PDZD9

Summary

PDZD9 (PDZ domain containing 9, HGNC:28740) is a protein-coding gene on chromosome 16p12.2, encoding PDZ domain-containing protein 9 (Q8IXQ8).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 180 total — 1 pathogenic, 3 likely-pathogenic
• MANE Select transcript: NM_001363519

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28740
Approved symbol	PDZD9
Name	PDZ domain containing 9
Location	16p12.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC50721
Ensembl gene	ENSG00000155714
Ensembl biotype	protein_coding
Entrez	255762

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 nonsense_mediated_decay

ENST00000424898, ENST00000523914, ENST00000537222

RefSeq mRNA: 3 — MANE Select: NM_001363519 NM_001363519, NM_001370530, NM_173806

CCDS: CCDS10602, CCDS92124

Canonical transcript exons

ENST00000424898 — 4 exons

Exon	Start	End
ENSE00003475342	21988602	21988791
ENSE00003625681	21983865	21984660
ENSE00003690579	21996322	21996501
ENSE00003903674	22001017	22001116

Expression profiles

Bgee: expression breadth ubiquitous, 118 present calls, max score 81.41.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0431 / max 42.8531, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
156739	0.0431	3

Top tissues by expression

124 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	81.41	gold quality
testis	UBERON:0000473	81.26	gold quality
right testis	UBERON:0004534	80.47	gold quality
cerebellar cortex	UBERON:0002129	66.21	gold quality
cerebellar hemisphere	UBERON:0002245	66.20	gold quality
cortical plate	UBERON:0005343	66.10	gold quality
cerebellum	UBERON:0002037	66.05	gold quality
right hemisphere of cerebellum	UBERON:0014890	65.02	gold quality
prefrontal cortex	UBERON:0000451	61.00	gold quality
Brodmann (1909) area 9	UBERON:0013540	60.68	gold quality
nucleus accumbens	UBERON:0001882	60.05	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	60.03	gold quality
primary visual cortex	UBERON:0002436	59.88	gold quality
frontal cortex	UBERON:0001870	59.70	gold quality
putamen	UBERON:0001874	59.60	gold quality
superior frontal gyrus	UBERON:0002661	59.47	gold quality
cerebral cortex	UBERON:0000956	58.64	gold quality
caudate nucleus	UBERON:0001873	58.39	gold quality
anterior cingulate cortex	UBERON:0009835	58.12	gold quality
brain	UBERON:0000955	57.95	gold quality
right frontal lobe	UBERON:0002810	57.90	gold quality
skeletal muscle tissue	UBERON:0001134	57.84	silver quality
adrenal tissue	UBERON:0018303	56.34	gold quality
hypothalamus	UBERON:0001898	55.25	gold quality
Ammon’s horn	UBERON:0001954	53.84	gold quality
muscle tissue	UBERON:0002385	53.38	silver quality
granulocyte	CL:0000094	53.25	gold quality
temporal lobe	UBERON:0001871	53.13	gold quality
amygdala	UBERON:0001876	53.05	gold quality
substantia nigra	UBERON:0002038	52.92	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

29 targeting PDZD9, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-142-3P	99.62	71.30	974
HSA-MIR-3120-3P	99.54	70.28	2669
HSA-MIR-514B-5P	99.50	68.19	1766
HSA-MIR-3123	99.47	67.15	2693
HSA-MIR-1324	99.46	66.57	1302
HSA-MIR-4762-3P	99.43	69.72	2363
HSA-MIR-4316	99.37	65.75	1360
HSA-MIR-10522-5P	99.26	68.50	2087
HSA-MIR-593-3P	99.22	67.28	1327
HSA-MIR-4263	99.18	69.25	2236
HSA-MIR-6814-5P	99.03	66.68	1273
HSA-MIR-6895-3P	98.79	65.69	996
HSA-MIR-2276-3P	98.76	67.75	1384
HSA-MIR-5197-3P	98.71	67.05	1905
HSA-MIR-3161	98.71	67.14	816
HSA-MIR-6818-3P	98.56	68.23	1307
HSA-MIR-4684-5P	98.29	67.99	1650
HSA-MIR-4778-5P	97.96	68.06	1634
HSA-MIR-1271-3P	97.56	64.85	865
HSA-MIR-550A-3-5P	97.56	65.35	823
HSA-MIR-550A-5P	97.56	65.35	823
HSA-MIR-7855-5P	97.39	67.18	925
HSA-MIR-4288	97.11	67.23	1636
HSA-MIR-4509	96.19	65.80	900
HSA-MIR-193A-5P	95.70	65.33	613

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Pdzd9	ENSMUSG00000030887
rattus_norvegicus	Pdzd9	ENSRNOG00000016292

Protein

Protein identifiers

PDZ domain-containing protein 9 — Q8IXQ8 (reviewed: Q8IXQ8)

All UniProt accessions (2): Q8IXQ8, E5RJ18

Isoforms (3)

UniProt ID	Names	Canonical?
Q8IXQ8-1	1	yes
Q8IXQ8-2	2
Q8IXQ8-3	3

RefSeq proteins (3): NP_001350448, NP_001357459, NP_776167 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001478	PDZ	Domain
IPR036034	PDZ_sf	Homologous_superfamily
IPR039179	PDZD9	Family

