CNBD1

Summary

CNBD1 (cyclic nucleotide binding domain containing 1, HGNC:26663) is a protein-coding gene on chromosome 8q21.3, encoding Cyclic nucleotide-binding domain-containing protein 1 (Q8NA66).

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 90 total
• MANE Select transcript: NM_173538

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26663
Approved symbol	CNBD1
Name	cyclic nucleotide binding domain containing 1
Location	8q21.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ35802
Ensembl gene	ENSG00000176571
Ensembl biotype	protein_coding
Entrez	168975

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 3 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000517748, ENST00000518476, ENST00000521593, ENST00000522105, ENST00000522427, ENST00000523299

RefSeq mRNA: 1 — MANE Select: NM_173538 NM_173538

CCDS: CCDS55259

Canonical transcript exons

ENST00000518476 — 11 exons

Exon	Start	End
ENSE00001260110	87351685	87351794
ENSE00001260115	87286539	87286671
ENSE00001260128	87284678	87284815
ENSE00001315057	87353636	87353786
ENSE00002089763	86866415	86866583
ENSE00002093136	86939596	86939754
ENSE00002118078	87382620	87382859
ENSE00003509806	87236919	87237112
ENSE00003560094	86905081	86905194
ENSE00003634134	87205993	87206138
ENSE00003666770	86887542	86887611

Expression profiles

Bgee: expression breadth ubiquitous, 110 present calls, max score 86.24.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0111 / max 11.7282, expressed in 3 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
89653	0.0077	3
205246	0.0034	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	86.24	gold quality
secondary oocyte	CL:0000655	85.68	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.88	gold quality
left testis	UBERON:0004533	79.01	gold quality
right testis	UBERON:0004534	78.41	gold quality
testis	UBERON:0000473	76.63	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	72.61	gold quality
monocyte	CL:0000576	68.20	gold quality
leukocyte	CL:0000738	67.01	gold quality
sperm	CL:0000019	64.74	gold quality
granulocyte	CL:0000094	59.52	gold quality
lower lobe of lung	UBERON:0008949	59.51	silver quality
blood	UBERON:0000178	54.89	gold quality
skin of hip	UBERON:0001554	54.64	gold quality
spleen	UBERON:0002106	53.60	gold quality
mucosa of transverse colon	UBERON:0004991	51.73	gold quality
right lung	UBERON:0002167	50.64	gold quality
descending thoracic aorta	UBERON:0002345	48.48	gold quality
pigmented layer of retina	UBERON:0001782	48.36	silver quality
right coronary artery	UBERON:0001625	48.26	gold quality
mucosa of stomach	UBERON:0001199	45.25	gold quality
upper leg skin	UBERON:0004262	44.20	gold quality
deltoid	UBERON:0001476	44.03	gold quality
upper lobe of lung	UBERON:0008948	44.01	gold quality
superior surface of tongue	UBERON:0007371	43.78	gold quality
middle temporal gyrus	UBERON:0002771	43.42	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
mucosa of paranasal sinus	UBERON:0005030	42.96	gold quality
upper lobe of left lung	UBERON:0008952	42.95	gold quality
epithelium of nasopharynx	UBERON:0001951	42.91	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.85

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): NR1I2

miRNA regulators (miRDB)

4 targeting CNBD1, 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-3180-5P	99.82	69.12	2422
HSA-MIR-885-5P	99.59	68.59	879
HSA-MIR-133A-5P	99.28	69.13	941
HSA-MIR-1912-5P	97.94	67.98	832

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cnbd1	ENSDARG00000091489
mus_musculus	Cnbd1	ENSMUSG00000073991
rattus_norvegicus	Cnbd1	ENSRNOG00000056330

Paralogs (4): PRKAR2B (ENSG00000005249), PRKAR1A (ENSG00000108946), PRKAR2A (ENSG00000114302), PRKAR1B (ENSG00000188191)

Protein

Protein identifiers

Cyclic nucleotide-binding domain-containing protein 1 — Q8NA66 (reviewed: Q8NA66)

All UniProt accessions (3): H0YAN5, H0YC59, Q8NA66

RefSeq proteins (1): NP_775809* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000595	cNMP-bd_dom	Domain
IPR014710	RmlC-like_jellyroll	Homologous_superfamily
IPR018490	cNMP-bd_dom_sf	Homologous_superfamily

