rs755438608
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2
The NM_194449.4(PHLPP1):βc.403_411delβ(p.Ala135_Ala137del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000356 in 1,486,830 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Uncertain significance (β ).
Frequency
Genomes: π 0.00042 ( 0 hom., cov: 31)
Exomes π: 0.00035 ( 2 hom. )
Consequence
PHLPP1
NM_194449.4 inframe_deletion
NM_194449.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.77
Genes affected
PHLPP1 (HGNC:20610): (PH domain and leucine rich repeat protein phosphatase 1) This gene encodes a member of the serine/threonine phosphatase family. The encoded protein promotes apoptosis by dephosphorylating and inactivating the serine/threonine kinase Akt, and functions as a tumor suppressor in multiple types of cancer. Increased expression of this gene may also play a role in obesity and type 2 diabetes by interfering with Akt-mediated insulin signaling. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP3
?
Nonframeshift variant in repetitive region in NM_194449.4
BS2
?
High AC in GnomAd4 at 62 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHLPP1 | NM_194449.4 | c.403_411del | p.Ala135_Ala137del | inframe_deletion | 1/17 | ENST00000262719.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHLPP1 | ENST00000262719.10 | c.403_411del | p.Ala135_Ala137del | inframe_deletion | 1/17 | 1 | NM_194449.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000416 AC: 62AN: 148970Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000588 AC: 51AN: 86784Hom.: 1 AF XY: 0.000496 AC XY: 24AN XY: 48420
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GnomAD4 exome AF: 0.000349 AC: 467AN: 1337750Hom.: 2 AF XY: 0.000386 AC XY: 254AN XY: 658462
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GnomAD4 genome ? AF: 0.000416 AC: 62AN: 149080Hom.: 0 Cov.: 31 AF XY: 0.000343 AC XY: 25AN XY: 72848
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Jan 30, 2017 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at