PISD

gene
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Also known as dJ858B16.2PSDC

Summary

PISD (phosphatidylserine decarboxylase, HGNC:8999) is a protein-coding gene on chromosome 22q12.2, encoding Phosphatidylserine decarboxylase proenzyme, mitochondrial (Q9UG56). Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer).

The protein encoded by this gene catalyzes the conversion of phosphatidylserine to phosphatidylethanolamine in the inner mitochondrial membrane. The encoded protein is active in phospholipid metabolism and interorganelle trafficking of phosphatidylserine.

Source: NCBI Gene 23761 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Liberfarb syndrome (Strong, GenCC)
  • Clinical variants (ClinVar): 195 total — 5 pathogenic, 2 likely-pathogenic
  • Phenotypes (HPO): 13
  • MANE Select transcript: NM_001326411

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:8999
Approved symbolPISD
Namephosphatidylserine decarboxylase
Location22q12.2
Locus typegene with protein product
StatusApproved
AliasesdJ858B16.2, PSDC
Ensembl geneENSG00000241878
Ensembl biotypeprotein_coding
OMIM612770
Entrez23761

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 16 protein_coding, 4 protein_coding_CDS_not_defined, 3 retained_intron, 1 nonsense_mediated_decay

ENST00000266095, ENST00000382151, ENST00000397500, ENST00000422020, ENST00000429683, ENST00000431201, ENST00000435900, ENST00000437808, ENST00000439502, ENST00000442379, ENST00000460723, ENST00000473770, ENST00000474017, ENST00000478893, ENST00000479851, ENST00000486675, ENST00000491342, ENST00000892604, ENST00000892605, ENST00000930689, ENST00000930690, ENST00000930691, ENST00000930692, ENST00000972531

RefSeq mRNA: 13 — MANE Select: NM_001326411 NM_001326411, NM_001326412, NM_001326413, NM_001326414, NM_001326415, NM_001326416, NM_001326417, NM_001326418, NM_001326419, NM_001326420, NM_001326421, NM_014338, NM_178022

CCDS: CCDS13899, CCDS87016

Canonical transcript exons

ENST00000439502 — 8 exons

ExonStartEnd
ENSE000019279303166214431662215
ENSE000034598133162164931621885
ENSE000035056823162055331620713
ENSE000035072463162099631621142
ENSE000035184853162133431621472
ENSE000035246163161849131619836
ENSE000036470923164810131648276
ENSE000036614753165069931650778

Expression profiles

Bgee: expression breadth ubiquitous, 276 present calls, max score 98.77.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.2193 / max 217.0966, expressed in 1817 samples.

FANTOM5 promoters (12 alternative TSS)

Promoter IDTPM avgSamples expressed
19372512.37371792
1937174.89501532
1937212.2674439
1937201.2556268
1937130.9115181
1937160.8020486
1937150.7825335
1937180.5486200
1937190.290682
1937260.048919

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cerebellar hemisphereUBERON:000224598.77gold quality
cerebellar cortexUBERON:000212998.75gold quality
right hemisphere of cerebellumUBERON:001489098.71gold quality
cerebellumUBERON:000203798.29gold quality
paraflocculusUBERON:000535197.58gold quality
cerebellar vermisUBERON:000472096.98gold quality
granulocyteCL:000009495.69gold quality
metanephros cortexUBERON:001053395.39gold quality
bloodUBERON:000017895.27gold quality
monocyteCL:000057694.97gold quality
mononuclear cellCL:000084294.52gold quality
leukocyteCL:000073894.49gold quality
right frontal lobeUBERON:000281093.87gold quality
omental fat padUBERON:001041493.78gold quality
peritoneumUBERON:000235893.77gold quality
spleenUBERON:000210693.72gold quality
adipose tissue of abdominal regionUBERON:000780893.60gold quality
pituitary glandUBERON:000000793.52gold quality
left adrenal glandUBERON:000123493.44gold quality
left adrenal gland cortexUBERON:003582593.43gold quality
adenohypophysisUBERON:000219693.42gold quality
right testisUBERON:000453493.40gold quality
left testisUBERON:000453393.37gold quality
right adrenal gland cortexUBERON:003582793.34gold quality
right adrenal glandUBERON:000123393.33gold quality
left uterine tubeUBERON:000130393.13gold quality
upper lobe of left lungUBERON:000895292.87gold quality
adrenal cortexUBERON:000123592.83gold quality
right lobe of thyroid glandUBERON:000111992.69gold quality
stromal cell of endometriumCL:000225592.59gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes8.66

