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: ENST00000260682
Querying Taster for transcript #2: ENST00000461906
MT speed 0.11 s - this script 2.541741 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
ENST00000260682(MANE Select)	CYP2C9	Deleterious	69\|31	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000461906	CYP2C9	Deleterious	70\|30	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

10:94942290C>A_1_ENST00000260682

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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

Chr10:94942290C>A (GRCh38)

Gene symbol

CYP2C9

Gene constraints

LOEUF: 1.61, LOF (oe): 1.27, misssense (oe): 1.23, synonymous (oe): 1.25 ? (gnomAD)

Ensembl transcript ID

ENST00000260682.8

Genbank transcript ID

NM_000771 (exact from MANE)

UniProt / AlphaMissense peptide

CP2C9_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.430C>A
g.3633C>A

AA changes

AAE:	R144S	?
Score:	110

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		144	N	F	G	M	G	K	R	S	I	E	D	R	V	Q	E	E	A	R	C	L	V	E	E	L
mutated	not conserved	144	N	F	G	M	G	K	R	S	I	E	D	S	V	Q	E	E	A	R	C	L	V	E	E
Ptroglodytes	all identical	144	N	F	G	M	G	K	R	S	I	E	D	R	V	Q	E	E	A	R	C	L	V	E	E
Mmulatta	not conserved	300	NTAVDL	F	G	A	G	T	E	T	T	S	T	T	L	R	Y	A	L	L	L	L	L	K	H
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	490	CHAIN		lost
141	157	HELIX		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.574	0
	-0.052	0.004
(flanking)	3.931	0.614

?

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

10

Strand

1

Original gDNA sequence snippet

GGAAGAGGAGCATTGAGGACCGTGTTCAAGAGGAAGCCCGC

Altered gDNA sequence snippet

GGAAGAGGAGCATTGAGGACAGTGTTCAAGAGGAAGCCCGC

Original cDNA sequence snippet

GGAAGAGGAGCATTGAGGACCGTGTTCAAGAGGAAGCCCGC

Altered cDNA sequence snippet

GGAAGAGGAGCATTGAGGACAGTGTTCAAGAGGAAGCCCGC

Wildtype AA sequence

MDSLVVLVLC LSCLLLLSLW RQSSGRGKLP PGPTPLPVIG NILQIGIKDI SKSLTNLSKV
YGPVFTLYFG LKPIVVLHGY EAVKEALIDL GEEFSGRGIF PLAERANRGF GIVFSNGKKW
KEIRRFSLMT LRNFGMGKRS IEDRVQEEAR CLVEELRKTK ASPCDPTFIL GCAPCNVICS
IIFHKRFDYK DQQFLNLMEK LNENIKILSS PWIQICNNFS PIIDYFPGTH NKLLKNVAFM
KSYILEKVKE HQESMDMNNP QDFIDCFLMK MEKEKHNQPS EFTIESLENT AVDLFGAGTE
TTSTTLRYAL LLLLKHPEVT AKVQEEIERV IGRNRSPCMQ DRSHMPYTDA VVHEVQRYID
LLPTSLPHAV TCDIKFRNYL IPKGTTILIS LTSVLHDNKE FPNPEMFDPH HFLDEGGNFK
KSKYFMPFSA GKRICVGEAL AGMELFLFLT SILQNFNLKS LVDPKNLDTT PVVNGFASVP
PFYQLCFIPV *

