Genetic Variant PDZD4:p.Asp637Tyr (chrX-153803770-GTC-ATA) – ACMG Classification: Uncertain_significance (2 pts)

Germline classification Cancer classification (beta)

Variant summary

Our verdict is . The variant received 2 ACMG points: 2P and 0B. O3_Moderate

The NM_001303512.2(PDZD4):c.1909_1911delGACinsTAT (p.Asp637Tyr) variant causes a missense change. Note: allele frequency estimates from gnomAD may be inaccurate for this variant type (MNP or indel longer than 3 bp) due to technology limitations. The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. 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

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.20

Publications

0 publications found

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]

PDZD4 links:

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new If you want to explore the variant's impact on the transcript NM_001303512.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

Absent or extremely rare in gnomAD (AC ≤ 2) — O3 moderate; GnomAD: AF = absent, AC = 0 — absent/extremely rare (O3 moderate [+2])

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001303512.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PDZD4	NM_001303512.2	MANE Select	c.1909_1911delGACinsTAT	p.Asp637Tyr	missense	N/A	NP_001290441.1	Q17RL8
PDZD4	NM_032512.5		c.1891_1893delGACinsTAT	p.Asp631Tyr	missense	N/A	NP_115901.2
PDZD4	NM_001303515.2		c.1666_1668delGACinsTAT	p.Asp556Tyr	missense	N/A	NP_001290444.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PDZD4	ENST00000393758.7	TSL:1 MANE Select	c.1909_1911delGACinsTAT	p.Asp637Tyr	missense	N/A	ENSP00000377355.3	Q17RL8
PDZD4	ENST00000164640.8	TSL:1	c.1891_1893delGACinsTAT	p.Asp631Tyr	missense	N/A	ENSP00000164640.4	Q76G19-1
PDZD4	ENST00000544474.5	TSL:1	c.1564_1566delGACinsTAT	p.Asp522Tyr	missense	N/A	ENSP00000442033.1	Q76G19-2

Frequencies

GnomAD3 genomes

Cov.:

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

6.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACGS-UK Somatic Oncogenicity v2025

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over