rs1064792893

Variant names:

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

Variant summary

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

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. 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. 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
• Publications: 0 publications found

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

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

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

-

Donald Williams Parsons Laboratory, Baylor College of Medicine

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs1064792893; hg19: chr12-54975790;