MutationT@ster 2025

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Querying Taster for transcript #1: ENST00000252486
MT speed 0.06 s - this script 2.519077 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
ENST00000252486(MANE Select)	APOE	Benign	65\|35	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected

MutationT@ster 2025

Variant:

19:44908822C>T_1_ENST00000252486

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Prediction:

BenignPermalink

Summary:

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

Model: simple_aae
Tree vote: 65|35 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr19:44908822C>T (GRCh38)

Gene symbol

APOE

Gene constraints

LOEUF: 1.32, LOF (oe): 0.81, misssense (oe): 1.15, synonymous (oe): 1.14 ? (gnomAD)

Ensembl transcript ID

ENST00000252486.9

Genbank transcript ID

NM_000041 (exact from MANE), NM_001302691 (by similarity), NM_001302689 (by similarity), NM_001302690 (by similarity)

UniProt / AlphaMissense peptide

APOE_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.526C>T
g.3032C>T

AA changes

AAE:	R176C	?
Score:	180

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs7412
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	4609	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		176	R	L	L	R	D	A	D	D	L	Q	K	R	L	A	V	Y	Q	A	G	A	R	E	G	A
mutated	not conserved	176	R	L	L	R	D	A	D	D	L	Q	K	C	L	A	V	Y
Ptroglodytes	all identical	176	R	L	L	R	D	A	D	D	L	Q	K	R	L	A	V	Y
Mmulatta	all identical	176	R	L	L	R	D	A	D	D	L	Q	K	R	L	A	V	Y
Fcatus	no homologue
Mmusculus	all identical	168	R	L	M	R	D	A	E	D	L	Q	K	R	L	A	V	Y
Ggallus	no homologue
Trubripes	not conserved	410	R	L	N	K	D	A	E	Q	I	H	N	T	I	A	T	Y	M	G	E	I	Q	L	R
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all conserved	162	R	L	S	K	D	S	E	D	L	K	K	K	L	S	Q	Y

Protein features

Start (aa)	End (aa)	Feature	Details
19	317	CHAIN		lost
80	255	REGION	Repeat	lost
149	180	HELIX		lost
168	189	REPEAT		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.519	0.093
	0.906	0.143
(flanking)	2.004	0.189

?

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

19

Strand

1

Original gDNA sequence snippet

ATGCCGATGACCTGCAGAAGCGCCTGGCAGTGTACCAGGCC

Altered gDNA sequence snippet

ATGCCGATGACCTGCAGAAGTGCCTGGCAGTGTACCAGGCC

Original cDNA sequence snippet

ATGCCGATGACCTGCAGAAGCGCCTGGCAGTGTACCAGGCC

Altered cDNA sequence snippet

ATGCCGATGACCTGCAGAAGTGCCTGGCAGTGTACCAGGCC

Wildtype AA sequence

MKVLWAALLV TFLAGCQAKV EQAVETEPEP ELRQQTEWQS GQRWELALGR FWDYLRWVQT
LSEQVQEELL SSQVTQELRA LMDETMKELK AYKSELEEQL TPVAEETRAR LSKELQAAQA
RLGADMEDVC GRLVQYRGEV QAMLGQSTEE LRVRLASHLR KLRKRLLRDA DDLQKRLAVY
QAGAREGAER GLSAIRERLG PLVEQGRVRA ATVGSLAGQP LQERAQAWGE RLRARMEEMG
SRTRDRLDEV KEQVAEVRAK LEEQAQQIRL QAEAFQARLK SWFEPLVEDM QRQWAGLVEK
VQAAVGTSAA PVPSDNH*

Mutated AA sequence

MKVLWAALLV TFLAGCQAKV EQAVETEPEP ELRQQTEWQS GQRWELALGR FWDYLRWVQT
LSEQVQEELL SSQVTQELRA LMDETMKELK AYKSELEEQL TPVAEETRAR LSKELQAAQA
RLGADMEDVC GRLVQYRGEV QAMLGQSTEE LRVRLASHLR KLRKRLLRDA DDLQKCLAVY
QAGAREGAER GLSAIRERLG PLVEQGRVRA ATVGSLAGQP LQERAQAWGE RLRARMEEMG
SRTRDRLDEV KEQVAEVRAK LEEQAQQIRL QAEAFQARLK SWFEPLVEDM QRQWAGLVEK
VQAAVGTSAA PVPSDNH*

Position of stopcodon in wt / mu CDS

954 / 954

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

318 / 318

Position of stopcodon in wt / mu cDNA

1023 / 1023

Position of start ATG in wt / mu cDNA

70 / 70

Last intron/exon boundary

305

Theoretical NMD boundary in CDS

185

Length of CDS

954

Coding sequence (CDS) position

526

cDNA position

595

gDNA position

3032

Chromosomal position

44908822

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

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