PDZD2

PDZ domain containing 2, the group of PDZ domain containing

Basic information

Region (hg38): 5:31639130-32110932

Previous symbols: [ "PDZK3" ]

Links

ENSG00000133401 ∙ NCBI:23037 ∙ OMIM:610697 ∙ HGNC:18486 ∙ Uniprot:O15018 ∙ 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 PDZD2 gene.

• Inborn genetic diseases (131 variants)
• not provided (19 variants)
• not specified (1 variants)
• PDZD2-related disorder (1 variants)
• PDZD2-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDZD2 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			1	5	3	9
missense			123	13	5	141
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	124	18	8

Variants in PDZD2

This is a list of pathogenic ClinVar variants found in the PDZD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-31799264-G-A		PDZD2-related disorder	Benign (Dec 31, 2019)
5-31799331-A-T		not specified	Uncertain significance (Oct 14, 2023)
5-31799337-C-G			Benign (Aug 08, 2018)
5-31799359-G-A		PDZD2-related disorder	Benign (May 31, 2019)
5-31799372-C-A		not specified	Uncertain significance (Dec 19, 2023)
5-31799415-C-T		PDZD2-related disorder	Benign (Feb 24, 2020)
5-31799440-C-T		PDZD2-related disorder	Benign (Nov 18, 2019)
5-31799519-C-T		not specified	Uncertain significance (Dec 21, 2022)
5-31799540-G-A		not specified	Uncertain significance (Oct 04, 2022)
5-31799547-G-T		not specified	Uncertain significance (Jun 22, 2021)
5-31799663-C-T		not specified	Uncertain significance (Dec 21, 2022)
5-31799664-G-A		not specified	Uncertain significance (Jul 14, 2021)
5-31983157-A-T		PDZD2-related disorder	Likely benign (May 02, 2019)
5-31983211-G-A		not specified	Uncertain significance (Apr 25, 2022)
5-31983245-C-T		PDZD2-related disorder	Likely benign (Oct 26, 2023)
5-31983255-A-T		not specified	Uncertain significance (Dec 20, 2022)
5-31983301-G-A		not specified	Likely benign (Jan 31, 2024)
5-31983322-G-A		PDZD2-related disorder	Likely benign (Aug 08, 2019)
5-31983337-G-A		not specified	Uncertain significance (Jan 03, 2024)
5-31983354-C-A		PDZD2-related disorder	Benign (Feb 18, 2019)
5-31983423-G-A		not specified	Uncertain significance (Jan 23, 2023)
5-31983435-G-A		not specified	Uncertain significance (Dec 20, 2021)
5-31983459-G-A		not specified	Uncertain significance (Jan 17, 2024)
5-31983522-G-C		not specified	Uncertain significance (Feb 10, 2022)
5-31983523-A-C		not specified	Uncertain significance (Oct 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDZD2	protein_coding	protein_coding	ENST00000438447	24	471521

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00306	125650	1	97	125748	0.000390

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.69	1439	1.63e+3	0.882	0.0000968	18372
Missense in Polyphen		404	544.8	0.74155		6266
Synonymous	-0.232	693	685	1.01	0.0000445	6023
Loss of Function	7.55	19	101	0.188	0.00000566	1210

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00138	0.00138
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000222	0.000217
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000327	0.000308
Middle Eastern	0.000222	0.000217
South Asian	0.000394	0.000359
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.162

Intolerance Scores

• loftool: 0.533
• rvis_EVS: 0.25
• rvis_percentile_EVS: 69.67

Haploinsufficiency Scores

• pHI: 0.115
• hipred: N
• hipred_score: 0.321
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.581

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdzd2

Gene ontology

• Biological process: cell adhesion
• Cellular component: extracellular region;nucleus;cytoplasm;endoplasmic reticulum;cell-cell junction