MutationT@ster 2025

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Querying Taster for transcript #1: ENST00000370575
MT speed 0.09 s - this script 2.550603 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
ENST00000370575(MANE Select)	PYROXD2	Deleterious	85\|15	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

10:98387303A>C_1_ENST00000370575

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 85|15 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:98387303A>C (GRCh38)

Gene symbol

PYROXD2

Gene constraints

LOEUF: 1.15, LOF (oe): 0.93, misssense (oe): 0.98, synonymous (oe): 0.92 ? (gnomAD)

Ensembl transcript ID

ENST00000370575.5

Genbank transcript ID

NM_032709 (exact from MANE)

UniProt / AlphaMissense peptide

PYRD2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1452T>G
g.27880T>G

AA changes

AAE:	F484L	?
Score:	22

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs4345897
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	5	5

Protein conservation

Species	Match	AA	Alignment
Human		484	E	Q	E	R	D	A	Y	A	D	R	V	F	D	C	I	E	V	Y	A	P	G	F	K	D
mutated	not conserved	484									D	R	V	L	D	C	I	E	V	Y	A	P	G	F	K
Ptroglodytes	all identical	484									D	R	V	F	D	C	I	E	V	Y	A	P	G	F	K
Mmulatta	all identical	547									D	R	V	F	D	C	I	E	V	Y	A	P	G	F	K
Fcatus	all identical	484									D	K	V	F	D	C	I	E	A	Y	A	P	G	F	K
Mmusculus	all identical	490			E	K	N	T	Y	A	D	K	V	F	D	C	I	E	A	Y	A	P	G	F	K
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	all identical	451	E	E	K	K	T	E	Y	A	K	H	V	F	S	E	I	D	A	Y	A	P	N	F	S
Xtropicalis	all identical	446	E	A	E	R	N	R	Y	A	D	T	V	F	D	W	I	E	K	Y	A	P	G	F	K

Protein features

Start (aa)	End (aa)	Feature	Details
1	581	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	5.923	1
	0.184	0.946
(flanking)	7.188	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

5

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

-1

Original gDNA sequence snippet

GTTTTTGGCACCCCAGTGTTTGATTGCATCGAGGTCTATGC

Altered gDNA sequence snippet

GTTTTTGGCACCCCAGTGTTGGATTGCATCGAGGTCTATGC

Original cDNA sequence snippet

GCTTATGCAGACAGAGTGTTTGATTGCATCGAGGTCTATGC

Altered cDNA sequence snippet

GCTTATGCAGACAGAGTGTTGGATTGCATCGAGGTCTATGC

Wildtype AA sequence

MAASGRGLCK AVAASPFPAW RRDNTEARGG LKPEYDAVVI GAGHNGLVAA AYLQRLGVNT
AVFERRHVIG GAAVTEEIIP GFKFSRASYL LSLLRPQIYT DLELKKHGLR LHLRNPYSFT
PMLEEGAGSK VPRCLLLGTD MAENQKQIAQ FSQKDAQVFP KYEEFMHRLA LAIDPLLDAA
PVDMAAFQHG SLLQRMRSLS TLKPLLKAGR ILGAQLPRYY EVLTAPITKV LDQWFESEPL
KATLATDAVI GAMTSPHTPG SGYVLLHHVM GGLEGMQGAW GYVQGGMGAL SDAIASSATT
HGASIFTEKT VAKVQVNSEG CVQGVVLEDG TEVRSKMVLS NTSPQITFLK LTPQEWLPEE
FLERISQLDT RSPVTKINVA VDRLPSFLAA PNAPRGQPLP HHQCSIHLNC EDTLLLHQAF
EDAMDGLPSH RPVIELCIPS SLDPTLAPPG CHVVSLFTQY MPYTLAGGKA WDEQERDAYA
DRVFDCIEVY APGFKDSVVG RDILTPPDLE RIFGLPGGNI FHCAMSLDQL YFARPVPLHS
GYRCPLQGLY LCGSGAHPGG GVMGAAGRNA AHVAFRDLKS M*

Mutated AA sequence

MAASGRGLCK AVAASPFPAW RRDNTEARGG LKPEYDAVVI GAGHNGLVAA AYLQRLGVNT
AVFERRHVIG GAAVTEEIIP GFKFSRASYL LSLLRPQIYT DLELKKHGLR LHLRNPYSFT
PMLEEGAGSK VPRCLLLGTD MAENQKQIAQ FSQKDAQVFP KYEEFMHRLA LAIDPLLDAA
PVDMAAFQHG SLLQRMRSLS TLKPLLKAGR ILGAQLPRYY EVLTAPITKV LDQWFESEPL
KATLATDAVI GAMTSPHTPG SGYVLLHHVM GGLEGMQGAW GYVQGGMGAL SDAIASSATT
HGASIFTEKT VAKVQVNSEG CVQGVVLEDG TEVRSKMVLS NTSPQITFLK LTPQEWLPEE
FLERISQLDT RSPVTKINVA VDRLPSFLAA PNAPRGQPLP HHQCSIHLNC EDTLLLHQAF
EDAMDGLPSH RPVIELCIPS SLDPTLAPPG CHVVSLFTQY MPYTLAGGKA WDEQERDAYA
DRVLDCIEVY APGFKDSVVG RDILTPPDLE RIFGLPGGNI FHCAMSLDQL YFARPVPLHS
GYRCPLQGLY LCGSGAHPGG GVMGAAGRNA AHVAFRDLKS M*

Position of stopcodon in wt / mu CDS

1746 / 1746

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

582 / 582

Position of stopcodon in wt / mu cDNA

1793 / 1793

Position of start ATG in wt / mu cDNA

48 / 48

Last intron/exon boundary

1722

Theoretical NMD boundary in CDS

1624

Length of CDS

1746

Coding sequence (CDS) position

1452

cDNA position

1499

gDNA position

27880

Chromosomal position

98387303

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

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