PALMD

Summary

PALMD (palmdelphin, HGNC:15846) is a protein-coding gene on chromosome 1p21.2, encoding Palmdelphin (Q9NP74).

Predicted to be involved in regulation of cell shape. Predicted to be located in dendritic spine and membrane. Predicted to be active in cytoplasm.

Source: NCBI Gene 54873 — RefSeq curated summary.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 102 total
• MANE Select transcript: NM_017734

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15846
Approved symbol	PALMD
Name	palmdelphin
Location	1p21.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20271, PALML
Ensembl gene	ENSG00000099260
Ensembl biotype	protein_coding
OMIM	610182
Entrez	54873

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 7 protein_coding, 2 retained_intron

ENST00000263174, ENST00000496843, ENST00000605497, ENST00000605613, ENST00000909490, ENST00000909491, ENST00000941535, ENST00000941536, ENST00000941537

RefSeq mRNA: 1 — MANE Select: NM_017734 NM_017734

CCDS: CCDS758

Canonical transcript exons

ENST00000263174 — 8 exons

Exon	Start	End
ENSE00000638540	99667642	99667766
ENSE00000777611	99662319	99662399
ENSE00000777622	99686676	99686790
ENSE00001298260	99646113	99646362
ENSE00003566496	99686930	99686963
ENSE00003576491	99687076	99687189
ENSE00003621050	99688775	99689872
ENSE00003655726	99694019	99694535

Expression profiles

Bgee: expression breadth ubiquitous, 268 present calls, max score 98.10.

FANTOM5 (CAGE): breadth broad, TPM avg 18.9272 / max 1115.5151, expressed in 855 samples.

FANTOM5 promoters (11 alternative TSS)

Promoter ID	TPM avg	Samples expressed
4181	14.2821	810
4183	2.2887	287
4182	0.5529	239
4180	0.5199	276
4177	0.3075	163
4174	0.2415	71
4176	0.2244	98
4179	0.2129	120
4184	0.1264	51
4178	0.0917	50

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
synovial joint	UBERON:0002217	98.10	gold quality
heart right ventricle	UBERON:0002080	97.70	gold quality
apex of heart	UBERON:0002098	97.61	gold quality
parotid gland	UBERON:0001831	97.54	gold quality
adipose tissue	UBERON:0001013	97.46	gold quality
tendon of biceps brachii	UBERON:0008188	97.37	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	97.36	gold quality
hindlimb stylopod muscle	UBERON:0004252	97.35	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	97.34	gold quality
subcutaneous adipose tissue	UBERON:0002190	97.33	gold quality
body of tongue	UBERON:0011876	97.08	gold quality
decidua	UBERON:0002450	97.04	gold quality
adipose tissue of abdominal region	UBERON:0007808	96.98	gold quality
omental fat pad	UBERON:0010414	96.94	gold quality
peritoneum	UBERON:0002358	96.92	gold quality
biceps brachii	UBERON:0001507	96.87	gold quality
connective tissue	UBERON:0002384	96.86	gold quality
cardiac ventricle	UBERON:0002082	96.82	gold quality
heart left ventricle	UBERON:0002084	96.78	gold quality
diaphragm	UBERON:0001103	96.67	gold quality
gluteal muscle	UBERON:0002000	96.34	gold quality
sural nerve	UBERON:0015488	96.32	gold quality
calcaneal tendon	UBERON:0003701	96.30	gold quality
skin of hip	UBERON:0001554	96.27	gold quality
pericardium	UBERON:0002407	96.19	gold quality
tendon	UBERON:0000043	96.13	gold quality
triceps brachii	UBERON:0001509	95.84	gold quality
gastrocnemius	UBERON:0001388	95.59	gold quality
muscle of leg	UBERON:0001383	95.55	gold quality
muscle organ	UBERON:0001630	95.30	gold quality

Single-cell (SCXA)

Detected in 10 experiment(s), a significant marker in 9.

