PCYT2

Summary

PCYT2 (phosphate cytidylyltransferase 2, ethanolamine, HGNC:8756) is a protein-coding gene on chromosome 17q25.3, encoding Ethanolamine-phosphate cytidylyltransferase (Q99447). Ethanolamine-phosphate cytidylyltransferase that catalyzes the second step in the synthesis of phosphatidylethanolamine (PE) from ethanolamine via the CDP-ethanolamine pathway.

This gene encodes an enzyme that catalyzes the formation of CDP-ethanolamine from CTP and phosphoethanolamine in the Kennedy pathway of phospholipid synthesis. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 5833 — RefSeq curated summary.

At a glance

• Gene–disease (curated): spastic paraplegia 82, autosomal recessive (Definitive, GenCC)
• Clinical variants (ClinVar): 106 total — 3 pathogenic, 6 likely-pathogenic
• Phenotypes (HPO): 15
• MANE Select transcript: NM_002861

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:8756
Approved symbol	PCYT2
Name	phosphate cytidylyltransferase 2, ethanolamine
Location	17q25.3
Locus type	gene with protein product
Status	Approved
Aliases	ET
Ensembl gene	ENSG00000185813
Ensembl biotype	protein_coding
OMIM	602679
Entrez	5833

Gene structure

Transcript identifiers

Ensembl transcripts: 41 — 35 protein_coding, 5 retained_intron, 1 nonsense_mediated_decay

ENST00000331285, ENST00000538721, ENST00000538936, ENST00000570388, ENST00000570391, ENST00000571105, ENST00000571581, ENST00000571944, ENST00000572157, ENST00000572473, ENST00000572924, ENST00000572995, ENST00000573401, ENST00000573636, ENST00000573927, ENST00000574155, ENST00000574343, ENST00000576343, ENST00000883679, ENST00000883680, ENST00000883681, ENST00000883682, ENST00000883683, ENST00000883684, ENST00000883685, ENST00000883686, ENST00000883687, ENST00000883688, ENST00000883689, ENST00000883690, ENST00000883691, ENST00000883692, ENST00000883693, ENST00000883694, ENST00000883695, ENST00000883696, ENST00000883697, ENST00000938179, ENST00000956686, ENST00000956687, ENST00000956688

RefSeq mRNA: 8 — MANE Select: NM_002861 NM_001184917, NM_001256433, NM_001256434, NM_001256435, NM_001282203, NM_001282204, NM_001330518, NM_002861

CCDS: CCDS11791, CCDS54178, CCDS58610, CCDS62364, CCDS82220

Canonical transcript exons

ENST00000538936 — 13 exons

Exon	Start	End
ENSE00001300996	81911267	81911399
ENSE00002237409	81900958	81904944
ENSE00003458860	81905382	81905447
ENSE00003476267	81907773	81907857
ENSE00003519226	81906464	81906546
ENSE00003533697	81905066	81905154
ENSE00003612711	81908568	81908634
ENSE00003624659	81907554	81907598
ENSE00003644142	81909514	81909602
ENSE00003657442	81908876	81909037
ENSE00003673108	81906100	81906177
ENSE00003679059	81906760	81906898
ENSE00003788869	81905670	81905735

Expression profiles

Bgee: expression breadth ubiquitous, 265 present calls, max score 99.00.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 26.4402 / max 327.0366, expressed in 1779 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
168853	25.5449	1779
168852	0.3764	172
168850	0.2616	36
168854	0.1911	59
168851	0.0564	10
168849	0.0098	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	99.00	gold quality
right testis	UBERON:0004534	98.74	gold quality
right lobe of liver	UBERON:0001114	97.37	gold quality
testis	UBERON:0000473	96.77	gold quality
sperm	CL:0000019	96.22	gold quality
male germ cell	CL:0000015	95.15	gold quality
apex of heart	UBERON:0002098	95.01	gold quality
mucosa of transverse colon	UBERON:0004991	94.68	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	94.40	gold quality
right frontal lobe	UBERON:0002810	93.94	gold quality
right hemisphere of cerebellum	UBERON:0014890	93.01	gold quality
right uterine tube	UBERON:0001302	92.85	gold quality
prefrontal cortex	UBERON:0000451	92.64	gold quality
liver	UBERON:0002107	92.50	gold quality
spinal cord	UBERON:0002240	92.44	gold quality
cingulate cortex	UBERON:0003027	92.40	gold quality
cerebellar hemisphere	UBERON:0002245	92.38	gold quality
anterior cingulate cortex	UBERON:0009835	92.29	gold quality
body of stomach	UBERON:0001161	92.23	gold quality
cerebellar cortex	UBERON:0002129	92.22	gold quality
small intestine Peyer’s patch	UBERON:0003454	92.15	gold quality
heart left ventricle	UBERON:0002084	91.97	gold quality
metanephros cortex	UBERON:0010533	91.84	gold quality
Brodmann (1909) area 9	UBERON:0013540	91.81	gold quality
amygdala	UBERON:0001876	91.77	gold quality
cardiac ventricle	UBERON:0002082	91.53	gold quality
nucleus accumbens	UBERON:0001882	91.50	gold quality
small intestine	UBERON:0002108	90.96	gold quality
putamen	UBERON:0001874	90.75	gold quality
caudate nucleus	UBERON:0001873	90.67	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	13.05

