NM_015085.5:c.35G>A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2PP3
The NM_015085.5(RAP1GAP2):c.35G>A(p.Gly12Asp) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
RAP1GAP2
NM_015085.5 missense
NM_015085.5 missense
Scores
4
10
4
Clinical Significance
Conservation
PhyloP100: 4.89
Publications
0 publications found
Genes affected
RAP1GAP2 (HGNC:29176): (RAP1 GTPase activating protein 2) This gene encodes a GTPase-activating protein that activates the small guanine-nucleotide-binding protein Rap1 in platelets. The protein interacts with synaptotagmin-like protein 1 and Rab27 and regulates secretion of dense granules from platelets at sites of endothelial damage. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.812
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_015085.5. 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 |
|---|---|---|---|---|---|---|---|---|---|
| RAP1GAP2 | TSL:1 MANE Select | c.35G>A | p.Gly12Asp | missense | Exon 1 of 25 | ENSP00000254695.8 | Q684P5-1 | ||
| RAP1GAP2 | TSL:1 | c.35G>A | p.Gly12Asp | missense | Exon 1 of 24 | ENSP00000389824.2 | Q684P5-2 | ||
| RAP1GAP2 | c.35G>A | p.Gly12Asp | missense | Exon 1 of 21 | ENSP00000575822.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1410808Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 696984
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1410808
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
696984
African (AFR)
AF:
AC:
0
AN:
32164
American (AMR)
AF:
AC:
0
AN:
36860
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25332
East Asian (EAS)
AF:
AC:
0
AN:
36790
South Asian (SAS)
AF:
AC:
0
AN:
79958
European-Finnish (FIN)
AF:
AC:
0
AN:
49860
Middle Eastern (MID)
AF:
AC:
0
AN:
5708
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1085600
Other (OTH)
AF:
AC:
0
AN:
58536
GnomAD4 genome
GnomAD4 genome
Cov.:
33
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
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D
MetaSVM
Uncertain
D
MutationAssessor
Benign
L
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Benign
N
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MutPred
Loss of MoRF binding (P = 0.0341)
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
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.