PLSCR5

Summary

PLSCR5 (phospholipid scramblase family member 5, HGNC:19952) is a protein-coding gene on chromosome 3q24, encoding Phospholipid scramblase family member 5 (A0PG75).

Predicted to enable phospholipid scramblase activity. Predicted to be involved in plasma membrane phospholipid scrambling. Predicted to be active in plasma membrane.

Source: NCBI Gene 389158 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 47 total
• MANE Select transcript: NM_001085420

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19952
Approved symbol	PLSCR5
Name	phospholipid scramblase family member 5
Location	3q24
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000231213
Ensembl biotype	protein_coding
Entrez	389158

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000443512, ENST00000482567, ENST00000492200

RefSeq mRNA: 2 — MANE Select: NM_001085420 NM_001085420, NM_001321245

CCDS: CCDS46931, CCDS82853

Canonical transcript exons

ENST00000443512 — 8 exons

Exon	Start	End
ENSE00001599343	146593920	146594140
ENSE00001610720	146585837	146585942
ENSE00001621141	146605200	146605346
ENSE00001684060	146586030	146586112
ENSE00001684211	146600288	146600463
ENSE00001732908	146589653	146589814
ENSE00001764529	146595041	146595083
ENSE00001779378	146591720	146591881

Expression profiles

Bgee: expression breadth broad, 27 present calls, max score 83.69.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1364 / max 28.0626, expressed in 44 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
44942	0.1364	44

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.69	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	52.77	gold quality
colonic epithelium	UBERON:0000397	46.03	gold quality
caudate nucleus	UBERON:0001873	41.69	gold quality
stromal cell of endometrium	CL:0002255	39.97	gold quality
putamen	UBERON:0001874	39.70	gold quality
prefrontal cortex	UBERON:0000451	37.72	gold quality
superior frontal gyrus	UBERON:0002661	37.28	silver quality
ganglionic eminence	UBERON:0004023	37.28	gold quality
adenohypophysis	UBERON:0002196	36.99	gold quality
right uterine tube	UBERON:0001302	36.81	silver quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
sural nerve	UBERON:0015488	36.14	gold quality
pituitary gland	UBERON:0000007	35.67	silver quality
hindlimb stylopod muscle	UBERON:0004252	35.57	gold quality
muscle layer of sigmoid colon	UBERON:0035805	35.32	gold quality
nucleus accumbens	UBERON:0001882	34.29	silver quality
frontal cortex	UBERON:0001870	33.67	gold quality
smooth muscle tissue	UBERON:0001135	33.63	gold quality
muscle tissue	UBERON:0002385	33.47	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
hypothalamus	UBERON:0001898	32.96	silver quality
substantia nigra	UBERON:0002038	32.44	gold quality
anterior cingulate cortex	UBERON:0009835	32.43	gold quality
brain	UBERON:0000955	32.26	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
placenta	UBERON:0001987	31.60	silver quality
endometrium	UBERON:0001295	31.56	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.43

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

25 targeting PLSCR5, 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-3646	100.00	73.56	5283
HSA-MIR-4262	100.00	73.26	3931
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-302C-5P	99.97	72.56	3642
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-544A	99.84	68.66	1965
HSA-MIR-6715A-3P	99.83	68.05	1473
HSA-MIR-448	99.79	72.37	2103
HSA-MIR-452-5P	99.65	69.63	1762
HSA-MIR-4676-3P	99.65	69.31	1733
HSA-MIR-892C-3P	99.65	69.38	1745
HSA-MIR-510-3P	99.54	70.06	2965
HSA-MIR-543	99.52	69.03	2595
HSA-MIR-548G-3P	99.48	68.67	2159
HSA-MIR-892C-5P	99.16	70.56	2116
HSA-MIR-6814-5P	99.03	66.68	1273
HSA-MIR-5701	98.97	69.54	1502
HSA-MIR-6715B-3P	98.80	68.07	1204

Cross-species orthologs

9 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch211-71m22.1	ENSDARG00000058638
danio_rerio	si:ch73-206p6.1	ENSDARG00000077468
danio_rerio	si:ch211-71m22.5	ENSDARG00000091266
mus_musculus	Plscr5	ENSMUSG00000095654
rattus_norvegicus	Plscr5	ENSRNOG00000047917
caenorhabditis_elegans	scrm-6	WBGENE00009753
caenorhabditis_elegans		WBGENE00013052
caenorhabditis_elegans		WBGENE00019530
caenorhabditis_elegans		WBGENE00019531

Paralogs (4): PLSCR4 (ENSG00000114698), PLSCR2 (ENSG00000163746), PLSCR3 (ENSG00000187838), PLSCR1 (ENSG00000188313)

Protein

Protein identifiers

Phospholipid scramblase family member 5 — A0PG75 (reviewed: A0PG75)

All UniProt accessions (1): A0PG75

UniProt curated annotations — full annotation on UniProt →

Domain organisation. The N-terminal proline-rich domain (PRD) is required for phospholipid scramblase activity.