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ATF3, CEBPB, DDIT3, EGR1, ESR1, FOS, NFKB1, RELA, SREBF1, SREBF2, ZHX2

miRNA regulators (miRDB)

58 targeting PCYT2, 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-4673	100.00	66.64	1490
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-185-3P	99.95	67.01	1743
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-6836-5P	99.60	65.62	1538
HSA-MIR-6132	99.60	65.83	1554
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-4472	99.56	66.08	1478
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-3960	99.41	66.11	96
HSA-MIR-940	99.37	66.14	2064
HSA-MIR-6808-5P	99.31	66.23	2150
HSA-MIR-6893-5P	99.31	66.25	2119
HSA-MIR-6878-3P	99.24	64.23	920
HSA-MIR-6744-3P	99.22	64.41	972
HSA-MIR-1911-3P	99.15	66.17	528
HSA-MIR-6809-5P	99.13	68.45	1223
HSA-MIR-4757-5P	99.12	64.51	981
HSA-MIR-4763-3P	99.10	67.83	2649
HSA-MIR-661	99.09	65.94	2062

Literature-anchored findings (GeneRIF, showing 7)

• The Pcyt2 promoter is driven by a functional CAAT box (-90/-73) and by negative (-385/-255) and positive regulatory elements (-255/-153) in the upstream regions. (PMID:16023412)
• EGR1 is an important transcriptional stimulator of the human PCYT2 and that conditions that modify EGR1 also affect the function of ECT and consequently PE synthesis (PMID:18583706)
• Pcyt2 expression is responsive to tumor nutritional micro-environment, up-regulated in response to metabolic stress under conditions of serum deprivation. (PMID:22339418)
• differences in phosphorylation between Pcyt2 isoforms (PMID:24519946)
• These results suggest that the N-terminal CT domain of hECT contributes to its catalytic reaction, but C-terminal CT domain does not. (PMID:24802409)
• Phosphoethanolamine Accumulation Protects Cancer Cells under Glutamine Starvation through Downregulation of PCYT2. (PMID:31577958)
• our data establish PCYT2 as a disease gene for a new complex hereditary spastic paraplegia and confirm that etherlipid homeostasis is important for the development and function of the brain (PMID:31637422)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	pcyt2	ENSDARG00000043003
mus_musculus	Pcyt2	ENSMUSG00000025137
rattus_norvegicus	Pcyt2	ENSRNOG00000036684
drosophila_melanogaster	Pect	FBGN0032482
caenorhabditis_elegans		WBGENE00016531
caenorhabditis_elegans	pcyt-2.1	WBGENE00021352

Paralogs (2): PCYT1B (ENSG00000102230), PCYT1A (ENSG00000161217)

Protein

Protein identifiers

Ethanolamine-phosphate cytidylyltransferase — Q99447 (reviewed: Q99447)

Alternative names: CTP:phosphoethanolamine cytidylyltransferase, Phosphorylethanolamine transferase

All UniProt accessions (9): Q99447, I3L102, I3L1C4, I3L1F9, I3L1L9, I3L1R7, I3L2Q1, I3L3V9, I3NI16

UniProt curated annotations — full annotation on UniProt →

Function. Ethanolamine-phosphate cytidylyltransferase that catalyzes the second step in the synthesis of phosphatidylethanolamine (PE) from ethanolamine via the CDP-ethanolamine pathway. Phosphatidylethanolamine is a dominant inner-leaflet phospholipid in cell membranes, where it plays a role in membrane function by structurally stabilizing membrane-anchored proteins, and participates in important cellular processes such as cell division, cell fusion, blood coagulation, and apoptosis.

