PTPDC1

Summary

PTPDC1 (protein tyrosine phosphatase domain containing 1, HGNC:30184) is a protein-coding gene on chromosome 9q22.32, encoding Protein tyrosine phosphatase domain-containing protein 1 (A2A3K4). May play roles in cilia formation and/or maintenance.

The protein encoded by this gene contains a characteristic motif of protein tyrosine phosphatases (PTPs). PTPs regulate activities of phosphoproteins through dephosphorylation. They are signaling molecules involved in the regulation of a wide variety of biological processes. The specific function of this protein has not yet been determined. Alternatively spliced transcript variants encoding distinct isoforms have been identified.

Source: NCBI Gene 138639 — RefSeq curated summary.

At a glance

• GWAS associations: 12
• Clinical variants (ClinVar): 92 total
• MANE Select transcript: NM_001253829

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30184
Approved symbol	PTPDC1
Name	protein tyrosine phosphatase domain containing 1
Location	9q22.32
Locus type	gene with protein product
Status	Approved
Aliases	PTP9Q22, FLJ37312
Ensembl gene	ENSG00000158079
Ensembl biotype	protein_coding
Entrez	138639

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000288976, ENST00000375360, ENST00000467049, ENST00000620992, ENST00000650567

RefSeq mRNA: 4 — MANE Select: NM_001253829 NM_001253829, NM_001253830, NM_152422, NM_177995

CCDS: CCDS6707, CCDS6708, CCDS75860

Canonical transcript exons

ENST00000620992 — 9 exons

Exon	Start	End
ENSE00003638753	94104275	94104385
ENSE00003716234	94107828	94109853
ENSE00003732732	94084464	94084774
ENSE00003888785	94085251	94085422
ENSE00003889995	94097321	94098579
ENSE00003890762	94087831	94087911
ENSE00003892411	94101566	94101751
ENSE00003894434	94095317	94095454
ENSE00003895834	94088145	94088263

Expression profiles

Bgee: expression breadth ubiquitous, 224 present calls, max score 90.57.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.9773 / max 217.0966, expressed in 1650 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
97441	4.7290	1601
97444	1.2100	245
97446	1.1344	285
97442	0.5666	285
97445	0.3372	153

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tibial nerve	UBERON:0001323	90.57	gold quality
endothelial cell	CL:0000115	88.10	gold quality
sural nerve	UBERON:0015488	86.83	gold quality
corpus callosum	UBERON:0002336	84.65	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.81	gold quality
tibia	UBERON:0000979	83.66	gold quality
Brodmann (1909) area 46	UBERON:0006483	83.07	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	82.94	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.79	gold quality
nucleus accumbens	UBERON:0001882	82.42	gold quality
visceral pleura	UBERON:0002401	82.00	gold quality
epithelial cell of pancreas	CL:0000083	81.96	silver quality
calcaneal tendon	UBERON:0003701	81.87	gold quality
Brodmann (1909) area 23	UBERON:0013554	81.87	gold quality
caudate nucleus	UBERON:0001873	81.78	gold quality
spinal cord	UBERON:0002240	81.49	gold quality
putamen	UBERON:0001874	81.38	gold quality
medial globus pallidus	UBERON:0002477	80.54	gold quality
tendon	UBERON:0000043	80.53	gold quality
right atrium auricular region	UBERON:0006631	80.50	gold quality
tendon of biceps brachii	UBERON:0008188	80.35	gold quality
apex of heart	UBERON:0002098	80.00	gold quality
primary visual cortex	UBERON:0002436	79.93	gold quality
cardiac atrium	UBERON:0002081	79.78	gold quality
Ammon’s horn	UBERON:0001954	79.60	gold quality
heart left ventricle	UBERON:0002084	79.58	gold quality
mucosa of stomach	UBERON:0001199	79.51	gold quality
adenohypophysis	UBERON:0002196	79.36	gold quality
cardiac ventricle	UBERON:0002082	79.16	gold quality
secondary oocyte	CL:0000655	79.13	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ENAD-17	no	1871.84
E-ANND-3	no	4.26

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

110 targeting PTPDC1, 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-5692A	100.00	74.40	6850
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-3671	99.90	73.04	3897

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	zgc:77752	ENSDARG00000042387
mus_musculus	Ptpdc1	ENSMUSG00000038042
rattus_norvegicus	Ptpdc1	ENSRNOG00000086607
caenorhabditis_elegans		WBGENE00020444

Paralogs (8): CDC14A (ENSG00000079335), CDC14B (ENSG00000081377), CDKN3 (ENSG00000100526), PALD1 (ENSG00000107719), PTP4A1 (ENSG00000112245), PTP4A2 (ENSG00000184007), PTP4A3 (ENSG00000184489), CDC14C (ENSG00000218305)

Protein

Protein identifiers

Protein tyrosine phosphatase domain-containing protein 1 — A2A3K4 (reviewed: A2A3K4)

All UniProt accessions (2): A0A087WTF0, A2A3K4

UniProt curated annotations — full annotation on UniProt →

Function. May play roles in cilia formation and/or maintenance.