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 3)

  • High-throughput mass spectrometry screening for inhibitors of PISD is reported. (PMID:17478478)
  • the biallelic hypomorphic PISD variant p.(Cys266Tyr) is associated with a novel Spondyloepimetaphyseal dysplasias form. (PMID:30488656)
  • Conditional targeting of phosphatidylserine decarboxylase to lipid droplets. (PMID:33593792)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriopisdENSDARG00000052462
mus_musculusPisdENSMUSG00000023452
ENSMUSG00000095041
rattus_norvegicusPisdENSRNOG00000018319
drosophila_melanogasterPisdFBGN0026576
caenorhabditis_elegansWBGENE00015159

Protein

Protein identifiers

Phosphatidylserine decarboxylase proenzyme, mitochondrialQ9UG56 (reviewed: Q9UG56)

All UniProt accessions (7): Q9UG56, B1AKM6, B1AKM8, B1AKM9, B1AKN0, F8WCS6, H0Y7P7

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer). Plays a central role in phospholipid metabolism and in the interorganelle trafficking of phosphatidylserine. May be involved in lipid droplet biogenesis at the endoplasmic reticulum membrane.

Subunit / interactions. Heterodimer of a large membrane-associated beta subunit and a small pyruvoyl-containing alpha subunit.

Subcellular location. Mitochondrion inner membrane Mitochondrion inner membrane. Cytoplasm Mitochondrion inner membrane Mitochondrion inner membrane. Lipid droplet.

Post-translational modifications. Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the carboxyl end of the proenzyme. The autoendoproteolytic cleavage occurs by a canonical serine protease mechanism, in which the side chain hydroxyl group of the serine supplies its oxygen atom to form the C-terminus of the beta chain, while the remainder of the serine residue undergoes an oxidative deamination to produce ammonia and the pyruvoyl prosthetic group on the alpha chain. During this reaction, the Ser that is part of the protease active site of the proenzyme becomes the pyruvoyl prosthetic group, which constitutes an essential element of the active site of the mature decarboxylase.

Disease relevance. Liberfarb syndrome (LIBF) [MIM:618889] An autosomal recessive multisystem disorder affecting the eye, ear, bone, and brain development. Clinical features include early-onset retinal degeneration, congenital cataracts, sensorineural hearing loss, microcephaly, intellectual disability, white matter changes, mild facial dysmorphism, and skeletal dysplasia with platyspondyly, scoliosis and short stature. The disease is caused by variants affecting the gene represented in this entry.

Cofactor. Binds 1 pyruvoyl group covalently per subunit.

Pathway. Phospholipid metabolism; phosphatidylethanolamine biosynthesis.

Similarity. Belongs to the phosphatidylserine decarboxylase family. PSD-B subfamily. Eukaryotic type I sub-subfamily.

Isoforms (2)

UniProt IDNamesCanonical?
Q9UG56-31, PISD-Myes
Q9UG56-22, PISD-LD

RefSeq proteins (13): NP_001313340, NP_001313341, NP_001313342, NP_001313343, NP_001313344, NP_001313345, NP_001313346, NP_001313347, NP_001313348, NP_001313349, NP_001313350, NP_055153, NP_821141 (=MANE)

Domains & families (InterPro)

IDNameType
IPR003817PS_DcarbxylaseFamily
IPR033177PSD-BFamily
IPR033661PSD_type1_eukFamily

Pfam: PF02666

Catalyzed reactions (Rhea), 1 shown:

  • a 1,2-diacyl-sn-glycero-3-phospho-L-serine + H(+) = a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + CO2 (RHEA:20828)

UniProt features (18 total): active site 4, chain 3, sequence variant 2, topological domain 2, transit peptide 1, site 1, modified residue 1, splice variant 1, mutagenesis site 1, region of interest 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UG56-F178.130.38

