PALM

Summary

PALM (paralemmin, HGNC:8594) is a protein-coding gene on chromosome 19p13.3, encoding Paralemmin-1 (O75781). Involved in plasma membrane dynamics and cell process formation.

This gene encodes a member of the paralemmin protein family. The product of this gene is a prenylated and palmitoylated phosphoprotein that associates with the cytoplasmic face of plasma membranes and is implicated in plasma membrane dynamics in neurons and other cell types. Several alternatively spliced transcript variants have been identified, but the full-length nature of only two transcript variants has been determined.

Source: NCBI Gene 5064 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 289 total
• MANE Select transcript: NM_002579

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:8594
Approved symbol	PALM
Name	paralemmin
Location	19p13.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0270, PALM1
Ensembl gene	ENSG00000099864
Ensembl biotype	protein_coding
OMIM	608134
Entrez	5064

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 6 protein_coding, 3 protein_coding_CDS_not_defined, 3 retained_intron

ENST00000264560, ENST00000338448, ENST00000586055, ENST00000586776, ENST00000587513, ENST00000589012, ENST00000590161, ENST00000592155, ENST00000592870, ENST00000593172, ENST00000633534, ENST00000964891

RefSeq mRNA: 2 — MANE Select: NM_002579 NM_001040134, NM_002579

CCDS: CCDS32857, CCDS32858

Canonical transcript exons

ENST00000338448 — 9 exons

Exon	Start	End
ENSE00001372523	746285	748329
ENSE00002843176	708935	709151
ENSE00003473277	727008	727088
ENSE00003493405	727564	727694
ENSE00003500293	736019	736078
ENSE00003564651	740352	740483
ENSE00003592874	726138	726189
ENSE00003621242	734173	734194
ENSE00003673466	731095	731245

Expression profiles

Bgee: expression breadth ubiquitous, 230 present calls, max score 98.90.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.1259 / max 213.1086, expressed in 1219 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
172736	12.0226	1187
172738	1.0849	579
172739	0.3488	139
172737	0.3118	160
172741	0.1482	57
172735	0.0978	39
172740	0.0833	44
172742	0.0192	12
172743	0.0093	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
amygdala	UBERON:0001876	98.90	gold quality
right frontal lobe	UBERON:0002810	98.87	gold quality
nucleus accumbens	UBERON:0001882	98.75	gold quality
cingulate cortex	UBERON:0003027	98.47	gold quality
anterior cingulate cortex	UBERON:0009835	98.45	gold quality
caudate nucleus	UBERON:0001873	98.36	gold quality
putamen	UBERON:0001874	98.34	gold quality
prefrontal cortex	UBERON:0000451	98.15	gold quality
ganglionic eminence	UBERON:0004023	98.08	gold quality
cortical plate	UBERON:0005343	97.71	gold quality
Brodmann (1909) area 9	UBERON:0013540	97.55	gold quality
neocortex	UBERON:0001950	97.30	gold quality
frontal cortex	UBERON:0001870	97.27	gold quality
ventricular zone	UBERON:0003053	97.26	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	97.26	gold quality
apex of heart	UBERON:0002098	97.03	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	97.02	gold quality
temporal lobe	UBERON:0001871	96.95	gold quality
telencephalon	UBERON:0001893	96.94	gold quality
sural nerve	UBERON:0015488	96.91	gold quality
forebrain	UBERON:0001890	96.71	gold quality
cerebral cortex	UBERON:0000956	96.62	gold quality
spinal cord	UBERON:0002240	96.59	gold quality
right hemisphere of cerebellum	UBERON:0014890	96.32	gold quality
hypothalamus	UBERON:0001898	96.27	gold quality
central nervous system	UBERON:0001017	96.21	gold quality
brain	UBERON:0000955	96.20	gold quality
Ammon’s horn	UBERON:0001954	96.13	gold quality
adenohypophysis	UBERON:0002196	96.13	gold quality
right ovary	UBERON:0002118	96.00	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.41

