PDZD4

PDZ domain containing 4, the group of PDZ domain containing

Basic information

Region (hg38): X:153802166-153830565

Previous symbols: [ "PDZK4" ]

Links

ENSG00000067840 ∙ NCBI:57595 ∙ OMIM:300634 ∙ HGNC:21167 ∙ Uniprot:Q76G19 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PDZD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDZD4 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4		4
missense			43	5		48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	9	0

Variants in PDZD4

This is a list of pathogenic ClinVar variants found in the PDZD4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-153803400-C-A		not specified	Uncertain significance (Oct 28, 2024)
X-153803412-C-T		not specified	Likely benign (Oct 06, 2021)
X-153803467-C-T			Likely benign (Dec 01, 2022)
X-153803473-C-G		Autism;Hypotonia;Hand tremor;Abnormal facial shape;Kyphoscoliosis	Uncertain significance (Oct 09, 2022)
X-153803643-G-A		not specified	Uncertain significance (May 18, 2022)
X-153803757-C-G		not specified	Uncertain significance (Mar 17, 2023)
X-153803869-G-C		not specified	Uncertain significance (Jun 05, 2023)
X-153803873-C-T		not specified	Uncertain significance (Mar 01, 2024)
X-153803916-T-C		not specified	Uncertain significance (Jan 09, 2025)
X-153803925-G-A		not specified	Uncertain significance (Oct 03, 2024)
X-153803954-C-A		not specified	Uncertain significance (Jan 21, 2025)
X-153804021-G-C		not specified	Uncertain significance (May 16, 2023)
X-153804024-G-A		not specified	Uncertain significance (Jun 06, 2023)
X-153804029-C-T		not specified	Uncertain significance (Oct 06, 2024)
X-153804030-G-A		not specified	Uncertain significance (Dec 07, 2021)
X-153804063-G-A		not specified	Uncertain significance (Nov 12, 2024)
X-153804082-G-C		not specified	Uncertain significance (Dec 01, 2022)
X-153804122-G-C		not specified	Uncertain significance (Nov 14, 2023)
X-153804122-G-T		not specified	Likely benign (May 07, 2024)
X-153804125-G-A		not specified	Uncertain significance (Jul 10, 2024)
X-153804153-G-A		not specified	Uncertain significance (May 13, 2022)
X-153804158-A-C		not specified	Uncertain significance (Jan 05, 2022)
X-153804167-T-C		not specified	Uncertain significance (Feb 28, 2023)
X-153804171-C-T		not specified	Uncertain significance (Sep 02, 2024)
X-153804206-G-A		not specified	Uncertain significance (Feb 06, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDZD4	protein_coding	protein_coding	ENST00000164640	8	28400

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.849	0.151	125594	4	3	125601	0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.70	239	389	0.614	0.0000393	4985
Missense in Polyphen		70	176.36	0.39692		1991
Synonymous	0.485	165	173	0.953	0.0000179	1597
Loss of Function	3.45	3	19.4	0.155	0.00000151	310

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000135	0.0000993
East Asian	0.0000722	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000503	0.0000352
Middle Eastern	0.0000722	0.0000544
South Asian	0.0000565	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.121
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.88

Haploinsufficiency Scores

• pHI: 0.468
• hipred: Y
• hipred_score: 0.718
• ghis: 0.561

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0335

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pdzd4
• Phenotype: normal phenotype

Gene ontology

• Biological process: protein ubiquitination
• Cellular component: cell cortex
• Molecular function: ubiquitin protein ligase activity