 0.00	-	wt: ccacccccag\|GACGCCCCTT mu: ccacccccat\|GACGCCCCTT

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

22

Strand

-1

Original gDNA sequence snippet

ACCCGCATCTCCCACCCCCAGGACGCCCCTTTCGCCCCAAC

Altered gDNA sequence snippet

ACCCGCATCTCCCACCCCCATGACGCCCCTTTCGCCCCAAC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MGLEALVPLA VIVAIFLLLV DLMHRRQRWA ARYPPGPLPL PGLGNLLHVD FQNTPYCFDQ
LRRRFGDVFS LQLAWTPVVV LNGLAAVREA LVTHGEDTAD RPPVPITQIL GFGPRSQGVF
LARYGPAWRE QRRFSVSTLR NLGLGKKSLE QWVTEEAACL CAAFANHSGR PFRPNGLLDK
AVSNVIASLT CGRRFEYDDP RFLRLLDLAQ EGLKEESGFL REVLNAVPVL LHIPALAGKV
LRFQKAFLTQ LDELLTEHRM TWDPAQPPRD LTEAFLAEME KAKGNPESSF NDENLRIVVA
DLFSAGMVTT STTLAWGLLL MILHPDVQRR VQQEIDDVIG QVRRPEMGDQ AHMPYTTAVI
HEVQRFGDIV PLGVTHMTSR DIEVQGFRIP KGTTLITNLS SVLKDEAVWE KPFRFHPEHF
LDAQGHFVKP EAFLPFSAGR RACLGEPLAR MELFLFFTSL LQHFSFSVPT GQPRPSHHGV
FAFLVSPSPY ELCAVPR*

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

20 / 20

Last intron/exon boundary

1334

Theoretical NMD boundary in CDS

1264

Length of CDS

1494

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

1921

Chromosomal position

42128945

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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MutationT@ster 2025

Variant:

22:42128945C>A_2_ENST00000359033

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Prediction:

DeleteriousPermalink

Summary:

Splice site lost

Model: without_aae
Tree vote: 200|0 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr22:42128945C>A (GRCh38)

Gene symbol

CYP2D6

Gene constraints

LOEUF: 1.71, LOF (oe): 1.33, misssense (oe): 1.13, synonymous (oe): 1.29 ? (gnomAD)

Ensembl transcript ID

ENST00000359033.4

Genbank transcript ID

NM_001025161 (by similarity)

UniProt / AlphaMissense peptide

CP2D6_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.353-1G>T
g.1921G>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	rs3892097
	Allele 'A' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.912	1
	5.88	1
(flanking)	5.983	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor lost	1921	wt: 0.00 / mu: 0.00	-	wt: ccacccccag\|GACGCCCCTT mu: ccacccccat\|GACGCCCCTT

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

22

Strand

-1

Original gDNA sequence snippet

ACCCGCATCTCCCACCCCCAGGACGCCCCTTTCGCCCCAAC

Altered gDNA sequence snippet

ACCCGCATCTCCCACCCCCATGACGCCCCTTTCGCCCCAAC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MGLEALVPLA VIVAIFLLLV DLMHRRQRWA ARYPPGPLPL PGLGNLLHVD FQNTPYCFDQ
LRRRFGDVFS LQLAWTPVVV LNGLAAVREA LVTHGEDTAD RPPVPITQIL GFGPRSQGRP
FRPNGLLDKA VSNVIASLTC GRRFEYDDPR FLRLLDLAQE GLKEESGFLR EVLNAVPVLL
HIPALAGKVL RFQKAFLTQL DELLTEHRMT WDPAQPPRDL TEAFLAEMEK AKGNPESSFN
DENLRIVVAD LFSAGMVTTS TTLAWGLLLM ILHPDVQRRV QQEIDDVIGQ VRRPEMGDQA
HMPYTTAVIH EVQRFGDIVP LGVTHMTSRD IEVQGFRIPK GTTLITNLSS VLKDEAVWEK
PFRFHPEHFL DAQGHFVKPE AFLPFSAGRR ACLGEPLARM ELFLFFTSLL QHFSFSVPTG
QPRPSHHGVF AFLVSPSPYE LCAVPR*

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

75 / 75

Last intron/exon boundary

1236

Theoretical NMD boundary in CDS

1111

Length of CDS

1341

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

1921

Chromosomal position

42128945

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

Back to summary table