PLCXD1

Summary

PLCXD1 (phosphatidylinositol specific phospholipase C X domain containing 1, HGNC:23148) is a protein-coding gene on chromosome Xp22.33 and Yp11.32, encoding PI-PLC X domain-containing protein 1 (Q9NUJ7).

This gene is the most terminal protein-coding gene in the pseudoautosomal (PAR) region on chromosomes X and Y. Alternate splicing results in multiple transcript variants.

Source: NCBI Gene 55344 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 83 total
• MANE Select transcript: NM_018390

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23148
Approved symbol	PLCXD1
Name	phosphatidylinositol specific phospholipase C X domain containing 1
Location	Xp22.33 and Yp11.32
Locus type	gene with protein product
Status	Approved
Aliases	FLJ11323
Ensembl gene	ENSG00000182378
Ensembl biotype	protein_coding
OMIM	300974
Entrez	55344

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 14 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000381657, ENST00000399012, ENST00000415337, ENST00000429181, ENST00000430923, ENST00000443019, ENST00000445062, ENST00000447472, ENST00000448477, ENST00000484611, ENST00000927795, ENST00000927796, ENST00000927797, ENST00000927798, ENST00000958535

RefSeq mRNA: 5 — MANE Select: NM_018390 NM_001370370, NM_001370371, NM_001370372, NM_001370373, NM_018390

CCDS: CCDS14103

Canonical transcript exons

ENST00000381657 — 7 exons

Exon	Start	End
ENSE00001489383	299097	303356
ENSE00001489388	281381	281684
ENSE00003811639	291499	291654
ENSE00003812308	284167	284314
ENSE00003812426	288733	288869
ENSE00003812724	290648	290776
ENSE00003812899	293035	293218

Expression profiles

Bgee: expression breadth ubiquitous, 251 present calls, max score 91.58.

FANTOM5 (CAGE): breadth broad, TPM avg 3.4421 / max 108.5483, expressed in 507 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
195312	2.2247	298
195311	1.0142	397
195313	0.1606	62
195314	0.0428	24

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cervix squamous epithelium	UBERON:0006922	91.58	silver quality
ventricular zone	UBERON:0003053	90.15	gold quality
right hemisphere of cerebellum	UBERON:0014890	89.54	gold quality
embryo	UBERON:0000922	89.28	gold quality
cerebellar hemisphere	UBERON:0002245	88.70	gold quality
cerebellar cortex	UBERON:0002129	88.57	gold quality
cervix epithelium	UBERON:0004801	88.30	gold quality
cerebellum	UBERON:0002037	88.16	gold quality
ganglionic eminence	UBERON:0004023	88.09	gold quality
lower esophagus mucosa	UBERON:0035834	88.03	gold quality
mucosa of sigmoid colon	UBERON:0004993	86.76	gold quality
tibia	UBERON:0000979	86.68	gold quality
upper arm skin	UBERON:0004263	86.42	gold quality
cortical plate	UBERON:0005343	85.78	gold quality
upper leg skin	UBERON:0004262	85.37	gold quality
squamous epithelium	UBERON:0006914	85.33	gold quality
CA1 field of hippocampus	UBERON:0003881	85.19	gold quality
colonic epithelium	UBERON:0000397	85.13	gold quality
cerebellar vermis	UBERON:0004720	85.07	gold quality
colonic mucosa	UBERON:0000317	84.94	gold quality
epithelium of esophagus	UBERON:0001976	84.74	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.50	gold quality
germinal epithelium of ovary	UBERON:0001304	84.48	gold quality
sural nerve	UBERON:0015488	84.41	gold quality
mammalian vulva	UBERON:0000997	84.37	gold quality
lower lobe of lung	UBERON:0008949	84.31	gold quality
esophagus squamous epithelium	UBERON:0006920	84.26	gold quality
body of stomach	UBERON:0001161	83.82	gold quality
Brodmann (1909) area 46	UBERON:0006483	83.72	gold quality
stomach	UBERON:0000945	83.55	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ENAD-27	no	4.23
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

111 targeting PLCXD1, 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-8485	100.00	77.57	4731
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-362-3P	99.91	66.38	1267
HSA-MIR-6499-3P	99.90	66.38	1212
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-383-3P	99.85	65.84	1359
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	zgc:112023	ENSDARG00000103253
mus_musculus	Plcxd1	ENSMUSG00000064247
rattus_norvegicus	Plcxd1	ENSRNOG00000049866
drosophila_melanogaster	CG10747	FBGN0032845
caenorhabditis_elegans		WBGENE00018184

Paralogs (2): PLCXD3 (ENSG00000182836), PLCXD2 (ENSG00000240891)

Protein

Protein identifiers

PI-PLC X domain-containing protein 1 — Q9NUJ7 (reviewed: Q9NUJ7)

All UniProt accessions (7): Q9NUJ7, A0A0A0MSZ3, A0A0A0MT29, A0A0A0MT41, C9JP92, K7EIC3, X6RFG1

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

Tissue specificity. Widely expressed.

