PDZD2

PDZ domain containing 2, the group of PDZ domain containing

Basic information

Region (hg38): 5:31639131-32110932

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.

• not_specified (414 variants)
• PDZD2-related_disorder (83 variants)
• not_provided (20 variants)
• Lissencephaly (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. These statistics are base on transcript: NM_000178140.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				37	16	53
missense			383	44	16	443
nonsense			1			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	384	81	32

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