X-153807340-G-A

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2

The NM_001303512.2(PDZD4):​c.344C>T​(p.Pro115Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000029 in 1,208,215 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 11 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000027 ( 0 hom., 0 hem., cov: 25)
Exomes 𝑓: 0.000029 ( 0 hom. 11 hem. )

Consequence

PDZD4
NM_001303512.2 missense

Scores

2
5
10

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.83
Variant links:
Genes affected
PDZD4 (HGNC:21167): (PDZ domain containing 4) Predicted to be located in cell cortex. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.2927454).
BS2
High Hemizygotes in GnomAdExome4 at 11 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PDZD4NM_001303512.2 linkc.344C>T p.Pro115Leu missense_variant Exon 3 of 8 ENST00000393758.7 NP_001290441.1 Q76G19Q17RL8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PDZD4ENST00000393758.7 linkc.344C>T p.Pro115Leu missense_variant Exon 3 of 8 1 NM_001303512.2 ENSP00000377355.3 Q17RL8

Frequencies

GnomAD3 genomes
AF:
0.0000266
AC:
3
AN:
112920
Hom.:
0
Cov.:
25
AF XY:
0.00
AC XY:
0
AN XY:
35064
show subpopulations
Gnomad AFR
AF:
0.0000643
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000188
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000292
AC:
32
AN:
1095295
Hom.:
0
Cov.:
31
AF XY:
0.0000304
AC XY:
11
AN XY:
361297
show subpopulations
Gnomad4 AFR exome
AF:
0.0000379
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:
0.0000369
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000266
AC:
3
AN:
112920
Hom.:
0
Cov.:
25
AF XY:
0.00
AC XY:
0
AN XY:
35064
show subpopulations
Gnomad4 AFR
AF:
0.0000643
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000188
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000660
Hom.:
0

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Jul 14, 2021
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.326C>T (p.P109L) alteration is located in exon 3 (coding exon 3) of the PDZD4 gene. This alteration results from a C to T substitution at nucleotide position 326, causing the proline (P) at amino acid position 109 to be replaced by a leucine (L). 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
0.24
BayesDel_addAF
Benign
-0.23
T
BayesDel_noAF
Benign
-0.57
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.53
D;T
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Uncertain
0.91
D;D
M_CAP
Pathogenic
0.47
D
MetaRNN
Benign
0.29
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.6
L;.
PrimateAI
Uncertain
0.76
T
PROVEAN
Uncertain
-4.2
D;.
REVEL
Benign
0.12
Sift
Benign
0.11
T;.
Sift4G
Benign
0.52
T;T
Polyphen
0.91
P;P
Vest4
0.40
MutPred
0.48
Loss of disorder (P = 0.0227);.;
MVP
0.22
MPC
0.35
ClinPred
0.62
D
GERP RS
5.6
Varity_R
0.29
gMVP
0.79

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1557077468; hg19: chrX-153072795; COSMIC: COSV99381357; API