Miscellaneous. The gene coding for this protein is located in the pseudoautosomal region 1 (PAR1) of X and Y chromosomes.

RefSeq proteins (5): NP_001357299, NP_001357300, NP_001357301, NP_001357302, NP_060860* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000909	PLipase_C_PInositol-sp_X_dom	Domain
IPR017946	PLC-like_Pdiesterase_TIM-brl	Homologous_superfamily
IPR042158	PLCXD1/2/3	Family
IPR051057	PI-PLC_domain	Family

Pfam: PF26146

UniProt features (2 total): chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NUJ7-F1	93.52	0.90

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 126 (showing top): BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, FISCHER_G1_S_CELL_CYCLE, MODULE_205, GOBP_LIPID_METABOLIC_PROCESS, LIU_CMYB_TARGETS_UP, LIU_VMYB_TARGETS_UP, NUYTTEN_EZH2_TARGETS_DN, XU_GH1_EXOGENOUS_TARGETS_DN, LINDGREN_BLADDER_CANCER_CLUSTER_1_DN, NUYTTEN_NIPP1_TARGETS_DN, GOMF_PHOSPHORIC_DIESTER_HYDROLASE_ACTIVITY, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ESTER_BONDS, GOMF_PHOSPHORIC_ESTER_HYDROLASE_ACTIVITY, STEIN_ESRRA_TARGETS_UP, GSE13762_CTRL_VS_125_VITAMIND_DAY12_DC_DN

GO Biological Process (1): lipid metabolic process (GO:0006629)

GO Molecular Function (1): phosphoric diester hydrolase activity (GO:0008081)

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
primary metabolic process	1
phosphoric ester hydrolase activity	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

496 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PLCXD1	GTPBP6	O43824	754
PLCXD1	ASMTL	O95671	743
PLCXD1	DHRSX	Q8N5I4	721
PLCXD1	PPP2R3B	Q9Y5P8	717
PLCXD1	SHOX	O15266	639
PLCXD1	ASMT	P46597	624
PLCXD1	AKAP17A	Q02040	622
PLCXD1	ZBED1	O96006	595
PLCXD1	SPRY3	O43610	580
PLCXD1	PUDP	Q08623	523
PLCXD1	GYG2	O15488	495
PLCXD1	GPR143	P51810	474
PLCXD1	PRKX	P51817	466
PLCXD1	ZNF850	A8MQ14	449
PLCXD1	P2RY8	Q86VZ1	441

IntAct

3 interactions, top by confidence:

A	B	Type	Score
M		psi-mi:“MI:0914”(association)	0.350
CCR1	UBA6	psi-mi:“MI:0914”(association)	0.350

BioGRID (9): NMT1 (Affinity Capture-MS), PLCXD1 (Affinity Capture-RNA), PLCXD1 (Positive Genetic), PLCXD1 (Affinity Capture-MS), PLCXD1 (Affinity Capture-MS), PLCXD1 (Affinity Capture-MS), PLCXD1 (Affinity Capture-MS), PLCXD1 (Proximity Label-MS), PLCXD1 (Affinity Capture-RNA)

ESM2 similar proteins: A0A0D4WTV1, A0AVT1, A3KMX8, A5PN38, A6H630, A6QNU9, B2RXA1, B8ZXI1, C0JB40, D3YUE4, O15886, O22585, O45228, O64407, O65015, P09194, P10538, P37830, P49221, P49915, Q0VAA5, Q1RML2, Q27Q54, Q29LW1, Q2KHV5, Q2VRL0, Q3THK7, Q4V7C6, Q567I4, Q58EK3, Q58EM4, Q5FX52, Q5R998, Q5RA96, Q63HM9, Q64319, Q6AXB1, Q6AYT5, Q6DJA3, Q6UXP7

Diamond homologs: A6QNU9, B2RXA1, P34024, Q0VAA5, Q567I4, Q58EK3, Q63HM9, Q8BLJ3, Q8CHS4, Q9NUJ7, Q55DH0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

1563 predictions. Top by Δscore:

Variant	Effect	Δscore
X:276395:G:GC	donor_loss	1.0000
X:276395:G:GG	donor_gain	1.0000
X:276396:T:G	donor_loss	1.0000
X:288727:TCTCA:T	acceptor_loss	1.0000
X:288729:TCA:T	acceptor_loss	1.0000
X:288730:CA:C	acceptor_loss	1.0000
X:288731:A:AG	acceptor_gain	1.0000
X:288731:AG:A	acceptor_gain	1.0000
X:288731:AGG:A	acceptor_gain	1.0000
X:288732:G:A	acceptor_gain	1.0000
X:288732:G:GG	acceptor_gain	1.0000
X:288732:GGG:G	acceptor_gain	1.0000
X:288732:GGGA:G	acceptor_gain	1.0000
X:288866:CCAG:C	donor_loss	1.0000
X:288867:CAGG:C	donor_loss	1.0000
X:288868:AG:A	donor_loss	1.0000
X:288869:GG:G	donor_loss	1.0000
X:288870:G:A	donor_loss	1.0000
X:288871:T:A	donor_loss	1.0000
X:290643:CACA:C	acceptor_loss	1.0000
X:290645:CA:C	acceptor_loss	1.0000
X:290646:A:AG	acceptor_gain	1.0000
X:290646:AG:A	acceptor_gain	1.0000
X:290647:G:GG	acceptor_gain	1.0000
X:290647:GG:G	acceptor_gain	1.0000
X:290647:GGCA:G	acceptor_gain	1.0000
X:291494:CCCAG:C	acceptor_loss	1.0000
X:291495:CCAGG:C	acceptor_loss	1.0000
X:291496:CA:C	acceptor_loss	1.0000
X:291497:A:AG	acceptor_gain	1.0000

AlphaMissense

2089 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
Y:288735:A:C	S44R	0.997
Y:288737:C:A	S44R	0.997
Y:288737:C:G	S44R	0.997
Y:299254:C:A	N297K	0.994
Y:299254:C:G	N297K	0.994
Y:288855:T:A	W84R	0.993
Y:288855:T:C	W84R	0.993
Y:288869:G:C	Q88H	0.993
Y:288869:G:T	Q88H	0.993
Y:290678:G:T	G99W	0.993
Y:284314:G:T	G43W	0.992
Y:288738:C:G	H45D	0.991
Y:291523:T:A	W140R	0.991
Y:291523:T:C	W140R	0.991
Y:288733:G:A	G43E	0.990
Y:290679:G:A	G99E	0.990
Y:290694:A:C	D104A	0.990
Y:290694:A:T	D104V	0.990
Y:291506:T:C	L134P	0.990
Y:291551:T:A	V149D	0.990
Y:284256:G:C	W23C	0.989
Y:284256:G:T	W23C	0.989
Y:290670:T:C	L96P	0.989
Y:290741:T:C	F120L	0.989
Y:290743:T:A	F120L	0.989
Y:290743:T:G	F120L	0.989
Y:284309:T:A	I41N	0.988
Y:290700:G:C	R106P	0.988
Y:291506:T:A	L134H	0.988
Y:291525:G:C	W140C	0.988

dbSNP variants (sampled 300 via entrez): RS1000189182 (X:286410 C>T), RS1000317355 (X:289820 C>A,G), RS1000327520 (X:290033 C>T), RS1000481119 (X:300688 A>G,T), RS1000568628 (X:303258 A>G), RS1000663888 (X:286178 C>T), RS1000747924 (X:281897 G>A), RS1000800320 (X:282172 A>G), RS1000868579 (X:292381 C>G), RS1000893783 (X:292444 G>A), RS1001028336 (X:276401 G>T), RS1001253043 (X:300593 C>T), RS1001402336 (X:276660 A>G), RS1001592557 (X:295597 T>C,G), RS1001769855 (X:295811 G>A)

Disease associations

OMIM: gene MIM:300974 | 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

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression, affects expression, decreases expression	4
Cadmium Chloride	increases abundance, increases expression	3
Benzo(a)pyrene	decreases expression	2
Methotrexate	increases expression	2
Tretinoin	decreases expression	2
dicrotophos	increases expression	1
methyleugenol	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
butyraldehyde	decreases expression	1
potassium chromate(VI)	increases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, increases expression	1
nickel sulfate	increases expression	1
hydroquinone	increases expression	1
ciglitazone	affects binding, increases expression	1
diallyl trisulfide	increases expression	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
licochalcone B	increases expression	1
bisphenol S	increases expression	1
Rosiglitazone	decreases expression	1
Sunitinib	decreases expression	1
Arsenic Trioxide	decreases expression	1
Ethanol	affects cotreatment, increases abundance, increases expression	1
Cadmium	increases abundance, increases expression	1
Coumestrol	affects cotreatment, increases expression	1
Demecolcine	decreases expression	1
Dexamethasone	increases expression	1
Doxorubicin	decreases expression	1

Clinical trials (associated diseases)

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