PCP4L1

Summary

PCP4L1 (Purkinje cell protein 4 like 1, HGNC:20448) is a protein-coding gene on chromosome 1q23.3, encoding Purkinje cell protein 4-like protein 1 (A6NKN8).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 13 total
• MANE Select transcript: NM_001102566

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20448
Approved symbol	PCP4L1
Name	Purkinje cell protein 4 like 1
Location	1q23.3
Locus type	gene with protein product
Status	Approved
Aliases	IQM1
Ensembl gene	ENSG00000248485
Ensembl biotype	protein_coding
Entrez	654790

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000504449, ENST00000874683

RefSeq mRNA: 1 — MANE Select: NM_001102566 NM_001102566

CCDS: CCDS53412

Canonical transcript exons

ENST00000504449 — 3 exons

Exon	Start	End
ENSE00002221094	161283668	161283722
ENSE00002250626	161284339	161285450
ENSE00002289271	161258745	161258983

Expression profiles

Bgee: expression breadth ubiquitous, 209 present calls, max score 99.82.

FANTOM5 (CAGE): breadth broad, TPM avg 6.2072 / max 531.8406, expressed in 395 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
6240	6.2072	395

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	99.82	gold quality
secondary oocyte	CL:0000655	99.80	gold quality
nucleus accumbens	UBERON:0001882	96.77	gold quality
pons	UBERON:0000988	96.56	gold quality
caudate nucleus	UBERON:0001873	96.44	gold quality
putamen	UBERON:0001874	95.95	gold quality
lateral globus pallidus	UBERON:0002476	94.40	gold quality
prefrontal cortex	UBERON:0000451	92.71	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	92.05	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	90.53	gold quality
Brodmann (1909) area 9	UBERON:0013540	89.78	gold quality
anterior cingulate cortex	UBERON:0009835	89.70	gold quality
primary visual cortex	UBERON:0002436	89.26	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.14	gold quality
right frontal lobe	UBERON:0002810	89.08	gold quality
frontal cortex	UBERON:0001870	89.02	gold quality
Brodmann (1909) area 46	UBERON:0006483	88.51	gold quality
adenohypophysis	UBERON:0002196	88.04	gold quality
neocortex	UBERON:0001950	87.84	gold quality
pituitary gland	UBERON:0000007	87.09	gold quality
forebrain	UBERON:0001890	86.85	gold quality
occipital lobe	UBERON:0002021	86.68	gold quality
nasal cavity mucosa	UBERON:0001826	86.43	gold quality
brain	UBERON:0000955	85.43	gold quality
nasal cavity epithelium	UBERON:0005384	85.35	gold quality
cerebral cortex	UBERON:0000956	84.83	gold quality
Brodmann (1909) area 23	UBERON:0013554	84.20	gold quality
hypothalamus	UBERON:0001898	84.09	gold quality
urinary bladder	UBERON:0001255	83.81	gold quality
esophagus mucosa	UBERON:0002469	83.53	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-MTAB-7316	yes	1148.63
E-CURD-114	yes	64.35
E-GEOD-84465	yes	7.15
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

37 targeting PCP4L1, 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-4455	100.00	65.48	1587
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-7845-5P	99.88	64.88	771
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-205-5P	99.81	70.05	1557
HSA-MIR-6794-5P	99.76	66.38	1048
HSA-MIR-4716-3P	99.69	66.73	1022
HSA-MIR-7157-5P	99.66	69.33	1829
HSA-MIR-3679-3P	99.64	69.88	1599
HSA-MIR-4310	99.59	68.84	2527
HSA-MIR-3614-5P	99.30	65.25	837
HSA-MIR-580-5P	99.28	70.94	1776
HSA-MIR-6744-3P	99.22	64.41	972
HSA-MIR-6734-3P	99.15	66.27	1627
HSA-MIR-4757-5P	99.12	64.51	981
HSA-MIR-4717-3P	99.06	66.34	1072
HSA-MIR-4651	99.06	67.57	2002
HSA-MIR-7702	99.06	65.95	698
HSA-MIR-6749-3P	99.00	65.73	1443
HSA-MIR-12135	98.99	70.26	1814
HSA-MIR-608	98.93	67.83	2013
HSA-MIR-7977	98.65	66.18	2590
HSA-MIR-138-1-3P	98.25	67.89	867
HSA-MIR-3179	98.22	65.90	1445
HSA-MIR-338-3P	98.14	67.38	1137
HSA-MIR-6783-5P	97.67	67.21	1528
HSA-MIR-4640-5P	97.42	66.33	1543
HSA-MIR-4726-5P	97.24	65.67	1299
HSA-MIR-6515-5P	97.08	65.48	1219