Tissue specificity. Strongest expression in liver, heart, and skeletal muscle.

Disease relevance. Spastic paraplegia 82, autosomal recessive (SPG82) [MIM:618770] A form of spastic paraplegia, a neurodegenerative disorder characterized by a slow, gradual, progressive weakness and spasticity of the lower limbs. Rate of progression and the severity of symptoms are quite variable. Initial symptoms may include difficulty with balance, weakness and stiffness in the legs, muscle spasms, and dragging the toes when walking. In some forms of the disorder, bladder symptoms (such as incontinence) may appear, or the weakness and stiffness may spread to other parts of the body. SPG82 is a complicated form characterized by global developmental delay with regression, spastic para- or tetraparesis, epilepsy and progressive cerebral and cerebellar atrophy. The disease is caused by variants affecting the gene represented in this entry.

Pathway. Phospholipid metabolism; phosphatidylethanolamine biosynthesis; phosphatidylethanolamine from ethanolamine: step 2/3.

Similarity. Belongs to the cytidylyltransferase family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q99447-1	1	yes
Q99447-2	2
Q99447-3	3
Q99447-4	4

RefSeq proteins (8): NP_001171846, NP_001243362, NP_001243363, NP_001243364, NP_001269132, NP_001269133, NP_001317447, NP_002852* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004821	Cyt_trans-like	Domain
IPR014729	Rossmann-like_a/b/a_fold	Homologous_superfamily
IPR041723	CCT	Domain
IPR044608	Ect1/PCYT2	Family

Pfam: PF01467

Enzyme classification (BRENDA):

• EC 2.7.7.14 — ethanolamine-phosphate cytidylyltransferase (BRENDA: 9 organisms, 25 substrates, 21 inhibitors, 34 Km, 11 kcat entries)

Substrate kinetics (BRENDA)

9 substrates with measured Km, best-characterized 9. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
CTP	0.0127–0.465	12
ETHANOLAMINE PHOSPHATE	0.053–0.88	12
2-AMINOETHYLARSONIC ACID	3	1
2-AMINOETHYLPHOSPHONATE	30	1
ETHANOLAMINE-PHOSPHATE	0.0121	1
PHOSPHOCHOLINE	6.2	1
PHOSPHODIMETHYLETHANOLAMINE	6.8	1
PHOSPHOETHANOLAMINE	0.072	1
PHOSPHOMONOMETHYLETHANOLAMINE	0.11	1

Catalyzed reactions (Rhea), 1 shown:

• phosphoethanolamine + CTP + H(+) = CDP-ethanolamine + diphosphate (RHEA:24592)

UniProt features (40 total): helix 13, strand 10, binding site 5, splice variant 3, sequence variant 3, modified residue 3, chain 1, region of interest 1, sequence conflict 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
3ELB	X-RAY DIFFRACTION	2
4XSV	X-RAY DIFFRACTION	2.7

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q99447-F1	86.65	0.69

Functional residue map

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

Ligand- & substrate-binding residues (5): 221–222; 229–232; 259; 307–310; 336–340

Post-translational modifications (3): 338, 341, 342

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-1483213	Synthesis of PE

MSigDB gene sets: 221 (showing top): E2F_Q4, E2F_Q4_01, GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, TSENG_IRS1_TARGETS_UP, TGCGCANK_UNKNOWN, PEREZ_TP63_TARGETS, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_PHOSPHOLIPID_BIOSYNTHETIC_PROCESS, EVI1_05, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, CEBP_Q2, AP1_Q4_01, E2F_Q3, AML_Q6

GO Biological Process (5): phosphatidylethanolamine biosynthetic process (GO:0006646), phospholipid biosynthetic process (GO:0008654), lipid metabolic process (GO:0006629), biosynthetic process (GO:0009058), organophosphate biosynthetic process (GO:0090407)

GO Molecular Function (5): ethanolamine-phosphate cytidylyltransferase activity (GO:0004306), catalytic activity (GO:0003824), protein binding (GO:0005515), transferase activity (GO:0016740), nucleotidyltransferase activity (GO:0016779)