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): PAX6

miRNA regulators (miRDB)

93 targeting PALM, 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-6748-5P	100.00	65.81	1057
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-7152-3P	99.97	67.47	849
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-5682	99.89	72.56	1005
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-4472	99.56	66.08	1478
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-4677-3P	99.49	67.91	1246
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-4688	99.48	64.68	828
HSA-MIR-3191-3P	99.45	63.94	356
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-4284	99.36	65.25	1293
HSA-MIR-128-1-5P	99.33	60.46	332
HSA-MIR-128-2-5P	99.33	60.83	311

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	palm1b	ENSDARG00000007818
danio_rerio	palm1a	ENSDARG00000026882
mus_musculus	Palm	ENSMUSG00000035863
rattus_norvegicus	Palm	ENSRNOG00000009760

Paralogs (3): PALMD (ENSG00000099260), PALM2AKAP2 (ENSG00000157654), PALM3 (ENSG00000187867)

Protein

Protein identifiers

Paralemmin-1 — O75781 (reviewed: O75781)

Alternative names: Paralemmin

All UniProt accessions (4): O75781, A0A087WTK8, A0A087WWY4, A0A087X1D6

UniProt curated annotations — full annotation on UniProt →

Function. Involved in plasma membrane dynamics and cell process formation. Isoform 1 and isoform 2 are necessary for axonal and dendritic filopodia induction, for dendritic spine maturation and synapse formation in a palmitoylation-dependent manner.

Subunit / interactions. Interacts with dopamine receptor DRD3.

Subcellular location. Cell membrane. Cell projection. Filopodium membrane. Axon. Dendrite. Dendritic spine. Basolateral cell membrane. Apicolateral cell membrane.

Tissue specificity. Widely expressed with highest expression in brain and testis and intermediate expression in heart and adrenal gland.

Similarity. Belongs to the paralemmin family.

Isoforms (2)

UniProt ID	Names	Canonical?
O75781-1	1, Paralemmin-L	yes
O75781-2	2, Paralemmin-S

RefSeq proteins (2): NP_001035224, NP_002570* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004965	Paralemmin	Family

Pfam: PF03285

UniProt features (28 total): modified residue 12, compositionally biased region 4, region of interest 3, lipid moiety-binding region 3, chain 1, propeptide 1, splice variant 1, sequence variant 1, mutagenesis site 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O75781-F1	70.68	0.33

Functional residue map

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

Post-translational modifications (15): 1, 116, 124, 141, 145, 162, 243, 245, 346, 367, 369, 384, 381, 383, 384

Mutagenesis-validated functional residues (1):

Position	Phenotype
381–383	inhibits axonal and dendritic filopodia formation and reduces axonal and dendritic branching.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 205 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, VERHAAK_AML_WITH_NPM1_MUTATED_DN, GOBP_RESPONSE_TO_NITROGEN_COMPOUND, GOBP_RESPONSE_TO_ELECTRICAL_STIMULUS, GOBP_REGULATION_OF_CELL_MORPHOGENESIS, LFA1_Q6, FOXO4_01, FOXO1_01, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_CELLULAR_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, RODWELL_AGING_KIDNEY_NO_BLOOD_DN, MODULE_66, GOBP_CELLULAR_RESPONSE_TO_ELECTRICAL_STIMULUS, TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_ERYTHROCYTE_UP

GO Biological Process (9): cytoskeleton organization (GO:0007010), adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway (GO:0007193), regulation of cell shape (GO:0008360), positive regulation of filopodium assembly (GO:0051491), synapse maturation (GO:0060074), negative regulation of dopamine receptor signaling pathway (GO:0060160), cellular response to electrical stimulus (GO:0071257), protein localization to plasma membrane (GO:0072659), intracellular protein localization (GO:0008104)

GO Molecular Function (2): D3 dopamine receptor binding (GO:0031750), protein binding (GO:0005515)

