rs1555526625
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_000546.6(TP53):c.269C>T(p.Ser90Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,684 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
TP53
NM_000546.6 missense
NM_000546.6 missense
Scores
2
10
7
Clinical Significance
Conservation
PhyloP100: 2.09
Genes affected
TP53 (HGNC:11998): (tumor protein p53) This gene encodes a tumor suppressor protein containing transcriptional activation, DNA binding, and oligomerization domains. The encoded protein responds to diverse cellular stresses to regulate expression of target genes, thereby inducing cell cycle arrest, apoptosis, senescence, DNA repair, or changes in metabolism. Mutations in this gene are associated with a variety of human cancers, including hereditary cancers such as Li-Fraumeni syndrome. Alternative splicing of this gene and the use of alternate promoters result in multiple transcript variants and isoforms. Additional isoforms have also been shown to result from the use of alternate translation initiation codons from identical transcript variants (PMIDs: 12032546, 20937277). [provided by RefSeq, Dec 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.37674814).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460684Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726616
GnomAD4 exome
AF:
AC:
2
AN:
1460684
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
726616
Gnomad4 AFR exome
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Gnomad4 SAS exome
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Gnomad4 FIN exome
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Gnomad4 OTH exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Li-Fraumeni syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 13, 2017 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. An experimental study in yeast has shown that this variant does not impair the transcriptional transactivation activity of the TP53 protein (PMID: 12826609). This variant has not been reported in the literature in individuals with TP53-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change replaces serine with phenylalanine at codon 90 of the TP53 protein (p.Ser90Phe). The serine residue is weakly conserved and there is a large physicochemical difference between serine and phenylalanine. - |
Hereditary cancer-predisposing syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2015 | The p.S90F variant (also known as c.269C>T), located in coding exon 3 of the TP53 gene, results from a C to T substitution at nucleotide position 269. The serine at codon 90 is replaced by phenylalanine, an amino acid with highly dissimilar properties. This alteration has been reported as a somatic mutation 2 times in various tumors, but not as a germline mutation by the IARC TP53 database (Petitjean A et al. IARC TP53 database [version R17, November 2013]. Hum Mutat. 2007 Jun;28(6):622-9). Functional studies show transactivation activity similar to wild type in yeast assays (IARC TP53 database: Kato S et al. Proc Natl Acad Sci USA. 2003 Jul 8;100(14):8424-9). This amino acid position is poorly conserved on limited sequence alignment. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of p.S90F remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;.;D;.;.;.;.;.;.;D;.;.;T;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;.;.;.;D;D;.;D;D;D;D;T;D;D;D
M_CAP
Uncertain
D
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Pathogenic
D
MutationAssessor
Uncertain
.;.;.;M;.;M;M;M;.;.;M;.;.;.;.;.
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;.;N;.;.;N;N;.;.;N;.;.;N;.;N
REVEL
Uncertain
Sift
Uncertain
D;D;.;T;.;.;T;T;.;.;T;.;.;D;.;D
Sift4G
Uncertain
D;D;D;D;D;D;D;D;D;D;D;D;D;.;D;.
Polyphen
P;.;.;B;.;P;D;P;.;.;B;.;.;D;.;.
Vest4
MutPred
Loss of glycosylation at S90 (P = 0.0079);Loss of glycosylation at S90 (P = 0.0079);.;Loss of glycosylation at S90 (P = 0.0079);.;Loss of glycosylation at S90 (P = 0.0079);Loss of glycosylation at S90 (P = 0.0079);Loss of glycosylation at S90 (P = 0.0079);.;.;Loss of glycosylation at S90 (P = 0.0079);.;Loss of glycosylation at S90 (P = 0.0079);Loss of glycosylation at S90 (P = 0.0079);Loss of glycosylation at S90 (P = 0.0079);Loss of glycosylation at S90 (P = 0.0079);
MVP
MPC
1.4
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at