PXDC1

Summary

PXDC1 (PX domain containing 1, HGNC:21361) is a protein-coding gene on chromosome 6p25.2, encoding PX domain-containing protein 1 (Q5TGL8).

Predicted to enable phosphatidylinositol binding activity.

Source: NCBI Gene 221749 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 38 total
• MANE Select transcript: NM_183373

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21361
Approved symbol	PXDC1
Name	PX domain containing 1
Location	6p25.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000168994
Ensembl biotype	protein_coding
Entrez	221749

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000380277, ENST00000380283, ENST00000477592, ENST00000485986

RefSeq mRNA: 1 — MANE Select: NM_183373 NM_183373

CCDS: CCDS4486

Canonical transcript exons

ENST00000380283 — 5 exons

Exon	Start	End
ENSE00000000102	3722619	3723736
ENSE00001156008	3738057	3738148
ENSE00001484468	3751276	3751713
ENSE00003488360	3727551	3727662
ENSE00003663317	3737079	3737196

Expression profiles

Bgee: expression breadth ubiquitous, 290 present calls, max score 98.79.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.1712 / max 439.6829, expressed in 1394 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
71482	11.7723	1345
71484	0.9730	677
71483	0.3198	153
71481	0.1061	33

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ascending aorta	UBERON:0001496	98.79	gold quality
thoracic aorta	UBERON:0001515	98.78	gold quality
aorta	UBERON:0000947	98.56	gold quality
descending thoracic aorta	UBERON:0002345	98.47	gold quality
popliteal artery	UBERON:0002250	98.41	gold quality
tibial artery	UBERON:0007610	98.40	gold quality
right coronary artery	UBERON:0001625	98.06	gold quality
saphenous vein	UBERON:0007318	98.04	gold quality
right lobe of liver	UBERON:0001114	97.93	gold quality
left coronary artery	UBERON:0001626	97.73	gold quality
coronary artery	UBERON:0001621	97.68	gold quality
blood vessel layer	UBERON:0004797	96.92	gold quality
subcutaneous adipose tissue	UBERON:0002190	96.26	gold quality
liver	UBERON:0002107	96.22	gold quality
vena cava	UBERON:0004087	96.22	gold quality
synovial joint	UBERON:0002217	96.12	gold quality
omental fat pad	UBERON:0010414	95.96	gold quality
peritoneum	UBERON:0002358	95.93	gold quality
right lung	UBERON:0002167	95.86	gold quality
adipose tissue of abdominal region	UBERON:0007808	95.73	gold quality
gall bladder	UBERON:0002110	95.62	gold quality
adipose tissue	UBERON:0001013	95.38	gold quality
upper lobe of left lung	UBERON:0008952	95.36	gold quality
lower esophagus muscularis layer	UBERON:0035833	95.33	gold quality
lower esophagus	UBERON:0013473	95.29	gold quality
placenta	UBERON:0001987	95.28	gold quality
upper lobe of lung	UBERON:0008948	95.27	gold quality
amniotic fluid	UBERON:0000173	95.23	gold quality
mucosa of stomach	UBERON:0001199	95.21	gold quality
connective tissue	UBERON:0002384	95.05	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-7051	no	375.14
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

45 targeting PXDC1, 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-186-5P	99.99	70.83	3707
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-3663-3P	99.84	70.39	798
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-3180-5P	99.82	69.12	2422
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-323A-3P	99.79	70.30	1739
HSA-MIR-577	99.78	69.13	2479
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-4699-3P	99.71	70.15	3142
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-892A	99.54	68.16	1141
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-4519	99.48	66.10	859
HSA-MIR-32-3P	99.36	68.20	2517
HSA-MIR-520A-5P	99.35	66.72	1632
HSA-MIR-525-5P	99.35	66.85	1615
HSA-MIR-4506	99.34	67.47	526
HSA-MIR-488-5P	99.28	68.12	821
HSA-MIR-1286	99.09	66.23	1046
HSA-MIR-6868-5P	99.06	65.69	1284
HSA-MIR-412-3P	98.86	66.89	712
HSA-MIR-1288-5P	98.85	67.01	734
HSA-MIR-6754-3P	98.84	66.60	889

Literature-anchored findings (GeneRIF, showing 1)

• We used allele specific expression in lymphoblastoid cell lines from 306 Hutterites related in a single pedigree to provide formal evidence for parent of origin effects. Our approach identified two putative novel imprinted genes, PXDC1 and PWAR6, with asymmetrical parent of origin gene expression. (PMID:30204804)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	pxdc1b	ENSDARG00000040309
danio_rerio	pxdc1a	ENSDARG00000055177
mus_musculus	Pxdc1	ENSMUSG00000021411
rattus_norvegicus	Pxdc1	ENSRNOG00000017093

