MutationT@ster 2025

NEVER press reload or F5 - unless you want to start from the very beginning.
Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000507166
Querying Taster for transcript #2: ENST00000257290
MT speed 0.05 s - this script 2.483497 s

Transcript summary:

Permalink

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
ENST00000257290(MANE Select)	PDGFRA	Deleterious	92\|8	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected

Some transcripts had annotation problems and are not shown

MutationT@ster 2025

Variant:

4:54274554G>C_2_ENST00000257290

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 92|8 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr4:54274554G>C (GRCh38)

Gene symbol

PDGFRA

Gene constraints

LOEUF: 0.26, LOF (oe): 0.17, misssense (oe): 0.73, synonymous (oe): 0.89 ? (gnomAD)

Ensembl transcript ID

ENST00000257290.10

Genbank transcript ID

NM_006206 (exact from MANE), NM_001347828 (by similarity), NM_001347829 (by similarity), NM_001347830 (by similarity)

UniProt / AlphaMissense peptide

PGFRA_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1582G>C
g.45275G>C

AA changes

AAE:	A528P	?
Score:	27

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

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

Protein conservation

Species	Match	AA	Alignment
Human		528	V	A	P	T	L	R	S	E	L	T	V	A	A	A	V	L	V	L	L	V	I	V	I	I
mutated	not conserved	528	V	A	P	T	L	R	S	E	L	T	V	P	A	A	V	L	V	L	L	V	I	V	I
Ptroglodytes	all identical	541	V	A	P	T	L	R	S	E	L	T	V	A	A	A	V	L	V	L	L	V	I	V	I
Mmulatta	all identical	529	V	A	P	T	L	R	S	E	L	T	V	A	A	A	V	L	V	L	L	V	I	V	I
Fcatus	all identical	528	V	A	P	T	L	R	S	E	L	T	V	A	A	A	V	L	V	L	L	V	I	V	I
Mmusculus	all identical	528	V	A	P	T	L	R	S	E	L	T	V	A	A	A	V	L	V	L	L	V	I	V	I
Ggallus	all identical	719	V	A	P	T	L	R	S	E	L	T	V	A	A	A	V	L	V	L	L	V	I	V	I
Trubripes	all identical	941	V	S	N	G	P	H	P	E	L	T	V	A	A	A	V	L	V	L	L	V	I	V	I
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all identical	531	V	A	P	T	L	R	S	E	L	T	V	A	A	A	V	L	V	L	L	V	I	V	I

Protein features

Start (aa)	End (aa)	Feature	Details
24	528	TOPO_DOM	Extracellular	lost
24	1089	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.703	1
	7.561	1
(flanking)	5.768	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

24

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

4

Strand

1

Original gDNA sequence snippet

TGCGTTCTGAACTCACGGTGGCTGCTGCAGTCCTGGTGCTG

Altered gDNA sequence snippet

TGCGTTCTGAACTCACGGTGCCTGCTGCAGTCCTGGTGCTG

Original cDNA sequence snippet

TGCGTTCTGAACTCACGGTGGCTGCTGCAGTCCTGGTGCTG

Altered cDNA sequence snippet

TGCGTTCTGAACTCACGGTGCCTGCTGCAGTCCTGGTGCTG

Wildtype AA sequence

MGTSHPAFLV LGCLLTGLSL ILCQLSLPSI LPNENEKVVQ LNSSFSLRCF GESEVSWQYP
MSEEESSDVE IRNEENNSGL FVTVLEVSSA SAAHTGLYTC YYNHTQTEEN ELEGRHIYIY
VPDPDVAFVP LGMTDYLVIV EDDDSAIIPC RTTDPETPVT LHNSEGVVPA SYDSRQGFNG
TFTVGPYICE ATVKGKKFQT IPFNVYALKA TSELDLEMEA LKTVYKSGET IVVTCAVFNN
EVVDLQWTYP GEVKGKGITM LEEIKVPSIK LVYTLTVPEA TVKDSGDYEC AARQATREVK
EMKKVTISVH EKGFIEIKPT FSQLEAVNLH EVKHFVVEVR AYPPPRISWL KNNLTLIENL
TEITTDVEKI QEIRYRSKLK LIRAKEEDSG HYTIVAQNED AVKSYTFELL TQVPSSILDL
VDDHHGSTGG QTVRCTAEGT PLPDIEWMIC KDIKKCNNET SWTILANNVS NIITEIHSRD
RSTVEGRVTF AKVEETIAVR CLAKNLLGAE NRELKLVAPT LRSELTVAAA VLVLLVIVII
SLIVLVVIWK QKPRYEIRWR VIESISPDGH EYIYVDPMQL PYDSRWEFPR DGLVLGRVLG
SGAFGKVVEG TAYGLSRSQP VMKVAVKMLK PTARSSEKQA LMSELKIMTH LGPHLNIVNL
LGACTKSGPI YIITEYCFYG DLVNYLHKNR DSFLSHHPEK PKKELDIFGL NPADESTRSY
VILSFENNGD YMDMKQADTT QYVPMLERKE VSKYSDIQRS LYDRPASYKK KSMLDSEVKN
LLSDDNSEGL TLLDLLSFTY QVARGMEFLA SKNCVHRDLA ARNVLLAQGK IVKICDFGLA
RDIMHDSNYV SKGSTFLPVK WMAPESIFDN LYTTLSDVWS YGILLWEIFS LGGTPYPGMM
VDSTFYNKIK SGYRMAKPDH ATSEVYEIMV KCWNSEPEKR PSFYHLSEIV ENLLPGQYKK
SYEKIHLDFL KSDHPAVARM RVDSDNAYIG VTYKNEEDKL KDWEGGLDEQ RLSADSGYII
PLPDIDPVPE EEDLGKRNRH SSQTSEESAI ETGSSSSTFI KREDETIEDI DMMDDIGIDS
SDLVEDSFL*