GO Cellular Component (2): cytoplasm (GO:0005737), endoplasmic reticulum membrane (GO:0005789)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Glycerophospholipid biosynthesis	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
phosphatidylethanolamine metabolic process	1
glycerophospholipid biosynthetic process	1
phospholipid metabolic process	1
lipid biosynthetic process	1
organophosphate biosynthetic process	1
primary metabolic process	1
metabolic process	1
biosynthetic process	1
organophosphate metabolic process	1
cytidylyltransferase activity	1
molecular_function	1
binding	1
catalytic activity	1
transferase activity, transferring phosphorus-containing groups	1
intracellular anatomical structure	1
cellular anatomical structure	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1

Protein interactions and networks

STRING

1612 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PCYT2	PISD	Q9UG56	984
PCYT2	SELENOI	Q9C0D9	795
PCYT2	ETNK2	Q9NVF9	784
PCYT2	CEPT1	Q9Y6K0	772
PCYT2	ETNK1	Q9HBU6	747
PCYT2	CHKB	Q9Y259	742
PCYT2	CHKA	P35790	716
PCYT2	CHPT1	Q8WUD6	688
PCYT2	PEMT	Q9UBM1	681
PCYT2	PTDSS2	Q9BVG9	602
PCYT2	CDIPT	O14735	590
PCYT2	FGFR2	P18443	553
PCYT2	TOR4A	Q9NXH8	537
PCYT2	ADISSP	Q9GZN8	513
PCYT2	PTDSS1	P48651	506

IntAct

38 interactions, top by confidence:

A	B	Type	Score
PCYT2	INPPL1	psi-mi:“MI:0915”(physical association)	0.640
PCYT2	INPPL1	psi-mi:“MI:0914”(association)	0.640
REL	PCYT2	psi-mi:“MI:0915”(physical association)	0.560
PSMA1	PCYT2	psi-mi:“MI:0915”(physical association)	0.560
INCA1	PCYT2	psi-mi:“MI:0915”(physical association)	0.560
CLVS2	PCYT2	psi-mi:“MI:0915”(physical association)	0.560
CASP6	PCYT2	psi-mi:“MI:0915”(physical association)	0.560
LAMP2	PCYT2	psi-mi:“MI:0915”(physical association)	0.560
PRPF40A	PCYT2	psi-mi:“MI:0915”(physical association)	0.560
PCYT2	HOXA1	psi-mi:“MI:0915”(physical association)	0.370
ADAMTS10	PCYT2	psi-mi:“MI:0915”(physical association)	0.370
CRIP2	PCYT2	psi-mi:“MI:0915”(physical association)	0.370
PCYT2	DNMT3B	psi-mi:“MI:0915”(physical association)	0.370
GDF9	PCYT2	psi-mi:“MI:0915”(physical association)	0.370
SETDB1	PCYT2	psi-mi:“MI:0915”(physical association)	0.370
PCYT2	KDM8	psi-mi:“MI:0915”(physical association)	0.370
PCYT2		psi-mi:“MI:0915”(physical association)	0.370
PRKN	BBOX1	psi-mi:“MI:0914”(association)	0.350
RAB26	CHM	psi-mi:“MI:0914”(association)	0.350
RIPPLY1	PGAM2	psi-mi:“MI:0914”(association)	0.350
SLC35G2	MAOB	psi-mi:“MI:0914”(association)	0.350
MRPL49	UBA6	psi-mi:“MI:0914”(association)	0.350
PCYT2	REL	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (48): PCYT2 (Affinity Capture-MS), INPPL1 (Affinity Capture-MS), KDM8 (Two-hybrid), PCYT2 (Co-fractionation), PCYT2 (Affinity Capture-MS), INPPL1 (Affinity Capture-MS), PCYT2 (Affinity Capture-MS), PCYT2 (Two-hybrid), PCYT2 (Two-hybrid), PCYT2 (Two-hybrid), INCA1 (Two-hybrid), PCYT2 (Negative Genetic), PCYT2 (Phenotypic Suppression), PCYT2 (Two-hybrid), INPPL1 (Affinity Capture-MS)

