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GeneBe

X-153803772-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate

The NM_001303512.2(PDZD4):c.1909G>T(p.Asp637Tyr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 25)

Consequence

PDZD4
NM_001303512.2 missense

Scores

13
3
1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.10
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.871

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PDZD4NM_001303512.2 linkuse as main transcriptc.1909G>T p.Asp637Tyr missense_variant 8/8 ENST00000393758.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PDZD4ENST00000393758.7 linkuse as main transcriptc.1909G>T p.Asp637Tyr missense_variant 8/81 NM_001303512.2 P4
PDZD4ENST00000164640.8 linkuse as main transcriptc.1891G>T p.Asp631Tyr missense_variant 8/81 A1Q76G19-1
PDZD4ENST00000544474.5 linkuse as main transcriptc.1564G>T p.Asp522Tyr missense_variant 6/61 Q76G19-2

Frequencies

GnomAD3 genomes
Cov.:
25
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
25

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
1.0
BayesDel_addAF
Pathogenic
0.34
D
BayesDel_noAF
Pathogenic
0.25
Cadd
Pathogenic
26
Dann
Uncertain
0.99
DEOGEN2
Pathogenic
0.80
D;.;T
FATHMM_MKL
Pathogenic
1.0
D
LIST_S2
Pathogenic
1.0
D;D;D
M_CAP
Pathogenic
0.60
D
MetaRNN
Pathogenic
0.87
D;D;D
MetaSVM
Uncertain
-0.15
T
MutationAssessor
Uncertain
2.7
M;.;.
MutationTaster
Benign
1.0
D;D;D
PrimateAI
Pathogenic
0.86
D
PROVEAN
Pathogenic
-8.7
D;D;.
REVEL
Pathogenic
0.67
Sift
Pathogenic
0.0
D;D;.
Sift4G
Pathogenic
0.0
D;D;D
Polyphen
1.0
D;.;D
Vest4
0.85
MutPred
0.58
Gain of catalytic residue at D631 (P = 0.0045);.;.;
MVP
0.68
MPC
2.2
ClinPred
1.0
D
GERP RS
5.7
Varity_R
0.97
gMVP
1.0

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

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-153069227; API