Similarity. Belongs to the protein-tyrosine phosphatase family. Non-receptor class PTPDC1 subfamily.

Isoforms (2)

UniProt ID	Names	Canonical?
A2A3K4-1	1	yes
A2A3K4-2	2

RefSeq proteins (4): NP_001240758, NP_001240759, NP_689635, NP_818931 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000340	Dual-sp_phosphatase_cat-dom	Domain
IPR000387	Tyr_Pase_dom	Domain
IPR003595	Tyr_Pase_cat	Domain
IPR016130	Tyr_Pase_AS	Active_site
IPR020422	TYR_PHOSPHATASE_DUAL_dom	Domain
IPR029021	Prot-tyrosine_phosphatase-like	Homologous_superfamily
IPR049573	PTPDC1_PTP	Domain
IPR050561	PTP	Family

Pfam: PF00782

UniProt features (13 total): sequence conflict 3, modified residue 3, chain 1, domain 1, region of interest 1, compositionally biased region 1, active site 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A2A3K4-F1	70.60	0.49

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 190 (phosphocysteine intermediate)

Post-translational modifications (3): 392, 394, 547

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 104 (showing top): LINDGREN_BLADDER_CANCER_CLUSTER_2A_DN, GOBP_CILIUM_ORGANIZATION, GOBP_ORGANELLE_ASSEMBLY, chr9q22, RFX1_02, GOBP_CELL_PROJECTION_ORGANIZATION, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, BOYLAN_MULTIPLE_MYELOMA_PCA3_UP, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ESTER_BONDS, GOMF_PHOSPHORIC_ESTER_HYDROLASE_ACTIVITY, GOMF_PROTEIN_TYROSINE_PHOSPHATASE_ACTIVITY, GABRIELY_MIR21_TARGETS, LINDGREN_BLADDER_CANCER_CLUSTER_1_UP, GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_DN, GOMF_PHOSPHOPROTEIN_PHOSPHATASE_ACTIVITY

GO Biological Process (5): cilium assembly (GO:0060271), protein dephosphorylation (GO:0006470), smoothened signaling pathway (GO:0007224), dephosphorylation (GO:0016311), cell projection organization (GO:0030030)

GO Molecular Function (4): protein tyrosine phosphatase activity (GO:0004725), phosphoprotein phosphatase activity (GO:0004721), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (3): nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
axoneme assembly	1
intraciliary transport involved in cilium assembly	1
cilium organization	1
protein localization to cilium	1
organelle assembly	1
trans-Golgi to periciliary membrane compartment transport	1
plasma membrane bounded cell projection assembly	1
ciliary transition zone assembly	1
dephosphorylation	1
protein modification process	1
cell surface receptor signaling pathway	1
phosphate-containing compound metabolic process	1
cellular component organization	1
phosphoprotein phosphatase activity	1
phosphatase activity	1
catalytic activity, acting on a protein	1
binding	1
catalytic activity	1
nuclear lumen	1
intracellular anatomical structure	1
cytoplasm	1

Protein interactions and networks

STRING

636 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PTPDC1	CCDC73	Q6ZRK6	534
PTPDC1	ERCC6L	Q2NKX8	509
PTPDC1	KLK9	Q9UKQ9	476
PTPDC1	CFAP20DC	Q6ZVT6	474
PTPDC1	IPPK	Q9H8X2	470
PTPDC1	LRRC4B	Q9NT99	452
PTPDC1	PLEKHN1	Q494U1	449
PTPDC1	ZNF396	Q96N95	446
PTPDC1	SMC5	Q8IY18	425
PTPDC1	OR1E2	P47887	410
PTPDC1	IQUB	Q8NA54	404
PTPDC1	TMEM212	A6NML5	399
PTPDC1	KIF20A	O95235	396
PTPDC1	ZNF462	Q96JM2	395
PTPDC1	GPER1	Q99527	393

IntAct

26 interactions, top by confidence:

