chr20-2836048-G-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_022760.6(PCED1A):​c.1108C>T​(p.Pro370Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000015 in 1,332,358 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000015 ( 0 hom. )

Consequence

PCED1A
NM_022760.6 missense

Scores

19

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.152
Variant links:
Genes affected
PCED1A (HGNC:16212): (PC-esterase domain containing 1A) The protein encoded by this gene is a member of the GDSL/SGNH superfamily. Members of this family are hydrolytic enzymes with esterase and lipase activity and broad substrate specificity. This protein belongs to the Pmr5-Cas1p-esterase subfamily in that it contains the catalytic triad comprised of serine, aspartate and histidine and lacks two conserved regions (glycine after strand S2 and GxND motif). A pseudogene of this gene has been identified on the long arm of chromosome 2. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Sep 2012]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.05604595).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PCED1ANM_022760.6 linkuse as main transcriptc.1108C>T p.Pro370Ser missense_variant 7/8 ENST00000360652.7 NP_073597.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PCED1AENST00000360652.7 linkuse as main transcriptc.1108C>T p.Pro370Ser missense_variant 7/81 NM_022760.6 ENSP00000353868 P1Q9H1Q7-1
PCED1AENST00000356872.7 linkuse as main transcriptc.955C>T p.Pro319Ser missense_variant 7/82 ENSP00000349334 Q9H1Q7-2
PCED1AENST00000474714.5 linkuse as main transcriptc.136-339C>T intron_variant 3 ENSP00000474824
PCED1AENST00000487501.2 linkuse as main transcriptn.307C>T non_coding_transcript_exon_variant 3/43

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000150
AC:
2
AN:
1332358
Hom.:
0
Cov.:
35
AF XY:
0.00000154
AC XY:
1
AN XY:
649522
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000191
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

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 submitterclinical testingAmbry GeneticsOct 29, 2021The c.1108C>T (p.P370S) alteration is located in exon 7 (coding exon 6) of the PCED1A gene. This alteration results from a C to T substitution at nucleotide position 1108, causing the proline (P) at amino acid position 370 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.068
BayesDel_addAF
Benign
-0.29
T
BayesDel_noAF
Benign
-0.65
CADD
Benign
14
DANN
Benign
0.73
DEOGEN2
Benign
0.011
T;.
Eigen
Benign
-0.99
Eigen_PC
Benign
-0.89
FATHMM_MKL
Benign
0.29
N
LIST_S2
Benign
0.59
T;T
M_CAP
Benign
0.0054
T
MetaRNN
Benign
0.056
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.4
L;.
MutationTaster
Benign
1.0
N;N
PrimateAI
Benign
0.31
T
PROVEAN
Benign
-0.11
N;N
REVEL
Benign
0.0040
Sift
Benign
0.36
T;T
Sift4G
Benign
0.18
T;T
Polyphen
0.0
B;B
Vest4
0.10
MutPred
0.23
Gain of glycosylation at P370 (P = 0.0783);.;
MVP
0.13
MPC
0.40
ClinPred
0.060
T
GERP RS
-0.48
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0
Varity_R
0.023
gMVP
0.23

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr20-2816694; API