chr16-15031819-T-C
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015027.4(PDXDC1):āc.1484T>Cā(p.Leu495Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000372 in 1,613,920 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000020 ( 0 hom., cov: 31)
Exomes š: 0.0000021 ( 0 hom. )
Consequence
PDXDC1
NM_015027.4 missense
NM_015027.4 missense
Scores
1
11
5
Clinical Significance
Conservation
PhyloP100: 4.87
Genes affected
PDXDC1 (HGNC:28995): (pyridoxal dependent decarboxylase domain containing 1) Enables cadherin binding activity. Predicted to be involved in carboxylic acid metabolic process. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]
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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 |
---|---|---|---|---|---|---|---|
PDXDC1 | NM_015027.4 | c.1484T>C | p.Leu495Ser | missense_variant | 17/23 | ENST00000396410.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDXDC1 | ENST00000396410.9 | c.1484T>C | p.Leu495Ser | missense_variant | 17/23 | 1 | NM_015027.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152116Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461804Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727214
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152116Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74318
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 11, 2023 | The c.1484T>C (p.L495S) alteration is located in exon 17 (coding exon 17) of the PDXDC1 gene. This alteration results from a T to C substitution at nucleotide position 1484, causing the leucine (L) at amino acid position 495 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;.;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D;D;D;D
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;.;D
Sift
Uncertain
D;D;D;.;D
Sift4G
Uncertain
D;D;D;D;D
Polyphen
0.64
.;P;.;.;.
Vest4
MutPred
0.67
.;Gain of disorder (P = 0.0132);.;.;.;
MVP
MPC
0.33
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at