Genetic Variant NM_001303512.2:c.1909_1911delGACinsTAT (chrX-153803770-GTC-ATA) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is The variant received 2 classification points (ACMG Germline Pathogenicity v2019). PM2

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, Jul 2025]

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 ACMG Germline Pathogenicity v2019

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 2 points.

Show applied only (1)

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	PM2Absent/extremely low in population databases		Absent from gnomAD (AR/unknown gene) — PM2; Absent from gnomAD at well-covered site (MOI: unknown) (threshold 0.001) — PM2 moderate.

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_001303512.2. You can select a different transcript below to see updated classification 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	Prot: NP_001290441.1 UniProt: F6S393Q17RL8
PDZD4 NM_032512.5		c.1891_1893delGACinsTAT p.Asp631Tyr	missense	N/A	Prot: NP_115901.2
PDZD4 NM_001303515.2		c.1666_1668delGACinsTAT p.Asp556Tyr	missense	N/A	Prot: NP_001290444.1

PDZD4 NM_001303512.2

MANE Select

HGVSc / HGVSpc.1909_1911delGACinsTATp.Asp637Tyr

Exon rankN/A

missense

Prot: NP_001290441.1UniProt: F6S393

Q17RL8

PDZD4 NM_032512.5

HGVSc / HGVSpc.1891_1893delGACinsTATp.Asp631Tyr

Exon rankN/A

missense

Prot: NP_115901.2

PDZD4 NM_001303515.2

HGVSc / HGVSpc.1666_1668delGACinsTATp.Asp556Tyr

Exon rankN/A

missense

Prot: NP_001290444.1

Ensembl Transcripts

Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
PDZD4 ENST00000393758.7	TSL:1MANE Select	c.1909_1911delGACinsTAT p.Asp637Tyr	missense	N/A	Prot: ENSP00000377355.3 UniProt: F6S393
PDZD4 ENST00000164640.8	TSL:1	c.1891_1893delGACinsTAT p.Asp631Tyr	missense	N/A	Prot: ENSP00000164640.4 UniProt: Q76G19-1
PDZD4 ENST00000544474.5	TSL:1	c.1564_1566delGACinsTAT p.Asp522Tyr	missense	N/A	Prot: ENSP00000442033.1 UniProt: Q76G19-2

PDZD4 ENST00000393758.7

TSL:1MANE Select

HGVSc / HGVSpc.1909_1911delGACinsTATp.Asp637Tyr

Exon rankN/A

missense

Prot: ENSP00000377355.3UniProt: F6S393

PDZD4 ENST00000164640.8

TSL:1

HGVSc / HGVSpc.1891_1893delGACinsTATp.Asp631Tyr

Exon rankN/A

missense

Prot: ENSP00000164640.4UniProt: Q76G19-1

PDZD4 ENST00000544474.5

TSL:1

HGVSc / HGVSpc.1564_1566delGACinsTATp.Asp522Tyr

Exon rankN/A

missense

Prot: ENSP00000442033.1UniProt: Q76G19-2

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 2 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:25
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:25

Showing 2 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
PhyloP100	Uncertain	6.2

Showing 1 of 1 scores

Splicing Scores

No splicing scores have been computed for this variant.

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.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACMG Germline Pathogenicity v2019

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational Scores

Splicing Scores

MaveDB functional evidence ?

Publications

Other links and lift over

MaveDB functional evidence