CNPY1

Summary

CNPY1 (canopy FGF signaling regulator 1, HGNC:27786) is a protein-coding gene on chromosome 7q36.3, encoding Protein canopy homolog 1 (Q3B7I2).

Cnpy1 is expressed in the midbrain-hindbrain (MHB) boundary in zebrafish, binds FGFR1 (MIM 136350), and plays a role in FGF signaling (Hirate and Okamoto, 2006 [PubMed 16488878]).

Source: NCBI Gene 285888 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 27 total — 7 pathogenic, 3 likely-pathogenic
• MANE Select transcript: NM_001393663

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27786
Approved symbol	CNPY1
Name	canopy FGF signaling regulator 1
Location	7q36.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000146910
Ensembl biotype	protein_coding
OMIM	612493
Entrez	285888

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000321736, ENST00000406197, ENST00000636372, ENST00000636446, ENST00000682997

RefSeq mRNA: 8 — MANE Select: NM_001393663 NM_001103176, NM_001369814, NM_001369815, NM_001369816, NM_001369818, NM_001369820, NM_001369821, NM_001393663

CCDS: CCDS43684, CCDS94241

Canonical transcript exons

ENST00000636446 — 5 exons

Exon	Start	End
ENSE00001147943	155507020	155507116
ENSE00003792436	155546429	155546559
ENSE00003798356	155545831	155545943
ENSE00003799539	155508894	155509097
ENSE00003800708	155501129	155503105

Expression profiles

Bgee: expression breadth broad, 49 present calls, max score 84.49.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3798 / max 74.6563, expressed in 83 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
87036	0.0768	25
87040	0.0689	4
87034	0.0684	36
87039	0.0642	35
87035	0.0333	13
87033	0.0323	22
87037	0.0293	11
87038	0.0064	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar hemisphere	UBERON:0002245	84.49	gold quality
cerebellar cortex	UBERON:0002129	84.43	gold quality
cerebellum	UBERON:0002037	84.27	gold quality
right hemisphere of cerebellum	UBERON:0014890	83.27	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.90	gold quality
ganglionic eminence	UBERON:0004023	58.42	gold quality
cortical plate	UBERON:0005343	50.96	gold quality
ventricular zone	UBERON:0003053	50.32	gold quality
substantia nigra	UBERON:0002038	48.99	gold quality
superior frontal gyrus	UBERON:0002661	42.74	gold quality
corpus callosum	UBERON:0002336	42.18	silver quality
bone marrow cell	CL:0002092	41.52	gold quality
body of pancreas	UBERON:0001150	41.18	gold quality
brain	UBERON:0000955	40.53	gold quality
sural nerve	UBERON:0015488	40.05	gold quality
pancreas	UBERON:0001264	39.94	gold quality
prefrontal cortex	UBERON:0000451	39.89	gold quality
mucosa of transverse colon	UBERON:0004991	37.99	silver quality
bone marrow	UBERON:0002371	37.89	gold quality
frontal cortex	UBERON:0001870	37.82	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
rectum	UBERON:0001052	37.03	silver quality
smooth muscle tissue	UBERON:0001135	36.30	silver quality
Brodmann (1909) area 9	UBERON:0013540	35.92	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	35.81	gold quality
apex of heart	UBERON:0002098	35.12	gold quality
islet of Langerhans	UBERON:0000006	35.06	silver quality
skeletal muscle tissue	UBERON:0001134	34.77	gold quality
cerebral cortex	UBERON:0000956	34.68	gold quality
mucosa of stomach	UBERON:0001199	34.49	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-GEOD-98556	no	34.93
E-ANND-3	no	1.15

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

73 targeting CNPY1, 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-3163	100.00	77.23	8605
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-219A-5P	99.91	73.36	735
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-4782-3P	99.88	73.31	735
HSA-MIR-6766-3P	99.88	73.38	732
HSA-MIR-4671-3P	99.88	72.46	1045
HSA-MIR-4503	99.85	71.45	1869
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-26A-5P	99.78	73.52	2303
HSA-MIR-26B-5P	99.78	73.51	2305
HSA-MIR-4255	99.72	67.70	1541
HSA-MIR-1200	99.71	70.42	1838
HSA-MIR-1179	99.71	68.70	1040
HSA-MIR-1208	99.70	68.28	1533
HSA-MIR-379-3P	99.69	69.60	1524
HSA-MIR-411-3P	99.69	69.63	1524
HSA-MIR-7154-5P	99.69	70.52	1900
HSA-MIR-580-3P	99.67	69.23	1841
HSA-MIR-378A-5P	99.65	66.33	1311
HSA-MIR-1303	99.65	69.77	1662
HSA-MIR-875-3P	99.63	69.47	2548
HSA-MIR-4756-3P	99.62	66.30	1319

