PDZD9

Gene

PDZ domain containing 9, the group of PDZ domain containing

Gene summary

No gene description available in the current model. Review primary literature for detailed gene function and characteristics.

Previous symbols:

C16orf65

MANE transcript

NM_001363519.1

Inheritance

—

ClinVar variants

U:21B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.59

Max pathogenic AF

—

Genomic locus

chr16:21,983,865-22,001,116

External References & Databases

Ensembl (ENSG00000155714)

Transcript & Mutation Effects

hg38 • Region Span ~17.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PDZD9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 23

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001363519.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			21 clinvar	2 clinvar		23
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	21	3	0	24

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001363519.1	RefSeq	NP_001350448.1	4	MANE Select
ENST00000424898.3	Ensembl	ENSP00000400514.2	4	MANE Select
NM_001370530.1	RefSeq	NP_001357459.1	3	Standard
NM_173806.4	RefSeq	NP_776167.2	3	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000537222
Coding exons: 3
Length: 17248
Individuals with no LoFs: 125346
Homozygous LoFs: 0
Heterozygous LoFs: 382
Defined: 125728
p: 0.00152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.827	79	103	0.770	0.00000472	1344
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00064	0.00062	rare
Latino/Admixed American	0.0011	0.00093	notable
Ashkenazi Jewish	0.00027	0.00020	rare
East Asian	0.00069	0.00065	rare
Finnish	0.0024	0.0022	notable
European (Non-Finnish)	0.0026	0.0024	notable
South Asian	0.000088	0.000065	rare
Other	0.0015	0.0013	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 0.04
RVIS percentile EVS: 56.64

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.283

Gene Damage Prediction

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