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GeneBe

rs1803118

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001641.4(APEX1):c.950C>T(p.Ala317Val) variant causes a missense change. The variant was absent in control chromosomes in GnomAD Genomes project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

APEX1
NM_001641.4 missense

Scores

8
10

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.21
Variant links:
Genes affected
APEX1 (HGNC:587): (apurinic/apyrimidinic endodeoxyribonuclease 1) The APEX gene encodes the major AP endonuclease in human cells. It encodes the APEX endonuclease, a DNA repair enzyme with apurinic/apyrimidinic (AP) activity. Such AP activity sites occur frequently in DNA molecules by spontaneous hydrolysis, by DNA damaging agents or by DNA glycosylases that remove specific abnormal bases. The AP sites are the most frequent pre-mutagenic lesions that can prevent normal DNA replication. Splice variants have been found for this gene; all encode the same protein. Disruptions in the biological functions related to APEX are associated with many various malignancies and neurodegenerative diseases.[provided by RefSeq, Dec 2019]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
APEX1NM_001641.4 linkuse as main transcriptc.950C>T p.Ala317Val missense_variant 5/5 ENST00000216714.8
APEX1NM_001244249.2 linkuse as main transcriptc.950C>T p.Ala317Val missense_variant 5/5
APEX1NM_080648.3 linkuse as main transcriptc.950C>T p.Ala317Val missense_variant 5/5
APEX1NM_080649.3 linkuse as main transcriptc.950C>T p.Ala317Val missense_variant 5/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
APEX1ENST00000216714.8 linkuse as main transcriptc.950C>T p.Ala317Val missense_variant 5/51 NM_001641.4 P1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.49
BayesDel_addAF
Benign
-0.013
T
BayesDel_noAF
Benign
-0.26
Cadd
Benign
20
Dann
Uncertain
0.98
DEOGEN2
Benign
0.32
T;T;T
Eigen
Uncertain
0.36
Eigen_PC
Uncertain
0.46
FATHMM_MKL
Uncertain
0.93
D
M_CAP
Benign
0.023
T
MetaRNN
Uncertain
0.64
D;D;D
MetaSVM
Benign
-0.73
T
MutationAssessor
Benign
1.6
L;L;L
MutationTaster
Benign
1.0
D;D;D;D
PrimateAI
Uncertain
0.74
T
PROVEAN
Uncertain
-2.5
N;N;N
REVEL
Benign
0.15
Sift
Benign
0.31
T;T;T
Sift4G
Benign
0.20
T;T;T
Polyphen
0.74
P;P;P
Vest4
0.59
MutPred
0.47
Gain of catalytic residue at A317 (P = 0.0013);Gain of catalytic residue at A317 (P = 0.0013);Gain of catalytic residue at A317 (P = 0.0013);
MVP
0.86
MPC
0.28
ClinPred
0.82
D
GERP RS
5.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.48
gMVP
0.55

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: rs1803118; hg19: chr14-20925660; API