Pfam: PF00595

UniProt features (5 total): splice variant 3, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IXQ8-F1	64.69	0.30

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 33 (showing top): LFA1_Q6, TGANTCA_AP1_C, HAND1E47_01, FOXJ2_02, chr16p12, PR_Q2, PR_01, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_129_MOUSE_DN, ZNF2_TARGET_GENES, ZNF213_TARGET_GENES, MIR4684_5P, MIR142_3P, MIR2276_3P, GSE13229_IMM_VS_INTMATURE_NKCELL_UP, GSE14026_TH1_VS_TH17_DN

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

318 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PDZD9	VWA3A	A6NCI4	753
PDZD9	FAM222B	Q8WU58	642
PDZD9	MISP3	Q96FF7	623
PDZD9	CFAP119	A1A4V9	598
PDZD9	OR51D1	Q8NGF3	533
PDZD9	TMCO6	Q96DC7	514
PDZD9	POLR3E	Q9NVU0	511
PDZD9	MPP4	Q96JB8	507
PDZD9	C16orf54	Q6UWD8	491
PDZD9	CEP152	O94986	482
PDZD9	FIMP1	Q96LL3	461
PDZD9	ASPHD1	Q5U4P2	458
PDZD9	OR2K2	Q8NGT1	454
PDZD9	MOSMO	Q8NHV5	435
PDZD9	REPS2	Q8NFH8	390

IntAct

28 interactions, top by confidence:

A	B	Type	Score
ABCC4	PDZD9	psi-mi:“MI:0407”(direct interaction)	0.440
ARHGEF16	PDZD9	psi-mi:“MI:0407”(direct interaction)	0.440
ASIC3	PDZD9	psi-mi:“MI:0407”(direct interaction)	0.440
ATP2B4	PDZD9	psi-mi:“MI:0407”(direct interaction)	0.440
CYSLTR2	PDZD9	psi-mi:“MI:0407”(direct interaction)	0.440
DGKK	PDZD9	psi-mi:“MI:0407”(direct interaction)	0.440
DGKZ	PDZD9	psi-mi:“MI:0407”(direct interaction)	0.440
DOCK4	PDZD9	psi-mi:“MI:0407”(direct interaction)	0.440
FRMPD4	PDZD9	psi-mi:“MI:0407”(direct interaction)	0.440
FZD7	PDZD9	psi-mi:“MI:0407”(direct interaction)	0.440
TAMALIN	PDZD9	psi-mi:“MI:0407”(direct interaction)	0.440
E6	PDZD9	psi-mi:“MI:0407”(direct interaction)	0.440
ORF putative E6	PDZD9	psi-mi:“MI:0407”(direct interaction)	0.440
KCNA5	PDZD9	psi-mi:“MI:0407”(direct interaction)	0.440
KIR3DL3	PDZD9	psi-mi:“MI:0407”(direct interaction)	0.440
MAP2K2	PDZD9	psi-mi:“MI:0407”(direct interaction)	0.440
PDZD9	PBK	psi-mi:“MI:0407”(direct interaction)	0.440
RALBP1	PDZD9	psi-mi:“MI:0407”(direct interaction)	0.440
RASSF6	PDZD9	psi-mi:“MI:0407”(direct interaction)	0.440
SLC15A5	PDZD9	psi-mi:“MI:0407”(direct interaction)	0.440
SLCO1C1	PDZD9	psi-mi:“MI:0407”(direct interaction)	0.440
TJP2	PDZD9	psi-mi:“MI:0407”(direct interaction)	0.440
E6	PDZD9	psi-mi:“MI:0915”(physical association)	0.400
E	PDZD9	psi-mi:“MI:0915”(physical association)	0.400
G3BP1	TMEM232	psi-mi:“MI:0914”(association)	0.350

BioGRID (10): PDZD9 (Synthetic Lethality), PDZD9 (Affinity Capture-MS), PDZD9 (Affinity Capture-MS), PDZD9 (Affinity Capture-MS), CAPRIN1 (Affinity Capture-MS), PDZD9 (Affinity Capture-MS), PDZD9 (Affinity Capture-MS), PDZD9 (Affinity Capture-MS), PLCL2 (Cross-Linking-MS (XL-MS)), APP (Reconstituted Complex)

ESM2 similar proteins: A2VE78, B2RWW0, B8A5Y1, C0HAC0, E2RSS3, F4JI46, F8W4H9, O42354, O94972, O94988, P0DM64, P23804, P56273, P56950, P56951, Q00987, Q503Y8, Q5BLK4, Q5R6E1, Q5SXH7, Q5VT97, Q5VYS8, Q60524, Q6IFT4, Q6INS1, Q6NKT5, Q6P4F7, Q6PCX9, Q6REY9, Q76N89, Q7YRZ8, Q7ZUW7, Q80Y19, Q8C2S5, Q8GYY5, Q8IVF5, Q8IXQ8, Q8K2H3, Q8K4P8, Q8N103