GO Cellular Component (19): nucleoplasm (GO:0005654), plasma membrane (GO:0005886), cytoplasmic side of plasma membrane (GO:0009898), postsynaptic density (GO:0014069), basolateral plasma membrane (GO:0016323), apicolateral plasma membrane (GO:0016327), filopodium (GO:0030175), axon (GO:0030424), cytoplasmic vesicle (GO:0031410), filopodium membrane (GO:0031527), dendritic spine (GO:0043197), neuron spine (GO:0044309), synaptic membrane (GO:0097060), postsynapse (GO:0098794), cytoplasm (GO:0005737), membrane (GO:0016020), dendrite (GO:0030425), cell projection (GO:0042995), synapse (GO:0045202)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
plasma membrane region	3
neuron projection	3
synapse	2
organelle organization	1
adenylate cyclase-modulating G protein-coupled receptor signaling pathway	1
adenylate cyclase inhibitor activity	1
regulation of cell morphogenesis	1
regulation of biological quality	1
filopodium assembly	1
regulation of filopodium assembly	1
positive regulation of plasma membrane bounded cell projection assembly	1
nervous system development	1
developmental maturation	1
synapse organization	1
G protein-coupled dopamine receptor signaling pathway	1
negative regulation of G protein-coupled receptor signaling pathway	1
regulation of dopamine receptor signaling pathway	1
response to electrical stimulus	1
cellular response to abiotic stimulus	1
protein localization to membrane	1
protein localization to cell periphery	1
macromolecule localization	1
dopamine receptor binding	1
binding	1
nuclear lumen	1
membrane	1
cell periphery	1
plasma membrane	1
cytoplasmic side of membrane	1
asymmetric synapse	1
postsynaptic specialization	1
basal plasma membrane	1
actin-based cell projection	1
cytoplasm	1
intracellular vesicle	1
filopodium	1
cell projection membrane	1
dendrite	1
neuron spine	1

Protein interactions and networks

STRING

523 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PALM	ZDHHC13	Q8IUH4	832
PALM	ZDHHC8	Q9ULC8	795
PALM	ZDHHC17	Q8IUH5	745
PALM	SYT7	O43581	736
PALM	SNAP25	P13795	591
PALM	SYT1	P21579	587
PALM	DLG4	P78352	561
PALM	PRXL2A	Q9BRX8	524
PALM	GAD2	Q05329	487
PALM	PALMD	Q9NP74	417
PALM	ZDHHC3	Q9NYG2	398
PALM	BASP1	P80723	384
PALM	ZDHHC2	Q9UIJ5	371
PALM	PALM2AKAP2	Q9Y2D5	366
PALM	GAS1	P54826	353
PALM	TCF21	O43680	353

IntAct

58 interactions, top by confidence:

A	B	Type	Score
MED21	MED19	psi-mi:“MI:0914”(association)	0.880
RABGGTB	YKT6	psi-mi:“MI:0914”(association)	0.740
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
KCNJ2	KCNJ18	psi-mi:“MI:2364”(proximity)	0.660
DMWD	PALM	psi-mi:“MI:0915”(physical association)	0.560
PALM	SPRED1	psi-mi:“MI:0915”(physical association)	0.560
FYTTD1	UBA6	psi-mi:“MI:0914”(association)	0.530
RABGGTB	PIPSL	psi-mi:“MI:0914”(association)	0.530
GJB7	PALM3	psi-mi:“MI:0914”(association)	0.530
RASGRF1	PALM	psi-mi:“MI:0915”(physical association)	0.400
COQ6	PALM	psi-mi:“MI:0915”(physical association)	0.400
ZNF624	PALM	psi-mi:“MI:0915”(physical association)	0.400
GPC1	SNAP23	psi-mi:“MI:0915”(physical association)	0.400
GPC1	GANAB	psi-mi:“MI:0915”(physical association)	0.400
PALM	HTT	psi-mi:“MI:0915”(physical association)	0.400
POT1	PALM	psi-mi:“MI:0915”(physical association)	0.370
FLNA	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
Flnb	RPL22	psi-mi:“MI:0914”(association)	0.350
Tmod3	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
Coro1c	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
DBN1	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
SYNPO	LMO7	psi-mi:“MI:0914”(association)	0.350
Myh9	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
	SNAP23	psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
rep	PALM	psi-mi:“MI:0914”(association)	0.350

