15-55356247-CCC-TCG

Variant names:

• chr15-55356247-CCC-TCG
• NM_001204450.2:c.2395_2397delGGGinsCGA
• CCPG1 p.Gly799Arg

Variant summary

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

The NM_001204450.2(CCPG1):​c.2395_2397delGGGinsCGA​(p.Gly799Arg) variant causes a missense change. 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. G799W) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CCPG1 NM_001204450.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.07
• Publications: 0 publications found

Genes affected

CCPG1 (HGNC:24227): (cell cycle progression 1) Involved in positive regulation of cell cycle and positive regulation of cell population proliferation. Predicted to be integral component of membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

DNAAF4-CCPG1 (HGNC:43019): (DNAAF4-CCPG1 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring dyslexia susceptibility 1 candidate 1 (DYX1C1) and cell cycle progression 1 (CCPG1) genes on chromosome 15. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus unlikely to produce a protein product. [provided by RefSeq, Mar 2011]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001204450.2. 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
	CCPG1	NM_001204450.2	MANE Select	c.2395_2397delGGGinsCGA	p.Gly799Arg	missense	N/A	NP_001191379.1	Q9ULG6-5
	CCPG1	NM_001204451.2		c.1246_1248delGGGinsCGA	p.Gly416Arg	missense	N/A	NP_001191380.1	Q9ULG6-3
	CCPG1	NM_004748.6		c.*3250_*3252delGGGinsCGA		3_prime_UTR	Exon 8 of 8	NP_004739.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCPG1	ENST00000442196.8	TSL:2 MANE Select	c.2395_2397delGGGinsCGA	p.Gly799Arg	missense	N/A	ENSP00000403400.3	Q9ULG6-5
	CCPG1	ENST00000310958.10	TSL:1	c.*3250_*3252delGGGinsCGA		3_prime_UTR	Exon 8 of 8	ENSP00000311656.6	Q9ULG6-1
	CCPG1	ENST00000946865.1		c.2491_2493delGGGinsCGA	p.Gly831Arg	missense	N/A	ENSP00000616924.1

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		7.1

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: chr15-55648445;