rs1064792893

Variant names:

• chr12-54582006-AC-TG
• rs1064792893
• NM_006741.4:c.372_373delGTinsCA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_006741.4(PPP1R1A):​c.372_373delGTinsCA​(p.GluSer124AspThr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: PPP1R1A NM_006741.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.36

Genes affected

PPP1R1A (HGNC:9286): (protein phosphatase 1 regulatory inhibitor subunit 1A) Predicted to enable protein serine/threonine phosphatase inhibitor activity. Predicted to be involved in intracellular signal transduction. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP1R1A	NM_006741.4	c.372_373delGTinsCA	p.GluSer124AspThr	missense_variant		ENST00000257905.13	NP_006732.3
PPP1R1A	XM_006719471.5	c.184-957_184-956delGTinsCA		intron_variant	Intron 3 of 4		XP_006719534.1
PPP1R1A	XM_005268995.5	c.247+725_247+726delGTinsCA		intron_variant	Intron 4 of 5		XP_005269052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1R1A	ENST00000257905.13	c.372_373delGTinsCA	p.GluSer124AspThr	missense_variant		1	NM_006741.4	ENSP00000257905.8

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

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Rosette-forming glioneuronal tumor Uncertain:1

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Donald Williams Parsons Laboratory, Baylor College of Medicine

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1064792893; hg19: chr12-54975790;