Protein

Protein identifiers

PX domain-containing protein 1 — Q5TGL8 (reviewed: Q5TGL8)

All UniProt accessions (2): Q5TGL8, H0Y3G1

RefSeq proteins (1): NP_899229* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR036871	PX_dom_sf	Homologous_superfamily
IPR040288	PXDC1	Family

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5TGL8-F1	70.33	0.43

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 152 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_UP, GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_UP, YAGI_AML_WITH_INV_16_TRANSLOCATION, CHX10_01, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_UP, chr6p25, KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN, CAIRO_HEPATOBLASTOMA_DN, GENTILE_UV_HIGH_DOSE_DN, ATTCTTT_MIR186, GENTILE_UV_RESPONSE_CLUSTER_D5, ONDER_CDH1_TARGETS_2_UP, CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN, HAN_SATB1_TARGETS_DN, TAATTA_CHX10_01

GO Biological Process (0):

GO Molecular Function (1): phosphatidylinositol binding (GO:0035091)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
anion binding	1

Protein interactions and networks

STRING

428 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PXDC1	FAM50B	Q9Y247	505
PXDC1	PRP4K	Q13523	472
PXDC1	SLC22A23	A1A5C7	445
PXDC1	RSBN1L	Q6PCB5	437
PXDC1	SLC22A3	O75751	423
PXDC1	ZNF316	A6NFI3	415
PXDC1	TMEM278	A6NKF7	415
PXDC1	KRTAP12-2	P59991	399
PXDC1	C12orf60	Q5U649	395
PXDC1	KRTAP10-2	P60368	393
PXDC1	KRTAP10-8	P60410	391
PXDC1	DNAAF9	Q5TEA3	380
PXDC1	SUPT3H	O75486	376
PXDC1	CALHM3	Q86XJ0	374
PXDC1	ERICH1	Q86X53	373

IntAct

13 interactions, top by confidence:

A	B	Type	Score
LIN7A	CASK	psi-mi:“MI:0914”(association)	0.830
LIN7C	ABLIM1	psi-mi:“MI:0914”(association)	0.530
LIN7B	CASK	psi-mi:“MI:0914”(association)	0.530
LIN7C	ABLIM1	psi-mi:“MI:0914”(association)	0.350
RABGAP1L	ACOT7	psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
CASK	ABLIM1	psi-mi:“MI:0914”(association)	0.350
RABGAP1L	HOXD13	psi-mi:“MI:0914”(association)	0.350
LIN7C	STK25	psi-mi:“MI:0914”(association)	0.350
APBA1	ABLIM1	psi-mi:“MI:0914”(association)	0.350
	PXDC1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (11): PXDC1 (Affinity Capture-MS), PXDC1 (Affinity Capture-MS), PXDC1 (Affinity Capture-MS), PXDC1 (Affinity Capture-MS), PXDC1 (Synthetic Lethality), PXDC1 (Affinity Capture-MS), PXDC1 (Affinity Capture-MS), PXDC1 (Affinity Capture-MS), PXDC1 (Affinity Capture-MS), PXDC1 (Affinity Capture-MS), PXDC1 (Affinity Capture-RNA)

ESM2 similar proteins: A1A4L0, A2AFR3, A6NI72, A8MVU1, F1LXF1, O15034, O43572, O77774, O88845, O95219, P11274, P14598, P21580, P57770, Q08BT5, Q08D85, Q14161, Q14CM0, Q3UGM2, Q4KLK8, Q5R4C2, Q5T6S3, Q5TGL8, Q60769, Q66H91, Q66T02, Q68FF6, Q6DFZ1, Q6IC98, Q6PAJ1, Q6RFZ7, Q6ZPY2, Q6ZWH5, Q8BIE6, Q8BY87, Q8C0Q9, Q8CB44, Q8JZU6, Q8K2Y9, Q8TBP0

Diamond homologs: Q08D85, Q4KLK8, Q5TGL8, Q8JZU6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	30
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1324 predictions. Top by Δscore:

Variant	Effect	Δscore
6:3727549:A:AC	donor_gain	1.0000
6:3727550:C:CC	donor_gain	1.0000
6:3727550:CAA:C	donor_gain	1.0000
6:3737197:C:CC	acceptor_gain	1.0000
6:3738053:TCA:T	donor_loss	1.0000
6:3738054:CACTT:C	donor_loss	1.0000
6:3738055:A:AC	donor_gain	1.0000
6:3738055:A:T	donor_loss	1.0000
6:3738056:C:CA	donor_gain	1.0000
6:3738056:C:T	donor_loss	1.0000
6:3738056:CTTT:C	donor_gain	1.0000
6:3738056:CTTTA:C	donor_gain	1.0000
6:3738092:TCTCC:T	donor_gain	1.0000
6:3738144:CAGTC:C	acceptor_gain	1.0000
6:3738145:AGTC:A	acceptor_gain	1.0000
6:3738146:GTC:G	acceptor_gain	1.0000
6:3738147:TC:T	acceptor_gain	1.0000
6:3738148:CC:C	acceptor_gain	1.0000
6:3738149:C:CC	acceptor_gain	1.0000
6:3738149:C:CG	acceptor_loss	1.0000
6:3738154:A:AC	acceptor_gain	1.0000
6:3738155:T:C	acceptor_gain	1.0000
6:3738155:T:TC	acceptor_gain	1.0000
6:3723732:CAAAT:C	acceptor_gain	0.9900
6:3723736:TC:T	acceptor_loss	0.9900
6:3723737:C:CA	acceptor_loss	0.9900
6:3723737:C:CC	acceptor_gain	0.9900
6:3723738:T:A	acceptor_loss	0.9900
6:3727543:ATAC:A	donor_loss	0.9900
6:3727544:TAC:T	donor_loss	0.9900

AlphaMissense

1520 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:3727640:A:C	F163L	0.998
6:3727640:A:T	F163L	0.998
6:3727642:A:G	F163L	0.998
6:3751369:G:T	R55S	0.996
6:3737165:A:G	F127S	0.995
6:3738085:A:G	L107P	0.995
6:3751399:A:G	W45R	0.995
6:3751399:A:T	W45R	0.995
6:3727641:A:G	F163S	0.994
6:3751418:G:C	F38L	0.994
6:3751418:G:T	F38L	0.994
6:3751420:A:G	F38L	0.994
6:3727635:A:G	L165S	0.993
6:3737174:A:G	L124P	0.993
6:3737187:A:G	S120P	0.993
6:3738106:A:G	L100P	0.993
6:3751319:A:C	F71L	0.993
6:3751319:A:T	F71L	0.993
6:3751321:A:G	F71L	0.993
6:3751374:A:G	L53P	0.993
6:3751514:A:C	F6L	0.993
6:3751514:A:T	F6L	0.993
6:3751516:A:G	F6L	0.993
6:3737168:A:G	F126S	0.992
6:3738088:A:G	L106P	0.992
6:3751487:G:C	F15L	0.992
6:3751487:G:T	F15L	0.992
6:3751489:A:G	F15L	0.992
6:3727644:C:T	G162E	0.991
6:3737147:T:A	D133V	0.991

dbSNP variants (sampled 300 via entrez): RS1000004263 (6:3728773 T>C), RS1000092839 (6:3741386 C>G), RS1000140862 (6:3726168 C>A), RS1000148426 (6:3730319 A>C), RS1000210307 (6:3744211 A>G,T), RS1000215018 (6:3726404 G>A,C), RS1000294490 (6:3749785 C>T), RS1000361541 (6:3739393 G>A), RS1000400344 (6:3750479 CCCGTCTCAATT>C), RS1000449623 (6:3731293 T>A,C), RS1000601618 (6:3743964 TG>T,TGG), RS1000794691 (6:3753522 C>T), RS1000808030 (6:3752111 G>A,T), RS1000857207 (6:3751232 G>A,C), RS1000907745 (6:3735241 C>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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, increases methylation	5
sodium arsenite	increases expression, decreases expression	3
Benzo(a)pyrene	decreases methylation, increases expression	3
Tetrachlorodibenzodioxin	increases expression	3
Cyclosporine	increases expression	3
mercuric bromide	increases expression, affects cotreatment	2
entinostat	affects cotreatment, increases expression	2
Panobinostat	affects cotreatment, increases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, increases expression	2
methylmercuric chloride	increases expression	1
bisphenol A	affects expression	1
lead acetate	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
potassium chromate(VI)	decreases expression	1
aflatoxin B2	increases methylation	1
cupric chloride	increases expression	1
nickel sulfate	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
perfluoro-n-nonanoic acid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	increases expression	1
licochalcone B	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
NSC 689534	affects binding, increases expression	1
Decitabine	increases expression	1
Sunitinib	increases expression	1
Leflunomide	increases expression	1

Clinical trials (associated diseases)

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