17-50143641-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_032595.5(PPP1R9B):c.1582G>A(p.Val528Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,614,040 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
PPP1R9B
NM_032595.5 missense
NM_032595.5 missense
Scores
3
5
3
Clinical Significance
Conservation
PhyloP100: 7.89
Genes affected
PPP1R9B (HGNC:9298): (protein phosphatase 1 regulatory subunit 9B) This gene encodes a scaffold protein that functions as a regulatory subunit of protein phosphatase 1a. Expression of this gene is particularly high in dendritic spines, suggesting that the encoded protein may play a role in receiving signals from the central nervous system. The encoded protein has putative tumor suppressor function and decreased expression has been observed in tumors. [provided by RefSeq, Feb 2014]
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ACMG classification
Classification made for transcript
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP1R9B | NM_032595.5 | c.1582G>A | p.Val528Ile | missense_variant | 3/10 | ENST00000612501.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP1R9B | ENST00000612501.2 | c.1582G>A | p.Val528Ile | missense_variant | 3/10 | 1 | NM_032595.5 | P1 | |
ENST00000451776.1 | n.209-1482C>T | intron_variant, non_coding_transcript_variant | 3 | ||||||
PPP1R9B | ENST00000513579.1 | n.118G>A | non_coding_transcript_exon_variant | 2/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152230Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000803 AC: 2AN: 249146Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135210
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GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461692Hom.: 0 Cov.: 35 AF XY: 0.00000413 AC XY: 3AN XY: 727132
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GnomAD4 genome AF: 0.00000656 AC: 1AN: 152348Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74510
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ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
not provided Other:1
not provided, no classification provided | literature only | Psychiatry Genetics Yale University | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Benign
DEOGEN2
Benign
T
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Pathogenic
D
MetaRNN
Uncertain
T
PrimateAI
Pathogenic
D
Sift4G
Pathogenic
D
Vest4
MVP
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at