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 (5): 378 (schiff-base intermediate with substrate; via pyruvic acid; for decarboxylase activity); 377–378 (cleavage (non-hydrolytic); by autocatalysis); 191 (charge relay system; for autoendoproteolytic cleavage activity); 267 (charge relay system; for autoendoproteolytic cleavage activity); 378 (charge relay system; for autoendoproteolytic cleavage activity)

Post-translational modifications (1): 378

Mutagenesis-validated functional residues (1):

PositionPhenotype
378loss of autocatalytic processing.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-1483213Synthesis of PE

MSigDB gene sets: 270 (showing top): GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_PHOSPHOLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, GOBP_REGULATION_OF_MITOCHONDRION_ORGANIZATION, MISSIAGLIA_REGULATED_BY_METHYLATION_UP, GOBP_PROTEIN_MATURATION, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, GOCC_MITOCHONDRIAL_ENVELOPE, GOBP_ORGANELLE_ASSEMBLY, GOBP_GLYCEROLIPID_BIOSYNTHETIC_PROCESS

GO Biological Process (7): phosphatidylethanolamine biosynthetic process (GO:0006646), regulation of mitochondrion organization (GO:0010821), protein autoprocessing (GO:0016540), mitochondrial protein catabolic process (GO:0035694), lipid droplet formation (GO:0140042), lipid metabolic process (GO:0006629), phospholipid biosynthetic process (GO:0008654)

GO Molecular Function (4): phosphatidylserine decarboxylase activity (GO:0004609), protein binding (GO:0005515), lyase activity (GO:0016829), carboxy-lyase activity (GO:0016831)

GO Cellular Component (8): nucleus (GO:0005634), mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), Golgi apparatus (GO:0005794), lipid droplet (GO:0005811), cytosol (GO:0005829), cytoplasm (GO:0005737), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Glycerophospholipid biosynthesis1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
intracellular membrane-bounded organelle3
cytoplasm3
cellular anatomical structure3
mitochondrion organization2
phosphatidylethanolamine metabolic process1
glycerophospholipid biosynthetic process1
regulation of organelle organization1
protein processing1
mitochondrion1
protein catabolic process1
lipid storage1
lipid droplet organization1
membraneless organelle assembly1
primary metabolic process1
phospholipid metabolic process1
lipid biosynthetic process1
organophosphate biosynthetic process1
carboxy-lyase activity1
binding1
catalytic activity1
carbon-carbon lyase activity1
organelle inner membrane1
mitochondrial membrane1
endomembrane system1
intracellular membraneless organelle1
intracellular anatomical structure1

Protein interactions and networks

STRING

1982 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PISDPCYT2Q99447984
PISDPTDSS2Q9BVG9792
PISDPTDSS1P48651792
PISDPEMTQ9UBM1775
PISDGLB1P16278773
PISDCEPT1Q9Y6K0715
PISDETNK2Q9NVF9662
PISDCDIPTO14735628
PISDSELENOIQ9C0D9626
PISDCHKAP35790623
PISDETNK1Q9HBU6621
PISDCHKBQ9Y259619
PISDPSDA5PKW4602
PISDPSD2Q9BQI7593
PISDCHPT1Q8WUD6572

IntAct

61 interactions, top by confidence:

ABTypeScore
WDR19TULP3psi-mi:“MI:0914”(association)0.860
STK16UNC119Bpsi-mi:“MI:0914”(association)0.530
CXCR4FANCApsi-mi:“MI:0914”(association)0.530
IFT140ACSL3psi-mi:“MI:0914”(association)0.510
CFTRPISDpsi-mi:“MI:0915”(physical association)0.370
RIPK4VWA8psi-mi:“MI:0914”(association)0.350
HSCBRBP5psi-mi:“MI:0914”(association)0.350
LRRK2psi-mi:“MI:0914”(association)0.350
NS3C15orf61psi-mi:“MI:0914”(association)0.350
TMEM223psi-mi:“MI:0914”(association)0.350
DNAJA2DENND11psi-mi:“MI:0914”(association)0.350
PISDIGLL5psi-mi:“MI:0914”(association)0.350
C1QAMANBApsi-mi:“MI:0914”(association)0.350
GPR182SLC12A8psi-mi:“MI:0914”(association)0.350
PCDHB3ESYT2psi-mi:“MI:0914”(association)0.350
CLEC4EESYT2psi-mi:“MI:0914”(association)0.350
HLA-CTMEM131Lpsi-mi:“MI:0914”(association)0.350
PCDHB7TMEM131Lpsi-mi:“MI:0914”(association)0.350
BRICD5TMEM131Lpsi-mi:“MI:0914”(association)0.350
SLC22A9TMEM131Lpsi-mi:“MI:0914”(association)0.350
HLA-DQA1TMEM131Lpsi-mi:“MI:0914”(association)0.350
LDLRAD1ZNF316psi-mi:“MI:0914”(association)0.350
MFSD4AUBXN8psi-mi:“MI:0914”(association)0.350
AQP3UBXN8psi-mi:“MI:0914”(association)0.350
NUBP2TK2psi-mi:“MI:0914”(association)0.350
HYAL1CDIPTpsi-mi:“MI:0914”(association)0.350
VSIG4TNFRSF10Bpsi-mi:“MI:0914”(association)0.350
BSGTNPO2psi-mi:“MI:0914”(association)0.350

