GeneBe

12-110720423-A-C

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_002710.4(PPP1CC):​c.*653T>G variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.00000308 in 324,450 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000031 ( 0 hom. )

Consequence

PPP1CC
NM_002710.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.61

Publications

1 publications found
Variant links:
Genes affected
PPP1CC (HGNC:9283): (protein phosphatase 1 catalytic subunit gamma) The protein encoded by this gene belongs to the protein phosphatase family, PP1 subfamily. PP1 is an ubiquitous serine/threonine phosphatase that regulates many cellular processes, including cell division. It is expressed in mammalian cells as three closely related isoforms, alpha, beta/delta and gamma, which have distinct localization patterns. This gene encodes the gamma isozyme. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.27).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PPP1CCNM_002710.4 linkc.*653T>G 3_prime_UTR_variant Exon 7 of 7 ENST00000335007.10 NP_002701.1 P36873-1A0A024RBP2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PPP1CCENST00000335007.10 linkc.*653T>G 3_prime_UTR_variant Exon 7 of 7 1 NM_002710.4 ENSP00000335084.5 P36873-1
PPP1CCENST00000550261.5 linkn.*363-219T>G intron_variant Intron 4 of 4 5 ENSP00000447528.2 F8W0V8
PPP1CCENST00000546904.1 linkn.1076T>G non_coding_transcript_exon_variant Exon 2 of 2 2
PPP1CCENST00000340766.9 linkc.944-219T>G intron_variant Intron 7 of 7 2 ENSP00000341779.5 P36873-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000308
AC:
1
AN:
324450
Hom.:
0
Cov.:
0
AF XY:
0.00000586
AC XY:
1
AN XY:
170678
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
8760
American (AMR)
AF:
0.00
AC:
0
AN:
11330
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
10740
East Asian (EAS)
AF:
0.0000410
AC:
1
AN:
24366
South Asian (SAS)
AF:
0.00
AC:
0
AN:
24560
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
22262
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
1504
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
201198
Other (OTH)
AF:
0.00
AC:
0
AN:
19730
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
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 v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.27
CADD
Benign
14
DANN
Benign
0.90
PhyloP100
6.6
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs11558236; hg19: chr12-111158228; API