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	cnpy1	ENSDARG00000003757
mus_musculus	Cnpy1	ENSMUSG00000044681
rattus_norvegicus	Cnpy1	ENSRNOG00000028311
drosophila_melanogaster	sel	FBGN0263260
caenorhabditis_elegans	Y47H9C.8	WBGENE00012951
caenorhabditis_elegans		WBGENE00017165
caenorhabditis_elegans		WBGENE00017169

Paralogs (2): CNPY2 (ENSG00000257727), (ENSG00000283128)

Protein

Protein identifiers

Protein canopy homolog 1 — Q3B7I2 (reviewed: Q3B7I2)

All UniProt accessions (3): Q3B7I2, A0A1B0GVE0, A0A804HIX2

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the canopy family.

RefSeq proteins (8): NP_001096646, NP_001356743, NP_001356744, NP_001356745, NP_001356747, NP_001356749, NP_001356750, NP_001380592* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR021852	DUF3456	Domain
IPR042415	CNPY	Family

Pfam: PF11938

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q3B7I2-F1	79.89	0.27

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 46 (showing top): GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_UP, GSE45365_NK_CELL_VS_CD8A_DC_DN, GLI1_TARGET_GENES, ZNF184_TARGET_GENES, ZNF563_TARGET_GENES, MIR944, MIR4503, MIR670_3P, MIR1200, MIR194_5P, MIR4768_3P, MIR378A_5P, MIR1273H_3P, GSE10422_WT_VS_BAFF_TRANSGENIC_LN_BCELL_DN, GSE15659_NAIVE_CD4_TCELL_VS_RESTING_TREG_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

408 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CNPY1	PSAPL1	Q6NUJ1	893
CNPY1	PSAP	P07292	801
CNPY1	FGF8	P55075	730
CNPY1	FGFR1	P11362	695
CNPY1	ACVR2A	P27037	649
CNPY1	CNPY4	Q8N129	584
CNPY1	RBM33	Q96EV2	541
CNPY1	EN2	P19622	531
CNPY1	CNPY3	Q9BT09	518
CNPY1	EN1	Q05925	477
CNPY1	FGF20	Q9NP95	467
CNPY1	CORIN	Q9Y5Q5	462
CNPY1	FGF4	P08620	455
CNPY1	FGF18	O76093	450
CNPY1	FGF22	Q9HCT0	448

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A4IID1, A7E2M3, A8MRC7, F6PTN1, O13156, O35427, O60879, O70566, O75575, O77836, O82597, O82793, P56159, P97785, Q0J035, Q0VCK9, Q2HXL0, Q3B7I2, Q43187, Q4R854, Q4VAB4, Q5F407, Q5I0R6, Q5M854, Q5R9K4, Q5R9K8, Q5REP8, Q5ZKJ0, Q61143, Q62997, Q68EQ9, Q6DHU1, Q6GQI7, Q6INE8, Q6NQB7, Q6R8G7, Q80ZK0, Q812G0, Q84WK5, Q8BXA5

Diamond homologs: Q2L6L1, Q3B7I2, Q4VAB4, Q5M7D4, Q7JXF7, Q9QXT0, Q9Y2B0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	7
Likely pathogenic	3
Uncertain significance	15
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (10)

Variant ID	HGVS	Classification
146358	GRCh38/hg38 7q36.3(chr7:155501171-159325876)x1	Pathogenic
2422565	NC_000007.13:g.(?152617597)(158500659_?)del	Pathogenic
253496	GRCh37/hg19 7q36.3(chr7:155100276-155768780)x1	Pathogenic
4682696	GRCh37/hg19 7q36.2-36.3(chr7:153906860-158923491)x3	Pathogenic
563418	GRCh37/hg19 7q36.2-36.3(chr7:153958355-159119707)x1	Pathogenic
980290	GRCh37/hg19 7q36.3(chr7:155319280-159119707)x1	Pathogenic
983166	GRCh37/hg19 7q36.2-36.3(chr7:152800000-159138663)x1	Pathogenic
149109	GRCh38/hg38 7q36.3(chr7:155379296-159335866)x3	Likely pathogenic
443709	GRCh37/hg19 7q36.2-36.3(chr7:154963758-157582526)x3	Likely pathogenic
563414	GRCh37/hg19 7q36.1-36.3(chr7:152578849-156183328)x3	Likely pathogenic

SpliceAI

1588 predictions. Top by Δscore:

Variant	Effect	Δscore
7:155482008:A:C	acceptor_gain	1.0000
7:155500971:T:TA	donor_gain	1.0000
7:155507115:CA:C	acceptor_gain	1.0000
7:155507117:C:CC	acceptor_gain	1.0000
7:155508963:T:TA	donor_gain	1.0000
7:155508968:T:A	donor_gain	1.0000
7:155508997:T:A	donor_gain	1.0000
7:155509015:T:TA	donor_gain	1.0000
7:155482006:CCA:C	acceptor_gain	0.9900
7:155482007:CA:C	acceptor_gain	0.9900
7:155507113:CACA:C	acceptor_gain	0.9900
7:155509098:C:CC	acceptor_gain	0.9900
7:155509098:CTAAG:C	acceptor_loss	0.9900
7:155509099:T:C	acceptor_loss	0.9900
7:155482005:CCCA:C	acceptor_gain	0.9800
7:155482007:C:T	acceptor_gain	0.9800
7:155482008:A:AC	acceptor_gain	0.9800
7:155482016:C:CT	acceptor_gain	0.9800
7:155502980:T:C	donor_gain	0.9800
7:155503037:A:AC	donor_gain	0.9800
7:155503037:ACT:A	donor_gain	0.9800
7:155503038:C:CC	donor_gain	0.9800
7:155503038:CTC:C	donor_gain	0.9800
7:155503038:CTCCT:C	donor_gain	0.9800
7:155508887:AGCTT:A	donor_loss	0.9800
7:155508888:GCTTA:G	donor_loss	0.9800
7:155508889:CTT:C	donor_loss	0.9800
7:155508890:TTACC:T	donor_loss	0.9800
7:155508891:T:TG	donor_loss	0.9800
7:155508892:A:AC	donor_gain	0.9800

AlphaMissense

1080 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:155508978:G:C	F20L	0.910
7:155508978:G:T	F20L	0.910
7:155508980:A:G	F20L	0.910
7:155508987:G:C	F17L	0.885
7:155508987:G:T	F17L	0.885
7:155508989:A:G	F17L	0.885
7:155508897:A:C	F47L	0.873
7:155508897:A:T	F47L	0.873
7:155508899:A:G	F47L	0.873
7:155508981:T:A	R19S	0.862
7:155508981:T:G	R19S	0.862
7:155508969:C:A	R23S	0.789
7:155508969:C:G	R23S	0.789
7:155508927:A:C	F37L	0.753
7:155508927:A:T	F37L	0.753
7:155508929:A:G	F37L	0.753
7:155508904:A:G	L45S	0.743
7:155508982:C:G	R19T	0.738
7:155508976:G:T	A21D	0.735
7:155507116:A:G	C49R	0.722
7:155508942:A:C	F32L	0.721
7:155508942:A:T	F32L	0.721
7:155508944:A:G	F32L	0.721
7:155508988:A:C	F17C	0.686
7:155508988:A:G	F17S	0.672
7:155508900:T:A	K46N	0.653
7:155508900:T:G	K46N	0.653
7:155508983:T:C	R19G	0.652
7:155507106:A:T	I52K	0.643
7:155507082:A:G	I60T	0.641

dbSNP variants (sampled 300 via entrez): RS1000039913 (7:155511721 C>A,T), RS1000071078 (7:155512034 A>G), RS1000102610 (7:155516259 T>A,C,G), RS1000190686 (7:155548153 G>A), RS1000197592 (7:155547028 A>G), RS1000250618 (7:155542804 C>T), RS1000267620 (7:155505644 T>C), RS1000313885 (7:155526089 G>A), RS1000331107 (7:155509184 A>T), RS1000404640 (7:155508934 A>C), RS1000502657 (7:155516089 T>C), RS1000599147 (7:155516312 G>A), RS1000631831 (7:155507436 A>G), RS1000646067 (7:155548382 G>C,T), RS1000647219 (7:155546330 C>T)

Disease associations

OMIM: gene MIM:612493 | disease phenotypes: MIM:142945

GenCC curated gene-disease

Mondo (1): holoprosencephaly 3 (MONDO:0007733)

Orphanet (1): Holoprosencephaly (Orphanet:2162)

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST006491_10	Circulating fibroblast growth factor 23 levels	4.000000e-07
GCST012490_421	Femur bone mineral density x serum urate levels interaction	2.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004531	urate measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C564181	Holoprosencephaly 3 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases methylation, increases methylation, affects methylation	2
Valproic Acid	decreases expression	2
bisphenol A	increases methylation	1
trichostatin A	decreases expression	1
mono-(2-ethylhexyl)phthalate	increases abundance, increases methylation	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
2-ethyl-5-carboxypentyl phthalate	increases abundance, increases methylation	1
mono(2-ethyl-5-hydroxyhexyl) phthalate	increases abundance, increases methylation	1
Carbamazepine	affects expression	1
Methapyrilene	increases methylation	1
Phthalic Acids	increases abundance, increases methylation	1

Clinical trials (associated diseases)

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