1-3707626-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_005427.4(TP73):​c.264G>T​(p.Glu88Asp) variant causes a missense change. The variant allele was found at a frequency of 0.00000372 in 1,612,792 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: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000034 ( 0 hom. )

Consequence

TP73
NM_005427.4 missense

Scores

1
5
13

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.35
Variant links:
Genes affected
TP73 (HGNC:12003): (tumor protein p73) This gene encodes a member of the p53 family of transcription factors involved in cellular responses to stress and development. It maps to a region on chromosome 1p36 that is frequently deleted in neuroblastoma and other tumors, and thought to contain multiple tumor suppressor genes. The demonstration that this gene is monoallelically expressed (likely from the maternal allele), supports the notion that it is a candidate gene for neuroblastoma. Many transcript variants resulting from alternative splicing and/or use of alternate promoters have been found for this gene, but the biological validity and the full-length nature of some variants have not been determined. [provided by RefSeq, Feb 2011]

Genome browser will be placed here

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;
BP4
Computational evidence support a benign effect (MetaRNN=0.21004999).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TP73NM_005427.4 linkc.264G>T p.Glu88Asp missense_variant 4/14 ENST00000378295.9 NP_005418.1 O15350-1A1PQX5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TP73ENST00000378295.9 linkc.264G>T p.Glu88Asp missense_variant 4/141 NM_005427.4 ENSP00000367545.4 O15350-1

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152148
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000342
AC:
5
AN:
1460644
Hom.:
0
Cov.:
31
AF XY:
0.00000275
AC XY:
2
AN XY:
726656
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000126
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152148
Hom.:
0
Cov.:
33
AF XY:
0.0000135
AC XY:
1
AN XY:
74326
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJul 05, 2024The c.264G>T (p.E88D) alteration is located in exon 4 (coding exon 3) of the TP73 gene. This alteration results from a G to T substitution at nucleotide position 264, causing the glutamic acid (E) at amino acid position 88 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.10
BayesDel_addAF
Uncertain
0.062
T
BayesDel_noAF
Benign
-0.15
CADD
Benign
21
DANN
Benign
0.74
DEOGEN2
Benign
0.24
T;.;.;.;.;.;.;.;T;.;.
Eigen
Benign
-0.28
Eigen_PC
Benign
-0.12
FATHMM_MKL
Uncertain
0.88
D
LIST_S2
Benign
0.85
T;T;T;T;T;.;.;T;T;T;T
M_CAP
Uncertain
0.17
D
MetaRNN
Benign
0.21
T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Pathogenic
0.99
D
MutationAssessor
Benign
1.5
L;L;L;L;L;L;L;.;.;.;.
PrimateAI
Uncertain
0.65
T
PROVEAN
Benign
0.42
N;.;N;N;N;.;.;N;N;N;N
REVEL
Uncertain
0.54
Sift
Benign
1.0
T;.;T;T;T;.;.;T;T;T;T
Sift4G
Benign
0.78
T;T;T;T;T;T;T;T;T;T;T
Polyphen
0.073
B;.;B;.;.;.;.;B;.;B;.
Vest4
0.39
MutPred
0.055
Loss of phosphorylation at Y85 (P = 0.1667);Loss of phosphorylation at Y85 (P = 0.1667);Loss of phosphorylation at Y85 (P = 0.1667);Loss of phosphorylation at Y85 (P = 0.1667);Loss of phosphorylation at Y85 (P = 0.1667);Loss of phosphorylation at Y85 (P = 0.1667);Loss of phosphorylation at Y85 (P = 0.1667);.;.;.;.;
MVP
0.78
MPC
0.13
ClinPred
0.34
T
GERP RS
4.6
Varity_R
0.090
gMVP
0.30

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1639780053; hg19: chr1-3624190; API