1-88805670-AGT-TCA

Variant names:

• chr1-88805670-AGG-TCA
• NM_006256.4:c.1675_1676+1delAGGinsTCA
• PKN2 p.560

Variant summary

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

The NM_006256.4(PKN2):​c.1675_1676+1delAGGinsTCA​(p.560) variant causes a splice donor, splice region, synonymous, intron 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.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PKN2 NM_006256.4 splice_donor, splice_region, synonymous, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.14
• Publications: 0 publications found

Genes affected

PKN2 (HGNC:9406): (protein kinase N2) Enables RNA polymerase binding activity; histone deacetylase binding activity; and protein serine/threonine kinase activity. Involved in several processes, including apical junction assembly; positive regulation of cell cycle; and positive regulation of viral genome replication. Located in several cellular components, including cleavage furrow; cytoskeleton; and midbody. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006256.4. 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
	PKN2	NM_006256.4	MANE Select	c.1675_1676+1delAGGinsTCA	p.560	splice_donor splice_region synonymous intron	N/A	NP_006247.1	Q16513-1
	PKN2	NM_001320709.2		c.1627_1628+1delAGGinsTCA	p.544	splice_donor splice_region synonymous intron	N/A	NP_001307638.1	Q16513-2
	PKN2	NM_001320707.2		c.1531_1532+1delAGGinsTCA	p.512	splice_donor splice_region synonymous intron	N/A	NP_001307636.1	Q16513-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PKN2	ENST00000370521.8	TSL:1 MANE Select	c.1675_1676+1delAGGinsTCA	p.560	splice_donor splice_region synonymous intron	N/A	ENSP00000359552.3	Q16513-1
	PKN2	ENST00000370513.9	TSL:1	c.1531_1532+1delAGGinsTCA	p.512	splice_donor splice_region synonymous intron	N/A	ENSP00000359544.5	Q16513-3
	PKN2	ENST00000316005.11	TSL:5	c.1675_1677delAGGinsTCA	p.Arg559Ser	missense	N/A	ENSP00000317851.7	B1AL79

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		5.1

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: chr1-89271353;