Experiment	Marker?	Max mean expression
E-MTAB-8205	yes	190.96
E-GEOD-134144	yes	46.21
E-GEOD-135922	yes	46.16
E-MTAB-6701	yes	29.40
E-MTAB-8410	yes	27.41
E-MTAB-6678	yes	12.71
E-MTAB-10553	yes	6.46
E-GEOD-130148	yes	4.82
E-MTAB-10596	no	228.49
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

52 targeting PALMD, 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-9-5P	100.00	72.28	2361
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-6744-5P	99.93	66.82	748
HSA-MIR-3682-5P	99.93	67.97	1163
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-202-5P	99.78	67.65	991
HSA-MIR-26A-5P	99.78	73.52	2303
HSA-MIR-26B-5P	99.78	73.51	2305
HSA-MIR-4679	99.76	69.19	1229
HSA-MIR-4719	99.73	72.10	3329
HSA-MIR-4465	99.71	72.56	2096
HSA-MIR-466	99.67	70.85	2863
HSA-MIR-1251-3P	99.64	67.21	1408
HSA-MIR-3679-3P	99.64	69.88	1599

Literature-anchored findings (GeneRIF, showing 6)

• findings define palmdelphin as a target of serine-46-phosphorylated p53 that controls cell death in response to DNA damage. (PMID:24810057)
• A transcriptome-wide association study (TWAS) reveals PALMD (palmdelphin) as significantly associated with CAVS. The CAVS risk alleles and increasing disease severity are both associated with decreased mRNA expression levels of PALMD in valve tissues. (PMID:29511167)
• Phenome-wide analyses establish a specific association between aortic valve PALMD expression and calcific aortic valve stenosis. (PMID:32859967)
• Palmdelphin Regulates Nuclear Resilience to Mechanical Stress in the Endothelium. (PMID:34636652)
• PALMD regulates aortic valve calcification via altered glycolysis and NF-kappaB-mediated inflammation. (PMID:35367413)
• Clinical importance and PI3K/Akt pathway-dependent anti-proliferative role of PALMD and DPT in breast cancer. (PMID:37556876)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	palmda	ENSDARG00000001913
danio_rerio	palmdb	ENSDARG00000034321
danio_rerio		ENSDARG00000116789
mus_musculus	Palmd	ENSMUSG00000033377
rattus_norvegicus	Palmd	ENSRNOG00000058609

Paralogs (3): PALM (ENSG00000099864), PALM2AKAP2 (ENSG00000157654), PALM3 (ENSG00000187867)

Protein

Protein identifiers

Palmdelphin — Q9NP74 (reviewed: Q9NP74)

Alternative names: Paralemmin-like protein

All UniProt accessions (4): Q9NP74, A0A0S2Z599, A0A0S2Z5E7, S4R313

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Interacts with GLUL.

Subcellular location. Cytoplasm. Cell projection. Dendrite. Dendritic spine.

Tissue specificity. Ubiquitous. Most abundant in cardiac and skeletal muscle.

Post-translational modifications. Phosphorylated.

Similarity. Belongs to the paralemmin family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9NP74-1	1	yes
Q9NP74-2	2
Q9NP74-3	3

RefSeq proteins (1): NP_060204* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004965	Paralemmin	Family

Pfam: PF03285

UniProt features (28 total): modified residue 10, region of interest 3, cross-link 3, sequence variant 3, compositionally biased region 3, splice variant 2, sequence conflict 2, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NP74-F1	65.92	0.20

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 (13): 271, 321, 370, 384, 385, 498, 515, 520, 125, 179, 179, 1, 135

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 133 (showing top): HNF3ALPHA_Q6, GOBP_REGULATION_OF_CELL_MORPHOGENESIS, JAEGER_METASTASIS_DN, PEREZ_TP63_TARGETS, CAGCTG_AP4_Q5, BILD_HRAS_ONCOGENIC_SIGNATURE, RICKMAN_METASTASIS_DN, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_DN, OCT1_06, HFH3_01, TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_DUCTAL_NORMAL_DN, AFP1_Q6, NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN, PEREZ_TP53_AND_TP63_TARGETS, GOCC_NEURON_PROJECTION

GO Biological Process (1): regulation of cell shape (GO:0008360)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (6): cytoplasm (GO:0005737), membrane (GO:0016020), dendritic spine (GO:0043197), 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	3
regulation of cell morphogenesis	1
regulation of biological quality	1
binding	1
intracellular anatomical structure	1
dendrite	1
neuron spine	1
postsynapse	1
neuron projection	1
dendritic tree	1
cell junction	1

Protein interactions and networks

STRING

558 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PALMD	NOPCHAP1	Q8N5I9	541
PALMD	RNF145	Q96MT1	509
PALMD	CLVS1	Q8IUQ0	476
PALMD	SLC71A1	Q96MC6	465
PALMD	IGSF21	Q96ID5	460
PALMD	ARSJ	Q5FYB0	454
PALMD	PLPPR5	Q32ZL2	447
PALMD	LRMDA	Q9H2I8	443
PALMD	COL20A1	Q9P218	439
PALMD	IFT38	Q96AJ1	434
PALMD	KLHL31	Q9H511	433
PALMD	KCNH7	Q9NS40	429
PALMD	RIC3	Q7Z5B4	428
PALMD	ACAD10	Q6JQN1	425
PALMD	PALM	O75781	417

