GeneBe

rs767283642

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001429.4(EP300):​c.2062C>G​(p.Leu688Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L688L) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)

Consequence

EP300
NM_001429.4 missense

Scores

2
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.11

Publications

0 publications found
Variant links:
Genes affected
EP300 (HGNC:3373): (E1A binding protein p300) This gene encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. It functions as histone acetyltransferase that regulates transcription via chromatin remodeling and is important in the processes of cell proliferation and differentiation. It mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein. This gene has also been identified as a co-activator of HIF1A (hypoxia-inducible factor 1 alpha), and thus plays a role in the stimulation of hypoxia-induced genes such as VEGF. Defects in this gene are a cause of Rubinstein-Taybi syndrome and may also play a role in epithelial cancer. [provided by RefSeq, Jul 2008]
EP300-AS1 (HGNC:50504): (EP300 antisense RNA 1)

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.192725).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001429.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
EP300
NM_001429.4
MANE Select
c.2062C>Gp.Leu688Val
missense
Exon 11 of 31NP_001420.2Q09472
EP300
NM_001362843.2
c.2054-1090C>G
intron
N/ANP_001349772.1A0A669KB12

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
EP300
ENST00000263253.9
TSL:1 MANE Select
c.2062C>Gp.Leu688Val
missense
Exon 11 of 31ENSP00000263253.7Q09472
EP300
ENST00000916082.1
c.2062C>Gp.Leu688Val
missense
Exon 11 of 31ENSP00000586141.1
EP300
ENST00000715703.1
c.2062C>Gp.Leu688Val
missense
Exon 11 of 31ENSP00000520505.1Q09472

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.064
BayesDel_addAF
Benign
-0.10
T
BayesDel_noAF
Benign
-0.38
CADD
Benign
15
DANN
Uncertain
0.98
DEOGEN2
Benign
0.37
T
Eigen
Benign
-0.37
Eigen_PC
Benign
-0.27
FATHMM_MKL
Uncertain
0.92
D
LIST_S2
Benign
0.82
T
M_CAP
Benign
0.014
T
MetaRNN
Benign
0.19
T
MetaSVM
Benign
-0.88
T
MutationAssessor
Benign
0.68
N
PhyloP100
1.1
PrimateAI
Benign
0.37
T
PROVEAN
Benign
-0.56
N
REVEL
Benign
0.12
Sift
Benign
0.23
T
Sift4G
Benign
0.77
T
Polyphen
0.34
B
Vest4
0.36
MutPred
0.13
Loss of glycosylation at P687 (P = 0.1143)
MVP
0.81
ClinPred
0.11
T
GERP RS
0.58
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.034
gMVP
0.18
Mutation Taster
=87/13
polymorphism

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs767283642; hg19: chr22-41542751; API