ESM2 similar proteins: A3AZW5, B8BDK0, B9F2L1, F4JHA2, K7TQE3, O81893, O82387, O88637, P0DKG8, Q00IB6, Q0IZQ2, Q0J0B2, Q0VD50, Q3U213, Q4R3W5, Q5EA75, Q5N870, Q5SNL7, Q5T8I9, Q5W9E7, Q5XVJ4, Q5Z6B1, Q67VC8, Q6ZLC4, Q7XAP4, Q7XD96, Q84MA1, Q84ZX8, Q852L0, Q8CAE2, Q8GWZ6, Q8L5Z4, Q8LRK8, Q922E4, Q93XN8, Q94ID2, Q99447, Q9AYT5, Q9FNF8, Q9HAN9

Diamond homologs: A1W0D6, A7H2L7, A8FMK8, C5A1S7, D3RZA9, D5EBS7, F4JJE0, O58466, O74975, O88637, P13259, P19836, P27623, P33412, P49583, P49584, P49585, P49586, P49587, Q55BZ4, Q5EA75, Q5HTW1, Q6TG09, Q811Q9, Q8RKI6, Q8SQW6, Q8TXT2, Q8U1T9, Q922E4, Q99447, Q9QZC4, Q9UTI6, Q9UZ37, Q9Y5K3, Q9ZV56, Q9ZVI9, B5I9H4, B6YXC8, C6A439, D3DZ18

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	6
Uncertain significance	64
Likely benign	12
Benign	9

Top pathogenic / likely-pathogenic (9)

Variant ID	HGVS	Classification
2373369	NM_002861.5(PCYT2):c.524_527del (p.Asp175fs)	Pathogenic
3024149	NM_002861.5(PCYT2):c.1058+1G>A	Pathogenic
3024150	NM_002861.5(PCYT2):c.689T>A (p.Val230Glu)	Pathogenic
2500196	NM_002861.5(PCYT2):c.903G>C (p.Lys301Asn)	Likely pathogenic
2575242	NM_002861.5(PCYT2):c.682G>A (p.Gly228Arg)	Likely pathogenic
2627104	NM_002861.5(PCYT2):c.969+5G>A	Likely pathogenic
3068607	NM_002861.5(PCYT2):c.781A>T (p.Lys261Ter)	Likely pathogenic
4277682	NM_002861.5(PCYT2):c.418C>T (p.Arg140Cys)	Likely pathogenic
812572	NM_002861.5(PCYT2):c.676C>T (p.His226Tyr)	Likely pathogenic

SpliceAI

2318 predictions. Top by Δscore:

Variant	Effect	Δscore
17:81902522:GCCTC:G	donor_gain	1.0000
17:81905152:CTC:C	acceptor_gain	1.0000
17:81905153:TC:T	acceptor_gain	1.0000
17:81905153:TCC:T	acceptor_loss	1.0000
17:81905154:CC:C	acceptor_gain	1.0000
17:81905154:CCT:C	acceptor_loss	1.0000
17:81905155:C:CC	acceptor_gain	1.0000
17:81905164:C:CT	acceptor_gain	1.0000
17:81905164:C:T	acceptor_gain	1.0000
17:81905165:A:T	acceptor_gain	1.0000
17:81905447:CCTGG:C	acceptor_loss	1.0000
17:81905664:CCTCA:C	donor_loss	1.0000
17:81905665:CTCAC:C	donor_loss	1.0000
17:81905666:TCAC:T	donor_loss	1.0000
17:81905667:CAC:C	donor_loss	1.0000
17:81905731:ACGTA:A	acceptor_gain	1.0000
17:81905732:CGTA:C	acceptor_gain	1.0000
17:81905732:CGTAC:C	acceptor_gain	1.0000
17:81905733:GTA:G	acceptor_gain	1.0000
17:81905734:TA:T	acceptor_gain	1.0000
17:81905735:AC:A	acceptor_loss	1.0000
17:81905736:C:CC	acceptor_gain	1.0000
17:81905736:C:T	acceptor_loss	1.0000
17:81905745:C:CT	acceptor_gain	1.0000
17:81905746:A:T	acceptor_gain	1.0000
17:81905747:G:C	acceptor_gain	1.0000
17:81905747:G:GC	acceptor_gain	1.0000
17:81906095:CTCA:C	donor_loss	1.0000
17:81906096:TCA:T	donor_loss	1.0000
17:81906097:CACC:C	donor_loss	1.0000