Mutated AA sequence

MDSLVVLVLC LSCLLLLSLW RQSSGRGKLP PGPTPLPVIG NILQIGIKDI SKSLTNLSKV
YGPVFTLYFG LKPIVVLHGY EAVKEALIDL GEEFSGRGIF PLAERANRGF GIVFSNGKKW
KEIRRFSLMT LRNFGMGKRS IEDSVQEEAR CLVEELRKTK ASPCDPTFIL GCAPCNVICS
IIFHKRFDYK DQQFLNLMEK LNENIKILSS PWIQICNNFS PIIDYFPGTH NKLLKNVAFM
KSYILEKVKE HQESMDMNNP QDFIDCFLMK MEKEKHNQPS EFTIESLENT AVDLFGAGTE
TTSTTLRYAL LLLLKHPEVT AKVQEEIERV IGRNRSPCMQ DRSHMPYTDA VVHEVQRYID
LLPTSLPHAV TCDIKFRNYL IPKGTTILIS LTSVLHDNKE FPNPEMFDPH HFLDEGGNFK
KSKYFMPFSA GKRICVGEAL AGMELFLFLT SILQNFNLKS LVDPKNLDTT PVVNGFASVP
PFYQLCFIPV *

Position of stopcodon in wt / mu CDS

1473 / 1473

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

491 / 491

Position of stopcodon in wt / mu cDNA

1498 / 1498

Position of start ATG in wt / mu cDNA

26 / 26

Last intron/exon boundary

1316

Theoretical NMD boundary in CDS

1240

Length of CDS

1473

Coding sequence (CDS) position

430

cDNA position

455

gDNA position

3633

Chromosomal position

94942290

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

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MutationT@ster 2025

Variant:

10:94942290C>A_2_ENST00000461906

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 70|30 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:94942290C>A (GRCh38)

Gene symbol

CYP2C9

Gene constraints

LOEUF: 1.43, LOF (oe): 0.86, misssense (oe): 1.23, synonymous (oe): 1.29 ? (gnomAD)

Ensembl transcript ID

ENST00000461906.1

Genbank transcript ID

UniProt / AlphaMissense peptide

CP2C9_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.430C>A
g.3633C>A

AA changes

AAE:	R144S	?
Score:	110

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		144	N	F	G	M	G	K	R	S	I	E	D	R	V	Q	E	E	A	R	C	L	V	E	E	L
mutated	not conserved	144	N	F	G	M	G	K	R	S	I	E	D	S	V	Q	E	E	A	R	C	L	V	E	E
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	490	CHAIN		lost
141	157	HELIX		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.574	0
	-0.052	0.004
(flanking)	3.931	0.614

?

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

10

Strand

1

Original gDNA sequence snippet

GGAAGAGGAGCATTGAGGACCGTGTTCAAGAGGAAGCCCGC

Altered gDNA sequence snippet

GGAAGAGGAGCATTGAGGACAGTGTTCAAGAGGAAGCCCGC

Original cDNA sequence snippet

GGAAGAGGAGCATTGAGGACCGTGTTCAAGAGGAAGCCCGC

Altered cDNA sequence snippet

GGAAGAGGAGCATTGAGGACAGTGTTCAAGAGGAAGCCCGC

Wildtype AA sequence

MDSLVVLVLC LSCLLLLSLW RQSSGRGKLP PGPTPLPVIG NILQIGIKDI SKSLTNLSKV
YGPVFTLYFG LKPIVVLHGY EAVKEALIDL GEEFSGRGIF PLAERANRGF GIVFSNGKKW
KEIRRFSLMT LRNFGMGKRS IEDRVQEEAR CLVEELRKTK GG*

Mutated AA sequence

MDSLVVLVLC LSCLLLLSLW RQSSGRGKLP PGPTPLPVIG NILQIGIKDI SKSLTNLSKV
YGPVFTLYFG LKPIVVLHGY EAVKEALIDL GEEFSGRGIF PLAERANRGF GIVFSNGKKW
KEIRRFSLMT LRNFGMGKRS IEDSVQEEAR CLVEELRKTK GG*

Position of stopcodon in wt / mu CDS

489 / 489

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

163 / 163

Position of stopcodon in wt / mu cDNA

514 / 514

Position of start ATG in wt / mu cDNA

26 / 26

Last intron/exon boundary

356

Theoretical NMD boundary in CDS

280

Length of CDS

489

Coding sequence (CDS) position

430

cDNA position

455

gDNA position

3633

Chromosomal position

94942290

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