IntAct

31 interactions, top by confidence:

A	B	Type	Score
ABLIM3	PALMD	psi-mi:“MI:0915”(physical association)	0.560
ELAVL4	PALMD	psi-mi:“MI:0915”(physical association)	0.560
PALMD	WFS1	psi-mi:“MI:0915”(physical association)	0.560
HTT	PALMD	psi-mi:“MI:0915”(physical association)	0.560
PALMD	ATP2A2	psi-mi:“MI:0915”(physical association)	0.400
PALMD	ANXA2	psi-mi:“MI:0915”(physical association)	0.400
Nedd1		psi-mi:“MI:0914”(association)	0.350
DBN1	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
Strn3	STK24	psi-mi:“MI:0914”(association)	0.350
TIMM13	OARD1	psi-mi:“MI:0914”(association)	0.350
BAG6	CNOT1	psi-mi:“MI:0914”(association)	0.350
SORT1	SH3PXD2B	psi-mi:“MI:0914”(association)	0.350
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
EZR	MACROD2	psi-mi:“MI:0914”(association)	0.350
NF2	SAP18	psi-mi:“MI:0914”(association)	0.350
SWSAP1	NACA	psi-mi:“MI:2364”(proximity)	0.270
DISC1	PALMD	psi-mi:“MI:0915”(physical association)	0.000
ABLIM3	PALMD	psi-mi:“MI:0915”(physical association)	0.000
ezrA	PALMD	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (155): PALMD (Affinity Capture-RNA), PALMD (Affinity Capture-RNA), PALMD (Affinity Capture-MS), PALMD (Affinity Capture-MS), PALMD (Affinity Capture-MS), PALMD (Affinity Capture-MS), PALMD (Affinity Capture-MS), PALMD (Affinity Capture-MS), PALMD (Affinity Capture-MS), PALMD (Affinity Capture-MS), PALMD (Synthetic Lethality), ABLIM3 (Two-hybrid), PALMD (Proximity Label-MS), PALMD (Proximity Label-MS), PALMD (Protein-peptide)

ESM2 similar proteins: A0A1B0GVS7, A2CE83, A2VDU1, A5D992, A8KBE0, O43597, O43609, O43610, P28290, Q02223, Q08AD1, Q08E39, Q14CH0, Q1L0X2, Q2PFN5, Q2TBG9, Q3UUD2, Q4R815, Q5R959, Q5RGQ8, Q5TB30, Q66H35, Q6AYK4, Q6DD45, Q6GPM0, Q6NRB7, Q6P995, Q6PEM6, Q6ZUJ8, Q7ZX27, Q866R9, Q86VY9, Q8BGN6, Q8C3K5, Q8C817, Q8IYD9, Q8N957, Q96HH4, Q9BZD6, Q9C004

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	86
Likely benign	3
Benign	5

Top pathogenic / likely-pathogenic (0)

SpliceAI

945 predictions. Top by Δscore:

Variant	Effect	Δscore
1:99662395:TGAAG:T	donor_loss	1.0000
1:99662397:AAG:A	donor_loss	1.0000
1:99662399:GGTA:G	donor_loss	1.0000
1:99662400:G:C	donor_loss	1.0000
1:99662401:T:A	donor_loss	1.0000
1:99686672:TCAG:T	acceptor_loss	1.0000
1:99686674:A:AG	acceptor_gain	1.0000
1:99686674:AG:A	acceptor_gain	1.0000
1:99686675:G:GA	acceptor_gain	1.0000
1:99686675:GG:G	acceptor_gain	1.0000
1:99686675:GGC:G	acceptor_gain	1.0000
1:99686675:GGCT:G	acceptor_gain	1.0000
1:99686675:GGCTT:G	acceptor_gain	1.0000
1:99686786:TAAGA:T	donor_gain	1.0000
1:99686787:AAGA:A	donor_gain	1.0000
1:99686788:AGA:A	donor_gain	1.0000
1:99686789:GA:G	donor_gain	1.0000
1:99686789:GAG:G	donor_gain	1.0000
1:99686791:G:GG	donor_gain	1.0000
1:99686791:G:T	donor_loss	1.0000
1:99686792:T:A	donor_loss	1.0000
1:99686925:TACA:T	acceptor_loss	1.0000
1:99686926:ACAGT:A	acceptor_loss	1.0000
1:99686927:CA:C	acceptor_loss	1.0000
1:99686928:A:AG	acceptor_gain	1.0000
1:99686928:A:G	acceptor_loss	1.0000
1:99686928:AGTCT:A	acceptor_gain	1.0000
1:99686929:G:C	acceptor_loss	1.0000
1:99686929:G:GA	acceptor_gain	1.0000
1:99686929:GT:G	acceptor_gain	1.0000