BioGRID (106): PALM (Affinity Capture-MS), PALM (Affinity Capture-MS), PALM (Affinity Capture-MS), PALM (Affinity Capture-MS), PALM (Affinity Capture-MS), PALM (Proximity Label-MS), PALM (Affinity Capture-MS), PALM (Affinity Capture-MS), PALM (Affinity Capture-MS), PALM (Affinity Capture-MS), PALM (Affinity Capture-MS), PALM (Affinity Capture-MS), PALM (Affinity Capture-MS), PALM (Proximity Label-MS), PALM (Proximity Label-MS)

ESM2 similar proteins: A0M8T5, A1X157, E7F5E1, O15169, O35625, O35867, O54931, O70239, O75781, Q07DW4, Q07DZ5, Q07E15, Q07E28, Q07E41, Q09YG9, Q09YI1, Q09YJ3, Q09YK4, Q09YM8, Q0VDN7, Q108T9, Q13625, Q2IBB2, Q2IBD4, Q2IBF8, Q2MJV8, Q2MJV9, Q2QL82, Q2QLB3, Q2QLG9, Q3MHH7, Q3UH68, Q4KM62, Q5U301, Q63028, Q6IPM2, Q8CG79, Q8N163, Q8VDP4, Q920Q0

Diamond homologs: A2TJV2, A6NDB9, O54931, O75781, Q2MJV8, Q2MJV9, Q3MHH7, Q4KM62, Q5U301, Q7ZX27, Q920Q0, Q9JHU2, Q9NP74, Q9Y2D5, Q9YGL6, Q9Z0P4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	149
Likely benign	102
Benign	28

Top pathogenic / likely-pathogenic (0)

SpliceAI

1978 predictions. Top by Δscore:

Variant	Effect	Δscore
19:709148:TGGA:T	donor_gain	1.0000
19:709149:GGA:G	donor_gain	1.0000
19:709149:GGAG:G	donor_gain	1.0000
19:709150:GA:G	donor_gain	1.0000
19:709150:GAG:G	donor_gain	1.0000
19:709152:G:GG	donor_gain	1.0000
19:709156:G:GG	donor_gain	1.0000
19:711071:A:T	donor_gain	1.0000
19:726187:GCA:G	donor_gain	1.0000
19:726190:G:GG	donor_gain	1.0000
19:727003:CACA:C	acceptor_loss	1.0000
19:727004:A:AG	acceptor_gain	1.0000
19:727004:ACAG:A	acceptor_gain	1.0000
19:727005:C:G	acceptor_gain	1.0000
19:727006:A:AG	acceptor_gain	1.0000
19:727006:AG:A	acceptor_gain	1.0000
19:727007:G:GC	acceptor_gain	1.0000
19:727007:GG:G	acceptor_gain	1.0000
19:727007:GGA:G	acceptor_gain	1.0000
19:727007:GGAGA:G	acceptor_gain	1.0000
19:727085:GAAG:G	donor_gain	1.0000
19:727086:AAGG:A	donor_loss	1.0000
19:727087:AGGTA:A	donor_loss	1.0000
19:727089:G:C	donor_loss	1.0000
19:727089:G:GG	donor_gain	1.0000
19:727523:T:TA	acceptor_gain	1.0000
19:727535:C:CA	acceptor_gain	1.0000
19:727562:A:AG	acceptor_gain	1.0000
19:727563:G:GG	acceptor_gain	1.0000
19:727681:GAC:G	donor_gain	1.0000