Pfam: PF00027

UniProt features (7 total): sequence variant 3, chain 1, region of interest 1, compositionally biased region 1, binding site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NA66-F1	71.62	0.15

Functional residue map

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

Ligand- & substrate-binding residues (1): 322–436

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 22 (showing top): LHX3_01, BRN2_01, NIKOLSKY_BREAST_CANCER_8Q12_Q22_AMPLICON, chr8q21, SIPA1_TARGET_GENES, MIR133A_5P, GSE8685_IL2_ACT_IL2_STARVED_VS_IL21_ACT_IL2_STARVED_CD4_TCELL_DN, LIU_TARGETS_OF_VMYB_VS_CMYB_UP, GSE7596_AKT_TRANSD_VS_CTRL_CD4_TCONV_WITH_TGFB_DN, DESCARTES_MAIN_FETAL_RETINAL_PIGMENT_CELLS, DESCARTES_FETAL_EYE_RETINAL_PIGMENT_CELLS, DESCARTES_FETAL_STOMACH_PDE1C_ACSM3_POSITIVE_CELLS, T3R_Q6, NCOA4_TARGET_GENES, SRPK1_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

280 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CNBD1	CNBD2	Q96M20	521
CNBD1	AKAP6	Q13023	503
CNBD1	NBEA	Q8NFP9	484
CNBD1	XIRP2	A4UGR9	467
CNBD1	OR10K1	Q8NGX5	431
CNBD1	SLC18B1	Q6NT16	422
CNBD1	ZBBX	A8MT70	391
CNBD1	CPNE3	O75131	391
CNBD1	ARL11	Q969Q4	384
CNBD1	WWP1	Q9H0M0	359
CNBD1	COL14A1	Q05707	357
CNBD1	FAM81B	Q96LP2	349
CNBD1	CFAP299	Q6V702	349
CNBD1	ZNF880	Q6PDB4	348
CNBD1	DNAAF10	Q96MX6	336

IntAct

12 interactions, top by confidence:

A	B	Type	Score
CNBD1	HMGA1	psi-mi:“MI:0915”(physical association)	0.400
FBXW7	CNBD1	psi-mi:“MI:2364”(proximity)	0.270
SMAD4	CNBD1	psi-mi:“MI:2364”(proximity)	0.270
CNBD1	SMARCA4	psi-mi:“MI:2364”(proximity)	0.270
CNBD1	SPOP	psi-mi:“MI:2364”(proximity)	0.270
SPOP	CNBD1	psi-mi:“MI:2364”(proximity)	0.270
CNBD1	AKT1	psi-mi:“MI:2364”(proximity)	0.270
CNBD1	BRAF	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (1): CNBD1 (Proximity Label-MS)

ESM2 similar proteins: A1A5R8, A6PVS8, B1ANS9, O54852, O95259, P21784, P33981, P34089, P53685, P55895, P59111, Q05C16, Q08AW4, Q14AW5, Q14DL3, Q38849, Q39128, Q4R945, Q60603, Q63472, Q65X23, Q68FF0, Q6AYL8, Q6K3T2, Q6NSI8, Q6ZTR5, Q86DA5, Q8BVT6, Q8GYY7, Q8MJD7, Q8NA66, Q8NCM2, Q8S8Y8, Q8TEU7, Q8WNU8, Q8WZ64, Q920E3, Q944Q0, Q95JR6, Q96L42

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	67
Likely benign	11
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3943 predictions. Top by Δscore:

Variant	Effect	Δscore
8:86866584:G:GG	donor_gain	1.0000
8:86887608:ACAG:A	donor_loss	1.0000
8:86887610:AGGT:A	donor_loss	1.0000
8:86887612:G:T	donor_loss	1.0000
8:86887613:T:A	donor_loss	1.0000
8:86905079:A:G	acceptor_gain	1.0000
8:86939590:GTTCA:G	acceptor_loss	1.0000
8:86939591:TTCA:T	acceptor_loss	1.0000
8:86939592:TCAG:T	acceptor_loss	1.0000
8:86939593:CAGG:C	acceptor_loss	1.0000
8:86939594:A:AG	acceptor_gain	1.0000
8:86939594:AG:A	acceptor_gain	1.0000
8:86939595:G:GC	acceptor_loss	1.0000
8:86939595:G:GG	acceptor_gain	1.0000
8:86939595:GG:G	acceptor_gain	1.0000
8:86939750:AAATT:A	donor_gain	1.0000
8:86939751:AATT:A	donor_gain	1.0000
8:86939751:AATTG:A	donor_loss	1.0000
8:86939752:ATT:A	donor_gain	1.0000
8:86939753:TT:T	donor_gain	1.0000
8:86939754:TGT:T	donor_loss	1.0000
8:86939755:G:A	donor_loss	1.0000
8:86939755:G:GG	donor_gain	1.0000
8:86939756:T:TC	donor_loss	1.0000
8:86939757:AA:A	donor_loss	1.0000
8:87205989:T:TA	acceptor_gain	1.0000
8:87236917:A:AG	acceptor_gain	1.0000
8:87236917:AGT:A	acceptor_gain	1.0000
8:87236918:G:GC	acceptor_gain	1.0000
8:87236918:GT:G	acceptor_gain	1.0000

AlphaMissense

2917 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:87353699:A:C	S406R	0.995
8:87353701:C:A	S406R	0.995
8:87353701:C:G	S406R	0.995
8:87286605:T:A	W326R	0.991
8:87286605:T:C	W326R	0.991
8:87206005:G:C	R148S	0.990
8:87206005:G:T	R148S	0.990
8:87284778:T:C	L291P	0.981
8:87206040:T:C	L160P	0.980
8:87206096:A:C	S179R	0.980
8:87206098:T:A	S179R	0.980
8:87206098:T:G	S179R	0.980
8:87353687:T:C	F402L	0.980
8:87353689:T:A	F402L	0.980
8:87353689:T:G	F402L	0.980
8:87284696:T:C	F264L	0.978
8:87284698:T:A	F264L	0.978
8:87284698:T:G	F264L	0.978
8:87206004:G:C	R148T	0.976
8:87353691:G:A	G403D	0.976
8:87284700:G:A	G265E	0.975
8:86887578:T:C	L42S	0.972
8:87353759:G:C	A426P	0.970
8:87286607:G:C	W326C	0.967
8:87286607:G:T	W326C	0.967
8:87351721:G:A	G360D	0.964
8:87284699:G:T	G265W	0.963
8:87206004:G:T	R148M	0.962
8:87236961:C:A	A207D	0.962
8:87286587:T:C	C320R	0.962

dbSNP variants (sampled 300 via entrez): RS1000001794 (8:87424726 T>C), RS1000003860 (8:87062102 T>G), RS1000010859 (8:87397942 T>A,C), RS1000013601 (8:87292010 G>T), RS1000016547 (8:86955402 A>C,G), RS1000018379 (8:87327967 T>C), RS1000024121 (8:87307863 A>G), RS1000027952 (8:86947541 G>A), RS1000028709 (8:86911557 A>C,G), RS1000036030 (8:87405411 C>T), RS1000036341 (8:87147348 C>A,T), RS1000038971 (8:86917644 G>A,C), RS1000056916 (8:87368612 G>A,C,T), RS1000061469 (8:87381217 G>A), RS1000063528 (8:87073834 G>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

5 associations (top):

Study	Trait	p-value
GCST001961_14	Anorexia nervosa	4.000000e-06
GCST002927_20	Mercury levels	3.000000e-06
GCST003542_48	Night sleep phenotypes	6.000000e-06
GCST007450_3	Normal facial asymmetry (deformation magnitude)	4.000000e-06
GCST010396_153	Gut microbiota (bacterial taxa, hurdle binary method)	2.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0009751	facial asymmetry measurement
EFO:0007874	gut microbiome measurement

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
bisphenol A	increases expression	1
perfluorooctanoic acid	increases expression	1
benzo(e)pyrene	increases methylation	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	affects binding, increases reaction	1
perfluoro-n-nonanoic acid	increases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
Benzo(a)pyrene	affects methylation	1
Catechin	affects cotreatment, decreases expression	1
Methapyrilene	increases methylation	1
Valproic Acid	decreases methylation	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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