rs1555912151
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 3P and 4B. PM4PP3BS2
The NM_001429.4(EP300):c.5556_5564delTGCCACTCC(p.Ala1853_Pro1855del) variant causes a disruptive inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,461,886 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000062 ( 1 hom. )
Consequence
EP300
NM_001429.4 disruptive_inframe_deletion
NM_001429.4 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.87
Publications
0 publications found
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]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_001429.4.
PP3
No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
BS2
High AC in GnomAdExome4 at 9 AD gene.
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. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| EP300 | MANE Select | c.5556_5564delTGCCACTCC | p.Ala1853_Pro1855del | disruptive_inframe_deletion | Exon 31 of 31 | NP_001420.2 | Q09472 | ||
| EP300 | c.5478_5486delTGCCACTCC | p.Ala1827_Pro1829del | disruptive_inframe_deletion | Exon 30 of 30 | NP_001349772.1 | A0A669KB12 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| EP300 | TSL:1 MANE Select | c.5556_5564delTGCCACTCC | p.Ala1853_Pro1855del | disruptive_inframe_deletion | Exon 31 of 31 | ENSP00000263253.7 | Q09472 | ||
| EP300 | c.5586_5594delTGCCACTCC | p.Ala1863_Pro1865del | disruptive_inframe_deletion | Exon 31 of 31 | ENSP00000586141.1 | ||||
| EP300 | c.5556_5564delTGCCACTCC | p.Ala1853_Pro1855del | disruptive_inframe_deletion | Exon 31 of 31 | ENSP00000520505.1 | Q09472 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461886Hom.: 1 AF XY: 0.00000688 AC XY: 5AN XY: 727242 show subpopulations
GnomAD4 exome
AF:
AC:
9
AN:
1461886
Hom.:
AF XY:
AC XY:
5
AN XY:
727242
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33480
American (AMR)
AF:
AC:
0
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
0
AN:
39700
South Asian (SAS)
AF:
AC:
2
AN:
86256
European-Finnish (FIN)
AF:
AC:
0
AN:
53416
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
7
AN:
1112010
Other (OTH)
AF:
AC:
0
AN:
60396
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.454
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, multiple submitters, no conflicts
Pathogenic
VUS
Benign
Condition
-
1
-
Inborn genetic diseases (1)
-
1
-
Rubinstein-Taybi syndrome due to EP300 haploinsufficiency (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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