Given REF is incompatible with our hg38 reference sequence (N). Please double check if it's correct.

Y-338615-G-A

Position:

• chrY-338615-G-A

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The ENST00000711115.1(PPP2R3B):​c.1566C>T​(p.Pro522Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov:)
• Consequence: PPP2R3B ENST00000711115.1 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0570

Genes affected

PPP2R3B (HGNC:13417): (protein phosphatase 2 regulatory subunit B''beta) Protein phosphatase 2 (formerly named type 2A) is one of the four major Ser/Thr phosphatases and is implicated in the negative control of cell growth and division. Protein phosphatase 2 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. The B'' family has been further divided into subfamilies. The product of this gene belongs to the beta subfamily of regulatory subunit B''. [provided by RefSeq, Apr 2010]

PPP2R3B_1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=3.05).
• BP6: Variant Y-338615-G-A is Benign according to our data. Variant chrY-338615-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2659854.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.057 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPP2R3B_1	NM_013239.5_1	c.1566C>T	p.Pro522Pro	synonymous_variant	12/13
PPP2R3B_1	XM_047442723.1	c.1566C>T	p.Pro522Pro	synonymous_variant	12/13		XP_047298679.1
PPP2R3B_1	XM_047442724.1	c.1482C>T	p.Pro494Pro	synonymous_variant	12/13		XP_047298680.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP2R3B	ENST00000711115.1	c.1566C>T	p.Pro522Pro	synonymous_variant	12/13			ENSP00000518592.1
PPP2R3B	ENST00000711112.1	n.711C>T		splice_region_variant, non_coding_transcript_exon_variant	5/5
PPP2R3B	ENST00000711113.1	n.1426C>T		non_coding_transcript_exon_variant	8/8
PPP2R3B	ENST00000711114.1	n.796C>T		non_coding_transcript_exon_variant	4/5

Frequencies

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

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

Alfa AF: 0.0000712 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jun 01, 2022

PPP2R3B: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	3.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs773605704; hg19: chrY-249350;