A	B	Type	Score
PTPDC1	MAPK1	psi-mi:“MI:0915”(physical association)	0.670
PTPDC1	MID2	psi-mi:“MI:0915”(physical association)	0.560
PTPDC1	TEX11	psi-mi:“MI:0915”(physical association)	0.560
PTPDC1	CRKL	psi-mi:“MI:0915”(physical association)	0.560
PTPDC1	DCAF7	psi-mi:“MI:0914”(association)	0.510
PTPDC1	LMTK2	psi-mi:“MI:0915”(physical association)	0.370
PTPDC1	AATK	psi-mi:“MI:0915”(physical association)	0.370
PTPDC1	ERBB4	psi-mi:“MI:0915”(physical association)	0.370
PTPDC1	ERBB3	psi-mi:“MI:0915”(physical association)	0.370
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
PCBD1	PTPDC1	psi-mi:“MI:0914”(association)	0.350
ARL2	PTPDC1	psi-mi:“MI:0914”(association)	0.350
PTPDC1	CASK	psi-mi:“MI:0914”(association)	0.350
PTPDC1	DDX3Y	psi-mi:“MI:0914”(association)	0.350
PTPDC1	YWHAQ	psi-mi:“MI:0914”(association)	0.350
DCAF7	PTPDC1	psi-mi:“MI:0915”(physical association)	0.000
BBS12	PTPDC1	psi-mi:“MI:0915”(physical association)	0.000
PTPDC1	MID2	psi-mi:“MI:0915”(physical association)	0.000
PTPDC1	TEX11	psi-mi:“MI:0915”(physical association)	0.000
PTPDC1	CRKL	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (102): PTPDC1 (Affinity Capture-MS), FBXO3 (Affinity Capture-MS), HARS (Affinity Capture-MS), MAPK1 (Affinity Capture-MS), MAPK3 (Affinity Capture-MS), PPP2CA (Affinity Capture-MS), PPP2R1A (Affinity Capture-MS), PPP2R2A (Affinity Capture-MS), PPP2R2D (Affinity Capture-MS), USP9X (Affinity Capture-MS), YWHAQ (Affinity Capture-MS), PPP2CA (Affinity Capture-MS), ARL2 (Affinity Capture-MS), PPP2R2D (Affinity Capture-MS), CASK (Affinity Capture-MS)

ESM2 similar proteins: A0A1W2PPD8, A1A5Q5, A2A3K4, A4H5X5, A7E379, B2RXH2, C0SUT9, D3ZKV9, F5HB62, O19132, O36371, O54705, O60291, O75164, O94953, P03177, P33802, P35228, Q1HVD1, Q29RJ0, Q3KSQ2, Q3U2K5, Q3UPF5, Q53WJ1, Q5R4R7, Q5R978, Q5RD88, Q5VW22, Q5VWQ0, Q6B0I6, Q6EEF3, Q6EMB2, Q6PI47, Q6X4W1, Q80T69, Q80TL4, Q8BFX3, Q8BW72, Q8CHB8, Q8K3Y6

Diamond homologs: A0A0R4IVA4, A1L1R5, A2A3K4, A4D256, A6N3Q4, A7E379, O60729, P35821, P81299, Q00684, Q196Z3, Q4CUJ8, Q59NH8, Q63739, Q6GQT0, Q6NT99, Q6NZK8, Q78EG7, Q86IL4, Q93096, Q9BVJ7, Q9TSM6, Q9UNH5, Q6NKR2, Q9ZQP1, A2VDT1, O61722, O70274, O75365, Q12974, Q5B323, Q5R7J8, Q6P9X4, Q6PFY9, Q9D658, Q9P7H1, Q9PUT6, O94526, Q16667, Q91FX3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	72
Likely benign	8
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1085 predictions. Top by Δscore:

Variant	Effect	Δscore
9:94084769:G:GG	donor_gain	1.0000
9:94088260:GGCA:G	donor_gain	1.0000
9:94088261:GCAG:G	donor_gain	1.0000
9:94088264:G:GG	donor_gain	1.0000
9:94095315:A:AG	acceptor_gain	1.0000
9:94095316:G:GG	acceptor_gain	1.0000
9:94095409:G:GT	donor_gain	1.0000
9:94095451:ACAGG:A	donor_loss	1.0000
9:94095452:CAGGT:C	donor_loss	1.0000
9:94095453:AGG:A	donor_loss	1.0000
9:94095454:GG:G	donor_loss	1.0000
9:94095455:G:C	donor_loss	1.0000
9:94095456:T:A	donor_loss	1.0000
9:94104273:AG:A	acceptor_gain	1.0000
9:94104274:GG:G	acceptor_gain	1.0000
9:94104381:CTAAG:C	donor_loss	1.0000
9:94104382:TAAGG:T	donor_loss	1.0000
9:94104383:AAGGT:A	donor_loss	1.0000
9:94104384:AG:A	donor_loss	1.0000
9:94104385:GG:G	donor_loss	1.0000
9:94104386:GT:G	donor_loss	1.0000
9:94104387:T:A	donor_loss	1.0000
9:94107826:A:C	acceptor_loss	1.0000
9:94107827:G:A	acceptor_loss	1.0000
9:94107827:GGTTA:G	acceptor_gain	1.0000
9:94088143:A:G	acceptor_gain	0.9900
9:94088144:GCCAT:G	acceptor_gain	0.9900
9:94095312:CCTA:C	acceptor_loss	0.9900
9:94095314:TAGTT:T	acceptor_loss	0.9900
9:94095315:A:AC	acceptor_loss	0.9900