Literature-anchored findings (GeneRIF, showing 1)

• Cloning and expression analysis of the mouse Pcp4l1 gene, and sequence comparison to human PCP4L1. (PMID:15053978)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Pcp4l1	ENSMUSG00000038370
rattus_norvegicus	Pcp4l1	ENSRNOG00000003209

Paralogs (1): PCP4 (ENSG00000183036)

Protein

Protein identifiers

Purkinje cell protein 4-like protein 1 — A6NKN8 (reviewed: A6NKN8)

All UniProt accessions (1): A6NKN8

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the PCP4 family.

RefSeq proteins (1): NP_001096036* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR052142	Calmodulin_Regulator_PCP4-like	Family

UniProt features (6 total): compositionally biased region 2, chain 1, domain 1, region of interest 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NKN8-F1	72.81	0.39

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 (1): 8

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 35 (showing top): SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_16, YOSHIMURA_MAPK8_TARGETS_UP, DODD_NASOPHARYNGEAL_CARCINOMA_DN, CHEN_LIVER_METABOLISM_QTL_CIS, WONG_ADULT_TISSUE_STEM_MODULE, OHGUCHI_LIVER_HNF4A_TARGETS_UP, KATSANOU_ELAVL1_TARGETS_DN, PRKDC_TARGET_GENES, ZNF350_TARGET_GENES, ZNF618_TARGET_GENES, MIR3662, MIR7977, MIR6783_5P, MIR3179

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

1204 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PCP4L1	BPIFB3	P59826	494
PCP4L1	TMEM192	Q8IY95	473
PCP4L1	GPR26	Q8NDV2	470
PCP4L1	NIM1K	Q8IY84	459
PCP4L1	SLC41A3	Q96GZ6	412
PCP4L1	IGFALS	P35858	412
PCP4L1	SLC16A7	O60669	404
PCP4L1	OR5BS1	A0A2R8YED5	403
PCP4L1	SOCS2	O14508	393
PCP4L1	PLA2G4D	Q86XP0	381
PCP4L1	NELFCD	Q8IXH7	375
PCP4L1	LENEP	Q9Y5L5	373
PCP4L1	FLYWCH2	Q96CP2	372
PCP4L1	IGFBP1	P08833	365
PCP4L1	GHRHR	Q02643	353
PCP4L1	SERPINA12	Q8IW75	353

IntAct

4 interactions, top by confidence:

A	B	Type	Score
PCP4L1	H1-2	psi-mi:“MI:0915”(physical association)	0.400
CFTR	PCP4L1	psi-mi:“MI:0915”(physical association)	0.370
IQCB1	PCP4L1	psi-mi:“MI:0914”(association)	0.350

BioGRID (3): HIST1H1C (Proximity Label-MS), PCP4L1 (PCA), PCP4L1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GV96, A0MZ66, A0MZ67, A2VDA9, A5PJI6, A6NKN8, A8R4Q8, E7F7X0, O14990, O19021, O42932, O62770, O62771, P13505, P36425, P48539, P54866, P63054, P63055, P84086, P84087, P84088, Q04504, Q0P561, Q148C4, Q15506, Q28IH8, Q3UYG8, Q4R615, Q5F3A1, Q5M8L3, Q5R4Q3, Q5ZM33, Q62252, Q62736, Q6DBA5, Q6GNQ4, Q6NWC9, Q6P3G4, Q6PUV4

Diamond homologs: A6NKN8, A8R4Q8, P48539, P63054, P63055, Q148C4, Q6W8Q3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	7
Likely benign	1
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

711 predictions. Top by Δscore:

