NM_181882.3:c.698A>T
Variant names:
Variant summary
Our verdict is . The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
Uncertain significance
The NM_181882.3(PRX):c.698A>T(p.Gln233Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PRX
NM_181882.3 missense
NM_181882.3 missense
Scores
5
14
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.55
Publications
0 publications found
Genes affected
PRX (HGNC:13797): (periaxin) This gene encodes a protein involved in peripheral nerve myelin upkeep. The encoded protein contains 2 PDZ domains which were named after PSD95 (post synaptic density protein), DlgA (Drosophila disc large tumor suppressor), and ZO1 (a mammalian tight junction protein). Two alternatively spliced transcript variants have been described for this gene which encode different protein isoforms and which are targeted differently in the Schwann cell. Mutations in this gene cause Charcot-Marie-Tooth neuoropathy, type 4F and Dejerine-Sottas neuropathy. [provided by RefSeq, Jul 2008]
PRX Gene-Disease associations (from GenCC):
- Charcot-Marie-Tooth disease type 4Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: PanelApp Australia, ClinGen
- Charcot-Marie-Tooth disease type 4FInheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Orphanet
- Charcot-Marie-Tooth disease type 3Inheritance: AD, AR Classification: MODERATE, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics
Genome browser will be placed here
new If you want to explore the variant's impact on the transcript NM_181882.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (REVEL=0.105).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_181882.3. 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 |
|---|---|---|---|---|---|---|---|---|---|
| PRX | TSL:1 MANE Select | c.698A>T | p.Gln233Leu | missense | Exon 7 of 7 | ENSP00000326018.6 | Q9BXM0-1 | ||
| PRX | TSL:1 | c.*903A>T | 3_prime_UTR | Exon 6 of 6 | ENSP00000291825.6 | Q9BXM0-2 | |||
| PRX | c.983A>T | p.Gln328Leu | missense | Exon 7 of 7 | ENSP00000501261.1 | A0A669KBF1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1397526Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 690958
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1397526
Hom.:
Cov.:
35
AF XY:
AC XY:
0
AN XY:
690958
African (AFR)
AF:
AC:
0
AN:
32386
American (AMR)
AF:
AC:
0
AN:
36798
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25210
East Asian (EAS)
AF:
AC:
0
AN:
37006
South Asian (SAS)
AF:
AC:
0
AN:
80102
European-Finnish (FIN)
AF:
AC:
0
AN:
36698
Middle Eastern (MID)
AF:
AC:
0
AN:
5454
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1085556
Other (OTH)
AF:
AC:
0
AN:
58316
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Uncertain
D
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
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
MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.
Publications
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