22-41178965-TGTA-TGTAGTA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001429.4(EP300):​c.*13_*15dupGTA variant causes a 3 prime UTR change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 24)

Consequence

EP300
NM_001429.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.23
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
EP300NM_001429.4 linkuse as main transcriptc.*13_*15dupGTA 3_prime_UTR_variant 31/31 ENST00000263253.9 NP_001420.2 Q09472Q7Z6C1
EP300NM_001362843.2 linkuse as main transcriptc.*13_*15dupGTA 3_prime_UTR_variant 30/30 NP_001349772.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
EP300ENST00000263253.9 linkuse as main transcriptc.*13_*15dupGTA 3_prime_UTR_variant 31/311 NM_001429.4 ENSP00000263253.7 Q09472
EP300ENST00000674155.1 linkuse as main transcriptc.*13_*15dupGTA 3_prime_UTR_variant 30/30 ENSP00000501078.1 A0A669KB12
ENSG00000232754ENST00000415054.1 linkuse as main transcriptn.82+4095_82+4097dupTAC intron_variant 3
EP300-AS1ENST00000420537.1 linkuse as main transcriptn.224-4144_224-4142dupTAC intron_variant 3

Frequencies

GnomAD3 genomes
Cov.:
24
GnomAD4 exome
Cov.:
25
GnomAD4 genome
Cov.:
24

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr22-41574969; API