MutationT@ster 2025

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Querying Taster for transcript #1: ENST00000260682
MT speed 0.07 s - this script 2.526699 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	Benign	68\|32	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected

MutationT@ster 2025

Variant:

10:94981296A>C_1_ENST00000260682

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Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 68|32 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr10:94981296A>C (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.1075A>C
g.42639A>C

AA changes

AAE:	I359L	?
Score:	5

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1057910
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	3705	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		359	T	D	A	V	V	H	E	V	Q	R	Y	I	D	L	L	P	T	S	L	P	H	A	V	T
mutated	all conserved	359	T	D	A	V	V	H	E	V	Q	R	Y	L	D	L	L	P	T	S	L	P	H	A	V
Ptroglodytes	all identical	359	T	D	A	V	V	H	E	V	Q	R	Y	I	D	L	L	P	T	S	L	P	H	A	V
Mmulatta	all identical	519						H	E	I	Q	R	Y	I	D	L	L	P	T	S	V	P	H	A	V
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
346	359	HELIX		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.135	0
	0.278	0
(flanking)	1.642	0.006

?

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

TGCACGAGGTCCAGAGATACATTGACCTTCTCCCCACCAGC

Altered gDNA sequence snippet

TGCACGAGGTCCAGAGATACCTTGACCTTCTCCCCACCAGC

Original cDNA sequence snippet

TGCACGAGGTCCAGAGATACATTGACCTTCTCCCCACCAGC

Altered cDNA sequence snippet

TGCACGAGGTCCAGAGATACCTTGACCTTCTCCCCACCAGC

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 IEDRVQEEAR CLVEELRKTK ASPCDPTFIL GCAPCNVICS
IIFHKRFDYK DQQFLNLMEK LNENIKILSS PWIQICNNFS PIIDYFPGTH NKLLKNVAFM
KSYILEKVKE HQESMDMNNP QDFIDCFLMK MEKEKHNQPS EFTIESLENT AVDLFGAGTE
TTSTTLRYAL LLLLKHPEVT AKVQEEIERV IGRNRSPCMQ DRSHMPYTDA VVHEVQRYLD
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

1075

cDNA position

1100

gDNA position

42639

Chromosomal position

94981296

Speed

0.07 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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