BioGRID (79): PISD (Affinity Capture-MS), PISD (Affinity Capture-MS), IFT140 (Affinity Capture-MS), WDR19 (Affinity Capture-MS), PISD (Affinity Capture-RNA), PISD (Affinity Capture-MS), PISD (Affinity Capture-MS), PISD (Affinity Capture-MS), PISD (Affinity Capture-RNA), PISD (Affinity Capture-MS), DHX29 (Two-hybrid), DAGLB (Two-hybrid), PISD (Two-hybrid), PISD (Affinity Capture-MS), PISD (Affinity Capture-MS)

ESM2 similar proteins: A0A3L7I2I8, B1WC37, D2XV59, O00178, O08582, O60733, O75648, P08760, P11029, P11497, P42694, P97570, P97819, Q05B63, Q13085, Q14749, Q28559, Q28DS0, Q29555, Q4R4U1, Q503J2, Q58DC5, Q5I0K3, Q5R5F8, Q5R8I8, Q5R962, Q5RB73, Q5SWU9, Q5ZKW0, Q6DC64, Q6DFV5, Q6IS24, Q6NYU2, Q6P4H8, Q6YJI5, Q7Z4G4, Q80YV4, Q8CIW5, Q8JGT5, Q8N0X4

Diamond homologs: A0Q562, A4IZN0, A7NAF0, B0TZM7, B2SFB2, B2UVC1, B3L2V1, B6JNM7, D3ZAW2, O25911, P27465, P39006, Q0BN99, Q10949, Q14J65, Q1CRQ1, Q1PCQ8, Q2A4Y0, Q58DH2, Q5NHR3, Q5R8I8, Q8BSF4, Q9GPP8, Q9UG56, Q9UTB5, Q9ZJN0, A1U4D6, A3D015, A4G529, A4VR22, A4XPX3, A5IIH5, A5W9U4, A6TH77, A6VD70, A6WSW1, A7ZV31, A8A7Q7, A9KEZ8, A9L3W8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic5
Likely pathogenic2
Uncertain significance95
Likely benign69
Benign11

Top pathogenic / likely-pathogenic (7)

Variant IDHGVSClassification
1470810NM_001326411.2(PISD):c.337dup (p.Ser113fs)Pathogenic
2807239NM_001326411.2(PISD):c.643del (p.Leu215fs)Pathogenic
3625651NM_001326411.2(PISD):c.175C>T (p.Arg59Ter)Pathogenic
4802627NM_001326411.2(PISD):c.51_52insT (p.Pro18fs)Pathogenic
694325NM_001326411.2(PISD):c.1006-12_1006-3delPathogenic
2696718NM_001326411.2(PISD):c.845-2A>GLikely pathogenic
2700183NM_001326411.2(PISD):c.698-2A>GLikely pathogenic