AlphaMissense

2500 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:727585:T:A	W54R	0.998
19:727585:T:C	W54R	0.998
19:727587:G:C	W54C	0.998
19:727587:G:T	W54C	0.998
19:740370:T:C	I174T	0.998
19:746288:T:A	V213D	0.998
19:746554:T:C	F302L	0.998
19:746555:T:C	F302S	0.998
19:746556:C:A	F302L	0.998
19:746556:C:G	F302L	0.998
19:740370:T:G	I174S	0.997
19:727577:G:C	R51P	0.996
19:727589:T:C	L55P	0.995
19:740364:T:A	V172D	0.995
19:746354:T:C	L235P	0.995
19:740370:T:A	I174N	0.994
19:746555:T:G	F302C	0.994
19:727015:G:C	R22P	0.993
19:727586:G:C	W54S	0.993
19:740471:G:C	D208H	0.993
19:746560:G:C	G304R	0.993
19:727569:G:C	K48N	0.992
19:727569:G:T	K48N	0.992
19:727564:T:C	S47P	0.991
19:740360:T:C	S171P	0.991
19:740463:T:A	V205D	0.991
19:740472:A:T	D208V	0.991
19:727084:T:C	L45P	0.990
19:740465:T:G	Y206D	0.990
19:727075:T:C	L42P	0.989

dbSNP variants (sampled 300 via entrez): RS1000026709 (19:710242 C>T), RS1000083541 (19:745294 T>C), RS1000131498 (19:711414 G>T), RS1000133440 (19:740696 C>T), RS1000157380 (19:728142 G>A), RS1000188191 (19:745856 C>T), RS1000270952 (19:732789 G>A), RS1000387874 (19:728346 G>T), RS1000426541 (19:715958 T>C), RS1000475053 (19:724205 C>A,T), RS1000495269 (19:727328 C>G,T), RS1000531876 (19:715297 T>G), RS1000532808 (19:720048 G>A,T), RS1000590603 (19:748674 T>C), RS1000713743 (19:727521 C>G,T)

Disease associations

OMIM: gene MIM:608134 | 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
GCST006950_42	Feeling worry	6.000000e-09
GCST008522_97	Bitter alcoholic beverage consumption	9.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0009589	worry measurement
EFO:0010092	bitter alcoholic beverage consumption measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, increases methylation, decreases expression	2
bisphenol S	increases expression, increases methylation	2
Air Pollutants	increases abundance, increases expression, decreases expression	2
Arsenic	increases methylation, affects cotreatment, decreases expression, increases abundance	2
Benzo(a)pyrene	affects methylation	2
Smoke	decreases expression	2
Tobacco Smoke Pollution	affects expression, decreases expression	2
Aflatoxin B1	increases expression, increases methylation	2
Particulate Matter	increases abundance, increases expression, decreases expression	2
FR900359	affects phosphorylation	1
bisphenol F	increases expression	1
2,5,2’,5’-tetrachlorobiphenyl	increases expression	1
sulforaphane	decreases expression	1
sodium arsenite	affects cotreatment, decreases expression, increases abundance	1
tobacco tar	decreases expression	1
manganese chloride	decreases expression, increases abundance, affects cotreatment	1
benzo(e)pyrene	increases methylation	1
coumarin	decreases phosphorylation	1
bisphenol B	increases expression	1
abrine	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
bisphenol AF	increases expression	1
Sunitinib	increases expression	1
Zoledronic Acid	decreases expression	1
Fulvestrant	increases methylation, affects cotreatment	1
Acetaminophen	increases expression	1
Cisplatin	increases expression, affects cotreatment	1
Estradiol	increases expression	1
Manganese	increases abundance, affects cotreatment, decreases expression	1
Methapyrilene	increases methylation	1

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B1ZU	Abcam HeLa PALM KO	Cancer cell line	Female
CVCL_TB98	HAP1 PALM (-) 1	Cancer cell line	Male
CVCL_TB99	HAP1 PALM (-) 2	Cancer cell line	Male
CVCL_TC00	HAP1 PALM (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

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