Similarity. Belongs to the phospholipid scramblase family.

Isoforms (2)

UniProt ID	Names	Canonical?
A0PG75-1	1	yes
A0PG75-2	2

RefSeq proteins (2): NP_001078889, NP_001308174 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005552	Scramblase	Family
IPR025659	Tubby-like_C	Homologous_superfamily

Pfam: PF03803

UniProt features (7 total): region of interest 2, chain 1, compositionally biased region 1, splice variant 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0PG75-F1	73.33	0.44

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 26 (showing top): chr3q24, GOBP_PLASMA_MEMBRANE_ORGANIZATION, GOBP_REGULATION_OF_MEMBRANE_LIPID_DISTRIBUTION, GOBP_ORGANOPHOSPHATE_ESTER_TRANSPORT, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, GOBP_PHOSPHOLIPID_TRANSPORT, GOBP_MEMBRANE_ORGANIZATION, GOBP_LIPID_LOCALIZATION, GOMF_LIPID_TRANSPORTER_ACTIVITY, GOMF_PHOSPHOLIPID_TRANSPORTER_ACTIVITY, GOMF_TRANSPORTER_ACTIVITY, GOBP_PLASMA_MEMBRANE_PHOSPHOLIPID_SCRAMBLING, GOMF_PHOSPHOLIPID_SCRAMBLASE_ACTIVITY, GOMF_INTRAMEMBRANE_LIPID_TRANSPORTER_ACTIVITY, ZNF486_TARGET_GENES

GO Biological Process (1): plasma membrane phospholipid scrambling (GO:0017121)

GO Molecular Function (1): phospholipid scramblase activity (GO:0017128)

GO Cellular Component (1): plasma membrane (GO:0005886)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
plasma membrane organization	1
phospholipid translocation	1
plasma membrane phospholipid scrambling	1
intramembrane lipid carrier activity	1
membrane	1
cell periphery	1

Protein interactions and networks

STRING

274 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PLSCR5	ANO6	Q4KMQ2	482
PLSCR5	FAM241B	Q96D05	476
PLSCR5	IQUB	Q8NA54	414
PLSCR5	NAXD	Q8IW45	400
PLSCR5	TMEM184B	Q9Y519	358
PLSCR5	BSPRY	Q5W0U4	357
PLSCR5	CGRRF1	Q99675	349
PLSCR5	ASTE1	Q2TB18	349
PLSCR5	OR6C2	Q9NZP2	349
PLSCR5	TMIGD1	Q6UXZ0	348
PLSCR5	OTOP2	Q7RTS6	348
PLSCR5	PLEKHN1	Q494U1	347
PLSCR5	HIRIP3	Q9BW71	345
PLSCR5	EPB42	P16452	323
PLSCR5	BAIAP2L2	Q6UXY1	318

IntAct

2 interactions, top by confidence:

A	B	Type	Score
PLSCR5	TTC1	psi-mi:“MI:0914”(association)	0.350

BioGRID (3): AMBRA1 (Affinity Capture-MS), TTC1 (Affinity Capture-MS), RWDD3 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0PG75, A2A3N6, A7T1N0, A8XKF2, B3H5L1, D4A2Z8, E9PU17, E9PX95, F1S5L4, F4IM84, O08619, O15162, O42857, O75386, P00488, P34751, P41879, P47140, P58195, P58196, P97564, Q05187, Q05B79, Q09306, Q0KHU5, Q28C60, Q3UW68, Q3ZBG9, Q5GJ77, Q5XI69, Q69RI8, Q6DCK1, Q6DNF3, Q6QBQ4, Q6S5G3, Q84M24, Q8IJH8, Q8VHK9, Q9DCW2, Q9FHK8

Diamond homologs: A0PG75, O15162, P58195, P58196, Q3ZBG9, Q6QBQ4, Q9DCW2, Q9JIZ9, Q9JJ00, Q9NRQ2, Q9NRY6, Q9NRY7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	45
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1090 predictions. Top by Δscore:

Variant	Effect	Δscore
3:146589647:A:AC	donor_gain	1.0000
3:146589647:ACTT:A	donor_loss	1.0000
3:146589648:C:CC	donor_gain	1.0000
3:146589648:CTT:C	donor_loss	1.0000
3:146589649:TTA:T	donor_loss	1.0000
3:146589650:TAC:T	donor_loss	1.0000
3:146589651:A:AC	donor_gain	1.0000
3:146589652:C:CC	donor_gain	1.0000
3:146589652:CA:C	donor_gain	1.0000
3:146589652:CAA:C	donor_gain	1.0000
3:146589652:CAAA:C	donor_gain	1.0000
3:146589652:CAAAG:C	donor_gain	1.0000
3:146589817:T:C	acceptor_gain	1.0000
3:146591878:CTAA:C	acceptor_gain	1.0000
3:146591879:TAA:T	acceptor_gain	1.0000
3:146591882:C:CC	acceptor_gain	1.0000
3:146594136:TATCA:T	acceptor_gain	1.0000
3:146594138:TCA:T	acceptor_gain	1.0000
3:146594139:CA:C	acceptor_gain	1.0000
3:146594139:CAC:C	acceptor_gain	1.0000
3:146594140:ACTAA:A	acceptor_loss	1.0000
3:146594141:C:CC	acceptor_gain	1.0000
3:146595037:TTA:T	donor_loss	1.0000
3:146595039:A:AC	donor_gain	1.0000
3:146595039:ACTT:A	donor_gain	1.0000
3:146595040:C:CT	donor_gain	1.0000
3:146595040:CTT:C	donor_gain	1.0000
3:146595040:CTTC:C	donor_gain	1.0000
3:146595042:T:TA	donor_gain	1.0000
3:146595080:CTAA:C	acceptor_gain	1.0000

AlphaMissense

1784 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:146589783:C:T	G216E	0.997
3:146589683:T:A	K249N	0.996
3:146589683:T:G	K249N	0.996
3:146591841:A:T	V165D	0.996
3:146589669:C:T	G254D	0.995
3:146594071:G:T	A101E	0.995
3:146593965:C:A	R136S	0.994
3:146593965:C:G	R136S	0.994
3:146589711:A:T	V240D	0.993
3:146589784:C:A	G216W	0.993
3:146591802:A:T	I178N	0.993
3:146589682:C:G	A250P	0.992
3:146591723:A:C	F204L	0.992
3:146591723:A:T	F204L	0.992
3:146591725:A:G	F204L	0.992
3:146586098:A:C	F264L	0.991
3:146586098:A:T	F264L	0.991
3:146586100:A:G	F264L	0.991
3:146589667:C:G	A255P	0.991
3:146589784:C:G	G216R	0.991
3:146589784:C:T	G216R	0.991
3:146591724:A:G	F204S	0.991
3:146591808:A:G	F176S	0.991
3:146593966:C:G	R136T	0.991
3:146594104:A:C	I90S	0.991
3:146589670:C:G	G254R	0.990
3:146594104:A:T	I90N	0.990
3:146589657:A:G	L258P	0.989
3:146589664:A:G	C256R	0.989
3:146589722:G:C	F236L	0.989

dbSNP variants (sampled 300 via entrez): RS1000242134 (3:146596561 T>C), RS1000274654 (3:146602209 G>C,T), RS1000361518 (3:146584620 G>A), RS1000416882 (3:146602683 C>G), RS1000450304 (3:146578303 C>T), RS1000636671 (3:146577771 C>T), RS1000871603 (3:146597230 T>C), RS1000903388 (3:146578038 G>A), RS1001003954 (3:146585316 C>T), RS1001023812 (3:146601262 T>C,G), RS1001048860 (3:146594909 C>A,G,T), RS1001052035 (3:146603471 G>A), RS1001144057 (3:146603094 G>T), RS1001231265 (3:146601529 C>T), RS1001273350 (3:146602807 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

2 associations (top):

Study	Trait	p-value
GCST001521_10	Subcutaneous adipose tissue	3.000000e-06
GCST010726_22	Periventricular white matter hyperintensities	8.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0005665	white matter hyperintensity measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
CGP 52608	affects binding, increases reaction	1
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1
Benzo(a)pyrene	decreases methylation	1
Catechin	increases expression, affects cotreatment	1
Triclosan	decreases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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