AlphaMissense

2562 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:81908882:G:C	H112D	1.000
17:81908963:A:G	W85R	1.000
17:81908963:A:T	W85R	1.000
17:81905081:C:G	R348P	0.999
17:81906115:G:C	S274R	0.999
17:81906115:G:T	S274R	0.999
17:81906117:T:G	S274R	0.999
17:81906125:C:G	R271P	0.999
17:81906128:T:A	E270V	0.999
17:81906787:A:C	Y217D	0.999
17:81906827:A:C	F203L	0.999
17:81906827:A:T	F203L	0.999
17:81906828:A:C	F203C	0.999
17:81906828:A:G	F203S	0.999
17:81906829:A:G	F203L	0.999
17:81907804:A:G	L154P	0.999
17:81907810:C:G	R152P	0.999
17:81907811:G:T	R152S	0.999
17:81907819:A:G	L149P	0.999
17:81907847:G:T	R140S	0.999
17:81908631:T:A	D115V	0.999
17:81908631:T:G	D115A	0.999
17:81908880:G:C	H112Q	0.999
17:81908880:G:T	H112Q	0.999
17:81908882:G:T	H112N	0.999
17:81908884:A:T	V111D	0.999
17:81908886:A:C	C110W	0.999
17:81908887:C:T	C110Y	0.999
17:81908961:C:A	W85C	0.999
17:81908961:C:G	W85C	0.999

dbSNP variants (sampled 300 via entrez): RS1000005344 (17:81910839 G>A,C), RS1000057746 (17:81910701 C>T), RS1000430804 (17:81902767 A>G), RS1000641262 (17:81907024 GACAC>G), RS1000738479 (17:81911673 C>T), RS1000839613 (17:81901539 T>C), RS1000902835 (17:81906293 G>A,T), RS1001118847 (17:81901763 C>T), RS1001138649 (17:81906801 C>T), RS1001218522 (17:81911105 G>A,C), RS1001358273 (17:81906101 C>T), RS1001801927 (17:81904681 C>T), RS1002197257 (17:81902296 C>T), RS1002247141 (17:81901878 CTG>C), RS1002248157 (17:81902112 C>A,G,T)

Disease associations

OMIM: gene MIM:602679 | disease phenotypes: MIM:618770

GenCC curated gene-disease

Disease	Classification	Inheritance
spastic paraplegia 82, autosomal recessive	Definitive	Autosomal recessive

Mondo (1): spastic paraplegia 82, autosomal recessive (MONDO:0032906)

Orphanet (1): Autosomal recessive spastic paraplegia type 82 (Orphanet:631073)

HPO phenotypes

15 total (15 of 15 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000639	Nystagmus
HP:0000648	Optic atrophy
HP:0000750	Delayed speech and language development
HP:0001249	Intellectual disability
HP:0001257	Spasticity
HP:0001347	Hyperreflexia
HP:0002059	Cerebral atrophy
HP:0002376	Developmental regression
HP:0003487	Babinski sign
HP:0007359	Focal-onset seizure
HP:0007663	Reduced visual acuity
HP:0025190	Bilateral tonic-clonic seizure with generalized onset
HP:0025336	Delayed ability to sit
HP:0031936	Delayed ability to walk

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

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases methylation, increases expression, affects expression	3
sodium arsenite	affects cotreatment, decreases expression, increases expression	3
Benzo(a)pyrene	affects methylation, decreases expression	3
Smoke	decreases expression, increases abundance, increases expression	3
Cyclosporine	decreases expression	2
Aflatoxin B1	affects expression, decreases expression	2
Particulate Matter	affects cotreatment, decreases expression, increases abundance	2
afuresertib	increases expression	1
bisphenol F	increases expression	1
pirinixic acid	affects binding, decreases expression, increases activity	1
beta-lapachone	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
periodate-oxidized adenosine	affects expression	1
cupric chloride	decreases expression	1
nickel sulfate	increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
K 7174	decreases expression	1
bisphenol B	increases expression	1
bisphenol S	affects cotreatment, increases methylation	1
jinfukang	affects cotreatment, increases expression	1
bisphenol AF	increases expression	1
Decitabine	increases expression	1
Arsenic Trioxide	decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Vorinostat	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	affects methylation	1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_D1PL	Abcam K-562 PCYT2 KO	Cancer cell line	Female
CVCL_D2L7	Abcam Raji PCYT2 KO	Cancer cell line	Male
CVCL_WQ22	Abcam Jurkat PCYT2 KO	Cancer cell line	Male

Clinical trials (associated diseases)

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