PDZD9

PDZ domain containing 9, the group of PDZ domain containing

Basic information

Region (hg38): 16:21983865-22001116

Previous symbols: [ "C16orf65" ]

Links

ENSG00000155714 ∙ NCBI:255762 ∙ ∙ HGNC:28740 ∙ Uniprot:Q8IXQ8 ∙ 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 PDZD9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDZD9 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		1
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in PDZD9

This is a list of pathogenic ClinVar variants found in the PDZD9 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-21984272-C-A		not specified	Uncertain significance (Dec 17, 2023)
16-21984317-A-C		not specified	Uncertain significance (Sep 15, 2021)
16-21984367-C-T		not specified	Uncertain significance (Jan 04, 2024)
16-21984446-C-T		not specified	Uncertain significance (Feb 28, 2023)
16-21984496-T-C		not specified	Uncertain significance (Dec 03, 2021)
16-21984509-C-T		not specified	Uncertain significance (Mar 19, 2024)
16-21984535-G-T		not specified	Uncertain significance (Jun 23, 2023)
16-21984571-T-C		not specified	Uncertain significance (Feb 07, 2023)
16-21984579-T-G		not specified	Uncertain significance (Mar 14, 2023)
16-21984595-A-G		not specified	Uncertain significance (Sep 12, 2023)
16-21988775-A-G			Likely benign (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDZD9	protein_coding	protein_coding	ENST00000537222	3	17248

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00280	0.815	125346	0	382	125728	0.00152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.827	79	103	0.770	0.00000472	1344
Missense in Polyphen		22	34.996	0.62864		454
Synonymous	-0.463	41	37.4	1.10	0.00000190	371
Loss of Function	1.09	5	8.43	0.593	5.06e-7	101

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00169	0.00167
Ashkenazi Jewish	0.000272	0.000198
East Asian	0.000686	0.000653
Finnish	0.00240	0.00222
European (Non-Finnish)	0.00264	0.00236
Middle Eastern	0.000686	0.000653
South Asian	0.0000883	0.0000653
Other	0.00155	0.00130

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.132
• hipred: N
• hipred_score: 0.173
• ghis: 0.380

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdzd9