9-129147457-CG-TA

Variant names:

• chr9-129147457-CG-TA
• NM_178000.3:c.965_966delCGinsTA
• PTPA p.Ser322Leu

Variant summary

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

The NM_178000.3(PTPA):​c.965_966delCGinsTA​(p.Ser322Leu) 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. Synonymous variant affecting the same amino acid position (i.e. S322S) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PTPA NM_178000.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.23
• Publications: 0 publications found

Genes affected

PTPA (HGNC:9308): (protein phosphatase 2 phosphatase activator) Protein phosphatase 2A is one of the four major Ser/Thr phosphatases and is implicated in the negative control of cell growth and division. Protein phosphatase 2A holoenzymes are heterotrimeric proteins composed of a structural subunit A, a catalytic subunit C, and a regulatory subunit B. The regulatory subunit is encoded by a diverse set of genes that have been grouped into the B/PR55, B'/PR61, and B''/PR72 families. These different regulatory subunits confer distinct enzymatic specificities and intracellular localizations to the holozenzyme. The product of this gene belongs to the B' family. This gene encodes a specific phosphotyrosyl phosphatase activator of the dimeric form of protein phosphatase 2A. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

ENSG00000235007 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178000.3. 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
	PTPA	NM_178000.3	MANE Select	c.965_966delCGinsTA	p.Ser322Leu	missense	N/A	NP_821067.1	Q15257-2
	PTPA	NM_178001.3		c.1070_1071delCGinsTA	p.Ser357Leu	missense	N/A	NP_821068.1	Q15257-1
	PTPA	NM_021131.5		c.965_966delCGinsTA	p.Ser322Leu	missense	N/A	NP_066954.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTPA	ENST00000393370.7	TSL:1 MANE Select	c.965_966delCGinsTA	p.Ser322Leu	missense	N/A	ENSP00000377036.2	Q15257-2
	PTPA	ENST00000358994.9	TSL:1	c.1115_1116delCGinsTA	p.Ser372Leu	missense	N/A	ENSP00000351885.5	A0A804CD06
	PTPA	ENST00000452489.6	TSL:1	c.860_861delCGinsTA	p.Ser287Leu	missense	N/A	ENSP00000394338.3	F6WIT2

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		4.2

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: chr9-131909736;