AlphaMissense

5306 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:94088169:C:A	N120K	0.998
9:94088169:C:G	N120K	0.998
9:94095430:T:C	C190R	0.998
9:94095432:T:G	C190W	0.998
9:94095439:G:T	G193W	0.998
9:94085328:T:C	C54R	0.997
9:94088171:T:C	L121P	0.997
9:94095337:T:A	W159R	0.997
9:94095337:T:C	W159R	0.997
9:94097374:G:C	A216P	0.997
9:94097411:T:A	I228K	0.997
9:94085330:T:G	C54W	0.996
9:94088227:T:C	F140L	0.996
9:94088229:C:A	F140L	0.996
9:94088229:C:G	F140L	0.996
9:94095343:G:C	D161H	0.996
9:94095344:A:T	D161V	0.996
9:94095440:G:A	G193E	0.996
9:94097335:T:C	C203R	0.996
9:94097337:T:G	C203W	0.996
9:94097390:G:C	R221P	0.996
9:94097399:G:C	R224P	0.996
9:94097411:T:G	I228R	0.996
9:94097447:T:C	F240S	0.996
9:94101650:T:A	W646R	0.996
9:94101650:T:C	W646R	0.996
9:94087851:C:A	A92D	0.995
9:94095344:A:C	D161A	0.995
9:94095397:T:C	F179L	0.995
9:94095399:T:A	F179L	0.995

dbSNP variants (sampled 300 via entrez): RS1000034449 (9:94052023 C>T), RS1000139584 (9:94102759 G>T), RS1000168053 (9:94035174 G>C), RS1000169901 (9:94108075 A>G), RS1000206576 (9:94030436 G>A), RS1000229871 (9:94080205 G>A), RS1000278221 (9:94103074 A>C,G), RS1000309231 (9:94103463 A>G), RS1000343050 (9:94096233 C>G), RS1000399779 (9:94073039 G>C), RS1000467199 (9:94065665 C>T), RS1000494496 (9:94044503 C>G), RS1000552724 (9:94052238 A>C), RS1000580386 (9:94080508 G>A,T), RS1000619232 (9:94087102 C>G,T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

12 associations (top):

Study	Trait	p-value
GCST000817_122	Height	1.000000e-09
GCST002232_6	Esophageal adenocarcinoma	2.000000e-06
GCST002782_209	Waist-to-hip ratio adjusted for body mass index	1.000000e-06
GCST002782_210	Waist-to-hip ratio adjusted for body mass index	5.000000e-07
GCST003059_16	Parkinson’s disease	1.000000e-06
GCST004064_77	Waist-hip ratio	4.000000e-08
GCST006867_107	Type 2 diabetes	1.000000e-08
GCST006979_364	Heel bone mineral density	6.000000e-10
GCST006979_365	Heel bone mineral density	1.000000e-13
GCST008362_185	Birth weight	1.000000e-11
GCST012227_463	Hip circumference adjusted for BMI	2.000000e-10
GCST012229_71	Hip index	2.000000e-10

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0004343	waist-hip ratio
EFO:0009270	heel bone mineral density
EFO:0004344	birth weight
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

35 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases expression	4
sodium arsenite	increases abundance, increases expression, decreases expression, affects cotreatment	3
Benzo(a)pyrene	increases expression, increases methylation, increases mutagenesis	3
Cyclosporine	increases expression	3
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
FR900359	decreases phosphorylation	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, increases methylation	1
trichostatin A	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
perfluorooctanoic acid	increases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
avobenzone	increases expression	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
NSC 689534	increases expression, affects binding	1
Decitabine	affects expression	1
Arsenic Trioxide	decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Leflunomide	increases expression	1
Acetaminophen	increases expression	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Caffeine	decreases phosphorylation	1
Cisplatin	affects expression	1
Copper	affects binding, increases expression	1
Doxorubicin	decreases expression	1
Manganese	affects cotreatment, decreases expression, increases abundance	1
Tetrachlorodibenzodioxin	affects expression	1

Clinical trials (associated diseases)

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