EPC1 p.Leu4Leu

Variant names:

• chr10-32346903-A-A
• NM_001272004.3:c.

Your query was ambiguous. Multiple possible variants found:

• chr10-32346904--
• chr10-32346906-G-A
• chr10-32346904-C-A
• chr10-32346904-C-G
• chr10-32346904-C-T
• chr10-32346904-CAG-TAA

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001272004.3(EPC1):​c. variant causes a exon region change involving the alteration of a non-conserved nucleotide. 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: 33)
• Consequence: EPC1 NM_001272004.3 exon_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 0 publications found

Genes affected

EPC1 (HGNC:19876): (enhancer of polycomb homolog 1) This gene encodes a member of the polycomb group (PcG) family. The encoded protein is a component of the NuA4 histone acetyltransferase complex and can act as both a transcriptional activator and repressor. The encoded protein has been linked to apoptosis, DNA repair, skeletal muscle differentiation, gene silencing, and adult T-cell leukemia/lymphoma. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]

EPC1-AS2 (HGNC:56646): (EPC1 antisense RNA 2)

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001272004.3. 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
	EPC1	NM_001272004.3	MANE Select	c.		exon_region	Exon 1 of 14	NP_001258933.1	Q9H2F5-2
	EPC1	NM_025209.5		c.		exon_region	Exon 1 of 15	NP_079485.1	Q9H2F5-1
	EPC1	NM_001382753.1		c.		exon_region	Exon 1 of 14	NP_001369682.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPC1	ENST00000319778.11	TSL:1 MANE Select	c.		exon_region	Exon 1 of 14	ENSP00000318559.6	Q9H2F5-2
	EPC1	ENST00000263062.8	TSL:1	c.		exon_region	Exon 1 of 15	ENSP00000263062.8	Q9H2F5-1
	EPC1	ENST00000375110.6	TSL:1	c.		intron	N/A	ENSP00000364251.2	Q9H2F5-3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr10-32635831;