rs765853588
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_000314.8(PTEN):c.210-48_210-44del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000055 in 1,455,674 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000046 ( 0 hom. )
Consequence
PTEN
NM_000314.8 intron
NM_000314.8 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.130
Genes affected
PTEN (HGNC:9588): (phosphatase and tensin homolog) This gene was identified as a tumor suppressor that is mutated in a large number of cancers at high frequency. The protein encoded by this gene is a phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase. It contains a tensin like domain as well as a catalytic domain similar to that of the dual specificity protein tyrosine phosphatases. Unlike most of the protein tyrosine phosphatases, this protein preferentially dephosphorylates phosphoinositide substrates. It negatively regulates intracellular levels of phosphatidylinositol-3,4,5-trisphosphate in cells and functions as a tumor suppressor by negatively regulating AKT/PKB signaling pathway. The use of a non-canonical (CUG) upstream initiation site produces a longer isoform that initiates translation with a leucine, and is thought to be preferentially associated with the mitochondrial inner membrane. This longer isoform may help regulate energy metabolism in the mitochondria. A pseudogene of this gene is found on chromosome 9. Alternative splicing and the use of multiple translation start codons results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Feb 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP6
?
Variant 10-87930997-TCCTAA-T is Benign according to our data. Variant chr10-87930997-TCCTAA-T is described in ClinVar as [Benign]. Clinvar id is 255813.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTEN | NM_000314.8 | c.210-48_210-44del | intron_variant | ENST00000371953.8 | |||
PTEN | NM_001304717.5 | c.729-48_729-44del | intron_variant | ||||
PTEN | NM_001304718.2 | c.-540-48_-540-44del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTEN | ENST00000371953.8 | c.210-48_210-44del | intron_variant | 1 | NM_000314.8 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151746Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000841 AC: 2AN: 237908Hom.: 0 AF XY: 0.00000777 AC XY: 1AN XY: 128712
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GnomAD4 exome AF: 0.00000460 AC: 6AN: 1303928Hom.: 0 AF XY: 0.00000305 AC XY: 2AN XY: 655784
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GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151746Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74112
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at