3-53292123-TGC-GGG

Variant names:

• chr3-53292123-TGC-GGG
• NM_018403.7:c.1327_1329delGCAinsCCC
• DCP1A p.Ala443Pro

Variant summary

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

The NM_018403.7(DCP1A):​c.1327_1329delGCAinsCCC​(p.Ala443Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A443T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: DCP1A NM_018403.7 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57
• Publications: 0 publications found

Genes affected

DCP1A (HGNC:18714): (decapping mRNA 1A) Decapping is a key step in general and regulated mRNA decay. The protein encoded by this gene is a decapping enzyme. This protein and another decapping enzyme form a decapping complex, which interacts with the nonsense-mediated decay factor hUpf1 and may be recruited to mRNAs containing premature termination codons. This protein also participates in the TGF-beta signaling pathway. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Feb 2014]

ENSG00000302984 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018403.7. 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
	DCP1A	NM_018403.7	MANE Select	c.1327_1329delGCAinsCCC	p.Ala443Pro	missense	N/A	NP_060873.4
	DCP1A	NM_001290204.2		c.1213_1215delGCAinsCCC	p.Ala405Pro	missense	N/A	NP_001277133.1	Q9NPI6-2
	DCP1A	NM_001290205.2		c.1111_1113delGCAinsCCC	p.Ala371Pro	missense	N/A	NP_001277134.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCP1A	ENST00000610213.6	TSL:1 MANE Select	c.1327_1329delGCAinsCCC	p.Ala443Pro	missense	N/A	ENSP00000476386.1	Q9NPI6-1
	DCP1A	ENST00000863998.1		c.1369_1371delGCAinsCCC	p.Ala457Pro	missense	N/A	ENSP00000534057.1
	DCP1A	ENST00000918281.1		c.1324_1326delGCAinsCCC	p.Ala442Pro	missense	N/A	ENSP00000588340.1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.6

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: chr3-53326153;