NM_014456.5:c.860A>G
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_014456.5(PDCD4):c.860A>G(p.Asp287Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000139 in 1,434,030 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
PDCD4
NM_014456.5 missense
NM_014456.5 missense
Scores
1
11
6
Clinical Significance
Conservation
PhyloP100: 8.95
Publications
0 publications found
Genes affected
PDCD4 (HGNC:8763): (programmed cell death 4) This gene is a tumor suppressor and encodes a protein that binds to the eukaryotic translation initiation factor 4A1 and inhibits its function by preventing RNA binding. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2010]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_014456.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PDCD4 | TSL:1 MANE Select | c.860A>G | p.Asp287Gly | missense | Exon 7 of 12 | ENSP00000280154.7 | Q53EL6-1 | ||
| PDCD4 | TSL:1 | c.827A>G | p.Asp276Gly | missense | Exon 8 of 13 | ENSP00000376816.2 | Q53EL6-2 | ||
| PDCD4 | c.860A>G | p.Asp287Gly | missense | Exon 7 of 13 | ENSP00000558068.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 0.00000139 AC: 2AN: 1434030Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 715000 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1434030
Hom.:
Cov.:
25
AF XY:
AC XY:
0
AN XY:
715000
show subpopulations
African (AFR)
AF:
AC:
2
AN:
32838
American (AMR)
AF:
AC:
0
AN:
44454
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25914
East Asian (EAS)
AF:
AC:
0
AN:
39458
South Asian (SAS)
AF:
AC:
0
AN:
85188
European-Finnish (FIN)
AF:
AC:
0
AN:
53344
Middle Eastern (MID)
AF:
AC:
0
AN:
5724
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1087598
Other (OTH)
AF:
AC:
0
AN:
59512
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
31
Alfa
AF:
Hom.:
Asia WGS
AF:
AC:
1
AN:
3478
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Uncertain
D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Uncertain
D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Benign
T
Polyphen
B
Vest4
MutPred
Gain of catalytic residue at C288 (P = 0.0811)
MVP
MPC
ClinPred
D
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
Publications
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