Variant	Effect	Δscore
1:161258979:GCGAG:G	donor_gain	0.9900
1:161258982:AGGTG:A	donor_loss	0.9900
1:161258983:GGT:G	donor_loss	0.9900
1:161258984:G:C	donor_loss	0.9900
1:161283667:GCTTA:G	acceptor_gain	0.9900
1:161283719:AAAGG:A	donor_loss	0.9900
1:161283720:AAGG:A	donor_loss	0.9900
1:161283723:G:GC	donor_loss	0.9900
1:161283724:TGAG:T	donor_loss	0.9900
1:161283725:GA:G	donor_loss	0.9900
1:161284041:A:T	donor_gain	0.9900
1:161284333:CTGCA:C	acceptor_loss	0.9900
1:161284334:TGCA:T	acceptor_loss	0.9900
1:161284335:GCA:G	acceptor_loss	0.9900
1:161284336:CAGGA:C	acceptor_loss	0.9900
1:161284337:A:AG	acceptor_gain	0.9900
1:161284337:A:AT	acceptor_loss	0.9900
1:161284338:G:GG	acceptor_gain	0.9900
1:161284436:C:T	donor_gain	0.9900
1:161283666:A:AG	acceptor_gain	0.9800
1:161283667:G:GG	acceptor_gain	0.9800
1:161283667:GCTT:G	acceptor_gain	0.9800
1:161284039:GGAAA:G	donor_gain	0.9800
1:161284040:GAAAG:G	donor_gain	0.9800
1:161284044:G:GG	donor_gain	0.9800
1:161283662:TTCCA:T	acceptor_loss	0.9700
1:161283663:TCCA:T	acceptor_loss	0.9700
1:161283664:CCAGC:C	acceptor_loss	0.9700
1:161283665:CAGCT:C	acceptor_loss	0.9700
1:161283666:A:AT	acceptor_loss	0.9700

AlphaMissense

445 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:161284429:T:A	I52N	0.999
1:161284429:T:C	I52T	0.999
1:161284440:T:C	F56L	0.999
1:161284442:C:A	F56L	0.999
1:161284442:C:G	F56L	0.999
1:161284429:T:G	I52S	0.998
1:161284416:G:C	A48P	0.997
1:161284420:C:A	A49D	0.997
1:161284425:G:C	A51P	0.997
1:161284433:G:C	Q53H	0.997
1:161284433:G:T	Q53H	0.997
1:161284441:T:C	F56S	0.997
1:161284441:T:G	F56C	0.997
1:161284393:T:C	L40P	0.996
1:161284417:C:A	A48D	0.994
1:161284419:G:C	A49P	0.994
1:161284449:T:C	F59L	0.994
1:161284451:T:A	F59L	0.994
1:161284451:T:G	F59L	0.994
1:161284387:T:A	I38N	0.993
1:161284387:T:G	I38S	0.993
1:161284423:T:C	L50P	0.993
1:161284393:T:A	L40Q	0.991
1:161284408:C:G	T45R	0.991
1:161284444:G:C	R57P	0.991
1:161284390:A:G	D39G	0.990
1:161284440:T:G	F56V	0.989
1:161284407:A:C	T45P	0.988
1:161284408:C:A	T45K	0.988
1:161284440:T:A	F56I	0.986

dbSNP variants (sampled 300 via entrez): RS1000010676 (1:161267955 C>A,T), RS1000023034 (1:161263627 G>A), RS1000178569 (1:161269408 A>G), RS1000294413 (1:161269764 C>T), RS1000377219 (1:161281941 G>A,C,T), RS1000381261 (1:161282107 G>A), RS1000472125 (1:161276364 G>A), RS1000634496 (1:161276684 A>C), RS1000676617 (1:161282441 A>G), RS1000708760 (1:161280830 CT>C,CTT), RS1000842347 (1:161261309 G>T), RS1001253633 (1:161279875 G>T), RS1001686443 (1:161258352 G>A), RS1001780580 (1:161282967 T>G), RS1001818885 (1:161262450 A>G)

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

1 associations (top):

Study	Trait	p-value
GCST001523_16	Visceral adipose tissue adjusted for BMI	8.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases methylation, affects cotreatment, increases expression, affects expression	9
sodium arsenite	decreases expression, increases expression	2
trichostatin A	increases expression	1
butyraldehyde	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
theaflavin-3,3’-digallate	affects expression	1
Sunitinib	decreases expression	1
Panobinostat	affects cotreatment, increases expression	1
Air Pollutants	increases expression, increases abundance	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Estradiol	affects cotreatment, decreases expression	1
Hydrogen Peroxide	affects cotreatment, increases expression	1
Lead	affects expression	1
Polychlorinated Biphenyls	affects expression	1
Dronabinol	decreases expression	1
Theophylline	affects cotreatment, increases expression	1
Aflatoxin M1	increases expression	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	increases expression	1
Lactic Acid	increases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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