Mutated AA sequence

MGTSHPAFLV LGCLLTGLSL ILCQLSLPSI LPNENEKVVQ LNSSFSLRCF GESEVSWQYP
MSEEESSDVE IRNEENNSGL FVTVLEVSSA SAAHTGLYTC YYNHTQTEEN ELEGRHIYIY
VPDPDVAFVP LGMTDYLVIV EDDDSAIIPC RTTDPETPVT LHNSEGVVPA SYDSRQGFNG
TFTVGPYICE ATVKGKKFQT IPFNVYALKA TSELDLEMEA LKTVYKSGET IVVTCAVFNN
EVVDLQWTYP GEVKGKGITM LEEIKVPSIK LVYTLTVPEA TVKDSGDYEC AARQATREVK
EMKKVTISVH EKGFIEIKPT FSQLEAVNLH EVKHFVVEVR AYPPPRISWL KNNLTLIENL
TEITTDVEKI QEIRYRSKLK LIRAKEEDSG HYTIVAQNED AVKSYTFELL TQVPSSILDL
VDDHHGSTGG QTVRCTAEGT PLPDIEWMIC KDIKKCNNET SWTILANNVS NIITEIHSRD
RSTVEGRVTF AKVEETIAVR CLAKNLLGAE NRELKLVAPT LRSELTVPAA VLVLLVIVII
SLIVLVVIWK QKPRYEIRWR VIESISPDGH EYIYVDPMQL PYDSRWEFPR DGLVLGRVLG
SGAFGKVVEG TAYGLSRSQP VMKVAVKMLK PTARSSEKQA LMSELKIMTH LGPHLNIVNL
LGACTKSGPI YIITEYCFYG DLVNYLHKNR DSFLSHHPEK PKKELDIFGL NPADESTRSY
VILSFENNGD YMDMKQADTT QYVPMLERKE VSKYSDIQRS LYDRPASYKK KSMLDSEVKN
LLSDDNSEGL TLLDLLSFTY QVARGMEFLA SKNCVHRDLA ARNVLLAQGK IVKICDFGLA
RDIMHDSNYV SKGSTFLPVK WMAPESIFDN LYTTLSDVWS YGILLWEIFS LGGTPYPGMM
VDSTFYNKIK SGYRMAKPDH ATSEVYEIMV KCWNSEPEKR PSFYHLSEIV ENLLPGQYKK
SYEKIHLDFL KSDHPAVARM RVDSDNAYIG VTYKNEEDKL KDWEGGLDEQ RLSADSGYII
PLPDIDPVPE EEDLGKRNRH SSQTSEESAI ETGSSSSTFI KREDETIEDI DMMDDIGIDS
SDLVEDSFL*

Position of stopcodon in wt / mu CDS

3270 / 3270

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

1090 / 1090

Position of stopcodon in wt / mu cDNA

3405 / 3405

Position of start ATG in wt / mu cDNA

136 / 136

Last intron/exon boundary

3257

Theoretical NMD boundary in CDS

3071

Length of CDS

3270

Coding sequence (CDS) position

1582

cDNA position

1717

gDNA position

45275

Chromosomal position

54274554

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

Back to summary table

Problem:

1

MutationT@ster 2025

Data problem

No NCBI gene ID found.

Back to summary table