Diamond homologs: A1A5G4, O88382, Q32KW7, Q4L1J4, Q4R989, Q6RHR9, Q86UL8, Q8IXQ8, Q96QZ7, Q9D9M4, Q9WVQ1, Q8VBX6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

180 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	3
Uncertain significance	90
Likely benign	51
Benign	12

Top pathogenic / likely-pathogenic (4)

Variant ID	HGVS	Classification
1177305	NM_003366.4(UQCRC2):c.323G>A (p.Gly108Asp)	Pathogenic
1311711	NM_003366.4(UQCRC2):c.1020dup (p.Ile341fs)	Likely pathogenic
1678323	NM_003366.4(UQCRC2):c.967-1G>A	Likely pathogenic
2506293	NM_003366.4(UQCRC2):c.729dup (p.Leu244fs)	Likely pathogenic

SpliceAI

642 predictions. Top by Δscore:

Variant	Effect	Δscore
16:21988601:CCTTG:C	donor_gain	1.0000
16:21984661:C:CC	acceptor_gain	0.9900
16:21988597:TTTA:T	donor_loss	0.9900
16:21988598:TTACC:T	donor_loss	0.9900
16:21988599:TA:T	donor_loss	0.9900
16:21988600:A:AT	donor_loss	0.9900
16:21988790:ACCT:A	acceptor_loss	0.9900
16:21988791:CCTG:C	acceptor_loss	0.9900
16:21988792:CTGA:C	acceptor_loss	0.9900
16:21988793:T:A	acceptor_loss	0.9900
16:21984657:TGTG:T	acceptor_gain	0.9800
16:21993465:G:C	acceptor_gain	0.9800
16:21996498:CTTT:C	acceptor_gain	0.9800
16:21996507:C:CT	acceptor_gain	0.9800
16:21984659:TG:T	acceptor_gain	0.9700
16:21984659:TGCT:T	acceptor_loss	0.9700
16:21984660:GCTGA:G	acceptor_loss	0.9700
16:21984661:C:G	acceptor_loss	0.9700
16:21984662:T:A	acceptor_loss	0.9700
16:21988648:G:A	donor_gain	0.9700
16:21988792:C:CC	acceptor_gain	0.9600
16:21996502:C:CC	acceptor_gain	0.9600
16:21984663:G:C	acceptor_loss	0.9500
16:21988788:TCAC:T	acceptor_gain	0.9500
16:21988789:CACC:C	acceptor_gain	0.9500
16:21984666:A:AC	acceptor_gain	0.9300
16:21992783:C:A	donor_gain	0.9300
16:21996508:A:T	acceptor_gain	0.9300
16:22001012:GTTA:G	donor_loss	0.9300
16:22001013:TTAC:T	donor_loss	0.9300

AlphaMissense

1745 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:21996408:A:G	L42P	0.992
16:21988782:A:T	L74Q	0.991
16:21988651:A:G	W118R	0.990
16:21988651:A:T	W118R	0.990
16:21988677:C:G	R109P	0.987
16:21996381:A:G	L51P	0.987
16:21988758:A:T	V82E	0.986
16:21988773:A:T	V77D	0.985
16:21988782:A:C	L74R	0.984
16:21988782:A:G	L74P	0.984
16:21988788:T:A	D72V	0.983
16:21988791:C:A	G71V	0.983
16:21996330:A:G	L68P	0.983
16:21996412:C:G	G41R	0.983
16:21988695:A:G	L103P	0.982
16:21988785:A:T	V73D	0.982
16:21996435:A:G	L33P	0.982
16:21988788:T:C	D72G	0.981
16:21996348:G:T	A62E	0.981
16:21988725:A:G	L93P	0.980
16:21988649:C:A	W118C	0.979
16:21988649:C:G	W118C	0.979
16:21988788:T:G	D72A	0.979
16:21996381:A:T	L51H	0.978
16:21988789:C:G	D72H	0.976
16:21996375:A:C	I53S	0.975
16:21996378:T:G	Q52P	0.975
16:21996408:A:T	L42H	0.973
16:21996411:C:T	G41D	0.973
16:21996414:A:G	L40S	0.973

dbSNP variants (sampled 300 via entrez): RS1000016179 (16:21967433 G>A,T), RS1000023294 (16:21961172 A>C), RS1000084276 (16:21977578 A>G), RS1000135137 (16:21968865 A>G), RS1000220662 (16:21982215 C>T), RS1000263754 (16:21970235 G>A), RS1000278612 (16:21988157 G>A), RS1000478860 (16:21963622 C>G,T), RS1000559440 (16:21977283 G>A), RS1000633811 (16:21974005 C>A,G,T), RS1000734273 (16:21990421 C>T), RS1000795013 (16:21980947 G>C), RS1000852734 (16:22001362 G>T), RS1000883560 (16:21995398 T>C), RS1000883863 (16:22000961 A>G,T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:615160

GenCC curated gene-disease

Mondo (1): mitochondrial complex III deficiency nuclear type 5 (MONDO:0014066)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST009936_20	Venous thromboembolism	9.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
Benzo(a)pyrene	affects methylation	1
Catechin	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.