NM_001258345.3:c.721_723delCCAinsAGT

Variant names:

• chr4-20727315-CCA-AGT
• NM_001258345.3:c.721_723delCCAinsAGT
• PACRGL p.Pro241Ser

Variant summary

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

The NM_001258345.3(PACRGL):​c.721_723delCCAinsAGT​(p.Pro241Ser) 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. P241T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PACRGL NM_001258345.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.34
• Publications: 0 publications found

Genes affected

PACRGL (HGNC:28442): (parkin coregulated like)

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001258345.3. 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
	PACRGL	NM_001258345.3	MANE Select	c.721_723delCCAinsAGT	p.Pro241Ser	missense	N/A	NP_001245274.1	Q8N7B6-1
	PACRGL	NM_145048.5		c.640_642delCCAinsAGT	p.Pro214Ser	missense	N/A	NP_659485.1	Q8N7B6-2
	PACRGL	NM_001317849.3		c.481_483delCCAinsAGT	p.Pro161Ser	missense	N/A	NP_001304778.1	D6RGK2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PACRGL	ENST00000503585.6	TSL:2 MANE Select	c.721_723delCCAinsAGT	p.Pro241Ser	missense	N/A	ENSP00000423881.1	Q8N7B6-1
	PACRGL	ENST00000360916.9	TSL:1	c.640_642delCCAinsAGT	p.Pro214Ser	missense	N/A	ENSP00000354171.4	Q8N7B6-2
	PACRGL	ENST00000508952.5	TSL:1	n.*348_*350delCCAinsAGT		non_coding_transcript_exon	Exon 8 of 8	ENSP00000425102.1	D6RBZ2

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		5.3

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: chr4-20728938;