16-21984367-C-T

Variant summary

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

The NM_001363519.1(PDZD9):​c.695G>A​(p.Ser232Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000356 in 1,461,754 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: 0.000036 ( 0 hom. )

Consequence

PDZD9
NM_001363519.1 missense

Scores

1
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.179
Variant links:
Genes affected
PDZD9 (HGNC:28740): (PDZ domain containing 9)

Genome browser will be placed here

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=0.0639064).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PDZD9NM_001363519.1 linkuse as main transcriptc.695G>A p.Ser232Asn missense_variant 4/4 ENST00000424898.3 NP_001350448.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PDZD9ENST00000424898.3 linkuse as main transcriptc.695G>A p.Ser232Asn missense_variant 4/45 NM_001363519.1 ENSP00000400514 P1Q8IXQ8-1
PDZD9ENST00000523914.5 linkuse as main transcriptc.*472G>A 3_prime_UTR_variant, NMD_transcript_variant 5/51 ENSP00000429211
PDZD9ENST00000537222.6 linkuse as main transcriptc.515G>A p.Ser172Asn missense_variant 3/33 ENSP00000441685 Q8IXQ8-3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000796
AC:
2
AN:
251412
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135882
show subpopulations
Gnomad AFR exome
AF:
0.0000615
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000879
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000356
AC:
52
AN:
1461754
Hom.:
0
Cov.:
31
AF XY:
0.0000261
AC XY:
19
AN XY:
727172
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:
0.0000468
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000756
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.00
AC:
0
ESP6500AA
AF:
0.000227
AC:
1
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.0000165
AC:
2

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 GeneticsJan 04, 2024The c.515G>A (p.S172N) alteration is located in exon 3 (coding exon 3) of the PDZD9 gene. This alteration results from a G to A substitution at nucleotide position 515, causing the serine (S) at amino acid position 172 to be replaced by an asparagine (N). 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
0.12
BayesDel_addAF
Benign
-0.45
T
BayesDel_noAF
Benign
-0.71
CADD
Benign
11
DANN
Benign
0.78
DEOGEN2
Benign
0.031
.;T
Eigen
Benign
-0.94
Eigen_PC
Benign
-1.0
FATHMM_MKL
Benign
0.066
N
M_CAP
Benign
0.014
T
MetaRNN
Benign
0.064
T;T
MetaSVM
Benign
-0.90
T
MutationAssessor
Benign
1.4
.;L
MutationTaster
Benign
1.0
N;N;N
PrimateAI
Benign
0.30
T
PROVEAN
Benign
-2.3
N;N
REVEL
Benign
0.038
Sift
Uncertain
0.0060
D;D
Sift4G
Benign
0.080
T;T
Vest4
0.10
MVP
0.15
MPC
0.60
ClinPred
0.17
T
GERP RS
-0.69
Varity_R
0.16
gMVP
0.055

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: rs376162472; hg19: chr16-21995688; API