AlphaMissense

3655 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:99667663:T:A	W50R	0.997
1:99667663:T:C	W50R	0.997
1:99688832:T:A	V191D	0.997
1:99688799:T:A	V180D	0.996
1:99688985:T:C	L242P	0.996
1:99689510:T:C	F417S	0.996
1:99667665:G:C	W50C	0.995
1:99667665:G:T	W50C	0.995
1:99667667:T:C	L51P	0.995
1:99686753:T:C	L110P	0.995
1:99646354:G:C	A13P	0.994
1:99662356:G:C	R28P	0.994
1:99688793:T:C	I178T	0.994
1:99688910:T:A	V217E	0.994
1:99689509:T:C	F417L	0.994
1:99689511:C:A	F417L	0.994
1:99689511:C:G	F417L	0.994
1:99667656:G:C	R47S	0.993
1:99667656:G:T	R47S	0.993
1:99688793:T:G	I178S	0.993
1:99688988:T:C	L243P	0.993
1:99689585:C:A	A442D	0.993
1:99694034:T:C	M543T	0.992
1:99646347:A:C	R10S	0.991
1:99646347:A:T	R10S	0.991
1:99688886:T:A	V209D	0.991
1:99688906:T:C	S216P	0.991
1:99688837:T:C	S193P	0.990
1:99689515:G:T	G419W	0.990
1:99688783:G:C	A175P	0.989

dbSNP variants (sampled 300 via entrez): RS1000082316 (1:99662952 T>A), RS1000089519 (1:99667027 A>G), RS1000132461 (1:99663923 A>T), RS1000201263 (1:99686331 G>A), RS1000251739 (1:99692730 A>G), RS1000409931 (1:99670134 A>G), RS1000458349 (1:99658185 C>A,T), RS1000468375 (1:99676208 G>T), RS1000517794 (1:99662684 A>C), RS1000589911 (1:99662468 A>G,T), RS1000600434 (1:99646328 C>G), RS1000656788 (1:99652789 T>G), RS1000693639 (1:99668417 C>A,T), RS1000728457 (1:99652526 C>A), RS1000811946 (1:99692424 A>G)

Disease associations

OMIM: gene MIM:610182 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

8 associations (top):

Study	Trait	p-value
GCST000442_2	Aortic root size	1.000000e-07
GCST003802_1	Response to citalopram or escitalopram in depression	1.000000e-07
GCST004651_1	Aortic root size	1.000000e-16
GCST005561_1	Aortic valve stenosis	1.000000e-22
GCST005785_1	Calcific aortic valve stenosis	2.000000e-14
GCST006979_994	Heel bone mineral density	2.000000e-09
GCST009155_1	Bicuspid aortic valve	2.000000e-08
GCST009870_2	Calcific aortic valve stenosis	1.000000e-16

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0000266	aortic stenosis
EFO:0009270	heel bone mineral density

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Cyclosporine	decreases expression	3
bisphenol A	affects expression	2
sodium arsenite	decreases expression	2
(+)-JQ1 compound	decreases expression, increases expression	2
Air Pollutants	decreases expression, increases abundance	2
Estradiol	affects cotreatment, decreases expression	2
Ethinyl Estradiol	affects expression, decreases expression	2
Nickel	decreases expression	2
Silicon Dioxide	decreases expression	2
Tobacco Smoke Pollution	decreases expression	2
Aflatoxin B1	decreases expression, decreases methylation	2
bisphenol F	increases expression	1
TAK-243	decreases sumoylation	1
glycidyl methacrylate	decreases expression	1
sodium arsenate	increases abundance, decreases expression	1
mono-(2-ethylhexyl)phthalate	increases expression	1
sulforaphane	decreases expression	1
cobaltous chloride	decreases expression	1
ferrous chloride	decreases expression	1
coumarin	increases phosphorylation	1
hydroquinone	decreases expression	1
CGP 52608	affects binding, increases reaction	1
nutlin 3	increases expression, affects cotreatment	1
bisphenol B	increases expression	1
abrine	decreases expression	1
licochalcone B	decreases expression	1
bisphenol S	increases expression	1
NSC 689534	affects binding, decreases expression	1
bisphenol AF	increases expression	1
Temozolomide	decreases expression	1

Clinical trials (associated diseases)

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