GeneBe

rs201794373

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_017917.4(PPP2R3C):​c.1174-11_1174-10delTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000143 in 1,397,024 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: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

PPP2R3C
NM_017917.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.673

Publications

0 publications found
Variant links:
Genes affected
PPP2R3C (HGNC:17485): (protein phosphatase 2 regulatory subunit B''gamma) This gene encodes a regulatory subunit of the serine/threonine phosphatase, protein phosphatase 2. This protein is localized to both nuclear and cytoplasmic regions depending on cell cycle phase. Homozygous conditional knockout mice for this gene exhibit reduced numbers and impaired proliferation of immune system B cells. This protein may regulate the expression of the P-glycoprotein ATP-binding cassette transporter through its phosphatase activity. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2015]
FAM177A1 (HGNC:19829): (family with sequence similarity 177 member A1) This gene encodes a member of a conserved protein family. Alternative splicing results in multiple transcript variants. This gene is thought to be associated with susceptibility to juvenile idiopathic arthritis. [provided by RefSeq, Apr 2017]
FAM177A1 Gene-Disease associations (from GenCC):
  • complex neurodevelopmental disorder
    Inheritance: AR Classification: MODERATE Submitted by: Ambry Genetics, G2P

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017917.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PPP2R3C
NM_017917.4
MANE Select
c.1174-11_1174-10delTT
intron
N/ANP_060387.2
PPP2R3C
NM_001305155.2
c.844-11_844-10delTT
intron
N/ANP_001292084.1Q969Q6-2
PPP2R3C
NM_001305156.2
c.844-11_844-10delTT
intron
N/ANP_001292085.1Q969Q6-2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PPP2R3C
ENST00000261475.10
TSL:1 MANE Select
c.1174-11_1174-10delTT
intron
N/AENSP00000261475.5Q969Q6-1
PPP2R3C
ENST00000553273.5
TSL:1
n.*840-11_*840-10delTT
intron
N/AENSP00000451075.1G3V228
PPP2R3C
ENST00000557217.5
TSL:1
n.*977-11_*977-10delTT
intron
N/AENSP00000452436.1G3V228

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000143
AC:
2
AN:
1397024
Hom.:
0
AF XY:
0.00000144
AC XY:
1
AN XY:
695438
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
30598
American (AMR)
AF:
0.00
AC:
0
AN:
36540
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
24368
East Asian (EAS)
AF:
0.00
AC:
0
AN:
38674
South Asian (SAS)
AF:
0.00
AC:
0
AN:
79412
European-Finnish (FIN)
AF:
0.0000199
AC:
1
AN:
50368
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5502
European-Non Finnish (NFE)
AF:
9.31e-7
AC:
1
AN:
1073954
Other (OTH)
AF:
0.00
AC:
0
AN:
57608
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.67

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs201794373; hg19: chr14-35554993; API