GeneBe

rs35434632

Variant names:

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_000944.5(PPP3CA):​c.*27_*44delTTTTTTTTTTTTTTTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000334 in 479,362 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000029 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000034 ( 0 hom. )

Consequence

PPP3CA
NM_000944.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.89
Variant links:
Genes affected
PPP3CA (HGNC:9314): (protein phosphatase 3 catalytic subunit alpha) Enables several functions, including ATPase binding activity; calmodulin binding activity; and calmodulin-dependent protein phosphatase activity. Involved in several processes, including calcineurin-NFAT signaling cascade; peptidyl-serine dephosphorylation; and response to calcium ion. Located in several cellular components, including cytosol; dendritic spine; and nucleoplasm. Part of calcineurin complex. Colocalizes with cytoplasmic side of plasma membrane. Implicated in developmental and epileptic encephalopathy 91. Biomarker of focal segmental glomerulosclerosis and schizophrenia. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High AC in GnomAdExome4 at 15 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PPP3CANM_000944.5 linkc.*27_*44delTTTTTTTTTTTTTTTTTT 3_prime_UTR_variant Exon 14 of 14 ENST00000394854.8 NP_000935.1 Q08209-1A0A0S2Z4C6
PPP3CANM_001130691.2 linkc.*27_*44delTTTTTTTTTTTTTTTTTT 3_prime_UTR_variant Exon 13 of 13 NP_001124163.1 Q08209-2A0A0S2Z4B5
PPP3CANM_001130692.2 linkc.*27_*44delTTTTTTTTTTTTTTTTTT 3_prime_UTR_variant Exon 12 of 12 NP_001124164.1 Q08209-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PPP3CAENST00000394854 linkc.*27_*44delTTTTTTTTTTTTTTTTTT 3_prime_UTR_variant Exon 14 of 14 1 NM_000944.5 ENSP00000378323.3 Q08209-1

Frequencies

GnomAD3 genomes
AF:
0.0000289
AC:
1
AN:
34564
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000466
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000337
AC:
15
AN:
444798
Hom.:
0
AF XY:
0.0000478
AC XY:
11
AN XY:
230308
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000616
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000200
Gnomad4 FIN exome
AF:
0.0000422
Gnomad4 NFE exome
AF:
0.0000189
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000289
AC:
1
AN:
34564
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
15202
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000466
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs35434632; hg19: chr4-101946977; API