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

2649 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
22:31619720:G:CF374L0.999
22:31619720:G:TF374L0.999
22:31619721:A:GF374S0.999
22:31619722:A:GF374L0.999
22:31620599:G:TA320D0.999
22:31620609:A:GS317P0.999
22:31620647:C:GR304P0.999
22:31620650:T:AE303V0.999
22:31621007:C:GR278P0.999
22:31621010:C:GR277P0.999
22:31621026:A:GW272R0.999
22:31621026:A:TW272R0.999
22:31621050:G:CH264D0.999
22:31621067:A:GL258P0.999
22:31621456:C:TG192E0.999
22:31621465:G:TP189Q0.999
22:31621467:G:CS188R0.999
22:31621467:G:TS188R0.999
22:31621469:T:GS188R0.999
22:31621696:G:TR171S0.999
22:31619697:A:GL382P0.998
22:31619710:A:GS378P0.998
22:31619713:C:GG377R0.998
22:31620627:A:GW311R0.998
22:31620627:A:TW311R0.998
22:31620632:C:TG309E0.998
22:31620633:C:AG309W0.998
22:31621456:C:AG192V0.998
22:31621457:C:GG192R0.998
22:31621457:C:TG192R0.998

dbSNP variants (sampled 300 via entrez): RS1000008618 (22:31650325 C>A), RS1000062272 (22:31644966 T>C), RS1000120985 (22:31624089 C>A,G,T), RS1000193756 (22:31650723 G>C), RS1000326244 (22:31661753 A>G), RS1000346713 (22:31632709 G>A), RS1000389755 (22:31618808 C>T), RS1000413619 (22:31644733 C>T), RS1000440339 (22:31627081 G>A), RS1000591210 (22:31662187 G>A,C,T), RS1000761041 (22:31638455 T>G), RS1000940448 (22:31657132 T>C), RS1000989189 (22:31644914 C>G,T), RS1001070561 (22:31651319 C>T), RS1001098053 (22:31632005 G>C)

Disease associations

OMIM: gene MIM:612770 | disease phenotypes: MIM:618889

GenCC curated gene-disease

DiseaseClassificationInheritance
Liberfarb syndromeStrongAutosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
Liberfarb syndromeModerateAR

Mondo (1): Liberfarb syndrome (MONDO:0030045)

Orphanet (1): Short stature-skeletal dysplasia-retinal degeneration-intellectual disability-sensorineural hearing loss syndrome (Orphanet:589442)

HPO phenotypes

13 total (13 of 13 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000252Microcephaly
HP:0000407Sensorineural hearing impairment
HP:0000543Optic disc pallor
HP:0000546Retinal degeneration
HP:0001249Intellectual disability
HP:0001263Global developmental delay
HP:0002650Scoliosis
HP:0002663Delayed epiphyseal ossification
HP:0004322Short stature
HP:0007737Spicular pigmentation of the retina
HP:0007814Retinal pigment epithelial mottling
HP:0031367Metaphyseal striations

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: enzyme — Decarboxylases

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Cadmium Chlorideincreases abundance, increases expression, decreases expression3
Ozoneaffects cotreatment, increases expression, affects expression, increases abundance2
Valproic Acidaffects expression, affects methylation, decreases expression2
aristolochic acid Iincreases expression1
triphenyl phosphateaffects expression1
bisphenol Adecreases methylation1
sodium arseniteincreases abundance, increases expression1
perfluorooctanoic aciddecreases expression1
methacrylaldehydeaffects cotreatment, increases expression1
beta-methylcholineaffects expression1
celastrolincreases expression1
perfluorooctane sulfonic acidincreases expression1
ICG 001decreases expression1
abrineincreases expression1
perfluorobutanesulfonic aciddecreases expression1
bisphenol Sdecreases methylation1
Temozolomideincreases expression1
Zoledronic Acidincreases expression1
Acroleinaffects cotreatment, increases expression1
Air Pollutantsaffects expression, increases abundance1
Arsenicincreases abundance, increases expression1
Benzo(a)pyreneincreases methylation1
Cadmiumincreases abundance, increases expression1
Diazinonincreases methylation1
Doxorubicindecreases expression1
Estradiolaffects cotreatment, decreases expression, increases expression1
Fluorouracilaffects response to substance1
Methotrexatedecreases expression1
Smokedecreases expression1
Tetrachlorodibenzodioxinaffects cotreatment, decreases expression1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

CellosaurusNameCategorySex
CVCL_E2GSHAP1 PISD (-) 2Cancer cell lineMale
CVCL_XR61HAP1 PISD (-) 1Cancer cell lineMale

Clinical trials (associated diseases)

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

  • Associated diseases: Liberfarb syndrome
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Liberfarb syndrome