CNPPD1

Summary

CNPPD1 (cyclin Pas1/PHO80 domain containing 1, HGNC:25220) is a protein-coding gene on chromosome 2q35, encoding Protein CNPPD1 (Q9BV87).

Predicted to enable cyclin-dependent protein serine/threonine kinase regulator activity. Predicted to be located in membrane. Predicted to be part of cyclin-dependent protein kinase holoenzyme complex. Predicted to be active in nucleus.

Source: NCBI Gene 27013 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 88 total
• MANE Select transcript: NM_015680

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25220
Approved symbol	CNPPD1
Name	cyclin Pas1/PHO80 domain containing 1
Location	2q35
Locus type	gene with protein product
Status	Approved
Aliases	CGI-57
Ensembl gene	ENSG00000115649
Ensembl biotype	protein_coding
Entrez	27013

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 14 protein_coding

ENST00000360507, ENST00000409789, ENST00000451647, ENST00000453038, ENST00000874461, ENST00000874462, ENST00000874463, ENST00000874464, ENST00000874465, ENST00000874466, ENST00000874467, ENST00000874468, ENST00000922693, ENST00000960025

RefSeq mRNA: 4 — MANE Select: NM_015680 NM_001321389, NM_001321390, NM_001321391, NM_015680

CCDS: CCDS2433

Canonical transcript exons

ENST00000360507 — 8 exons

Exon	Start	End
ENSE00000785973	219176223	219176331
ENSE00000785974	219175591	219175672
ENSE00000785975	219174988	219175108
ENSE00000785979	219174146	219174207
ENSE00000785980	219173350	219173467
ENSE00001075441	219174778	219174906
ENSE00001433017	219171897	219173128
ENSE00001433990	219176760	219176925

Expression profiles

Bgee: expression breadth ubiquitous, 285 present calls, max score 97.19.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 19.0399 / max 167.2645, expressed in 1811 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
34026	11.9546	1796
34029	4.4813	1621
34025	1.3214	908
34027	1.2826	803

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	97.19	gold quality
right adrenal gland	UBERON:0001233	97.02	gold quality
right adrenal gland cortex	UBERON:0035827	96.94	gold quality
left adrenal gland	UBERON:0001234	96.89	gold quality
left adrenal gland cortex	UBERON:0035825	96.69	gold quality
lower esophagus mucosa	UBERON:0035834	96.66	gold quality
metanephros cortex	UBERON:0010533	96.62	gold quality
granulocyte	CL:0000094	96.48	gold quality
adrenal cortex	UBERON:0001235	96.48	gold quality
apex of heart	UBERON:0002098	96.34	gold quality
transverse colon	UBERON:0001157	96.18	gold quality
lower esophagus	UBERON:0013473	96.16	gold quality
lower esophagus muscularis layer	UBERON:0035833	96.15	gold quality
mucosa of stomach	UBERON:0001199	95.96	gold quality
right lobe of thyroid gland	UBERON:0001119	95.82	gold quality
small intestine Peyer’s patch	UBERON:0003454	95.82	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	95.74	gold quality
blood	UBERON:0000178	95.72	gold quality
monocyte	CL:0000576	95.70	gold quality
esophagus	UBERON:0001043	95.70	gold quality
skin of leg	UBERON:0001511	95.70	gold quality
esophagus mucosa	UBERON:0002469	95.55	gold quality
leukocyte	CL:0000738	95.49	gold quality
right coronary artery	UBERON:0001625	95.47	gold quality
mononuclear cell	CL:0000842	95.42	gold quality
gastrocnemius	UBERON:0001388	95.40	gold quality
adrenal gland	UBERON:0002369	95.31	gold quality
left lobe of thyroid gland	UBERON:0001120	95.25	gold quality
adult mammalian kidney	UBERON:0000082	95.16	gold quality
renal medulla	UBERON:0000362	95.14	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-110499	no	710.50
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting CNPPD1, 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-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-1283	99.69	72.42	3009
HSA-MIR-4530	99.69	66.47	1509
HSA-MIR-7-5P	99.67	70.53	1809
HSA-MIR-452-5P	99.65	69.63	1762
HSA-MIR-4676-3P	99.65	69.31	1733
HSA-MIR-892C-3P	99.65	69.38	1745
HSA-MIR-1915-3P	99.58	66.79	1988
HSA-MIR-510-3P	99.54	70.06	2965
HSA-MIR-5584-5P	99.49	68.22	2814
HSA-MIR-548G-3P	99.48	68.67	2159
HSA-MIR-548B-3P	99.38	67.26	1000
HSA-MIR-532-3P	99.34	65.76	1195
HSA-MIR-1253	99.12	67.08	1688
HSA-MIR-3168	99.08	67.75	1384
HSA-MIR-3117-5P	99.04	67.93	618
HSA-MIR-4738-3P	98.98	67.98	1846
HSA-MIR-7851-3P	98.72	64.88	980
HSA-MIR-6840-3P	98.68	65.95	1923
HSA-MIR-4463	98.56	66.05	1071
HSA-MIR-1910-3P	98.44	67.51	1695
HSA-MIR-4277	98.34	67.17	1323
HSA-MIR-6732-3P	98.17	67.52	802
HSA-MIR-6511A-5P	98.13	67.47	1770
HSA-MIR-1224-3P	97.24	65.92	851
HSA-MIR-4433B-3P	97.22	63.62	663

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	cnppd1	ENSDARG00000027078
mus_musculus	Cnppd1	ENSMUSG00000033159
rattus_norvegicus	Cnppd1	ENSRNOG00000018325
drosophila_melanogaster	CG40191	FBGN0058191
caenorhabditis_elegans		WBGENE00017311

Protein

Protein identifiers

Protein CNPPD1 — Q9BV87 (reviewed: Q9BV87)

Alternative names: Cyclin Pas1/PHO80 domain-containing protein 1

All UniProt accessions (3): C9J597, C9JF31, Q9BV87

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the CNPPD1 family.

RefSeq proteins (4): NP_001308318, NP_001308319, NP_001308320, NP_056495* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013922	Cyclin_PHO80-like	Family

Pfam: PF08613

UniProt features (8 total): sequence variant 5, chain 1, transmembrane region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BV87-F1	69.88	0.35

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 156 (showing top): GCM_GSPT1, MORF_SNRP70, MORF_UBE2I, FOXO4_01, FREAC3_01, USF_01, HFH4_01, GCM_DDX11, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP, NRF2_01, GCM_NF2, MORF_PDPK1, MORF_IKBKG, MORF_AATF, CTTTGTA_MIR524

GO Biological Process (1): regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)

GO Molecular Function (2): cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538), protein kinase binding (GO:0019901)

GO Cellular Component (3): cyclin-dependent protein kinase holoenzyme complex (GO:0000307), nucleus (GO:0005634), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cyclin-dependent protein serine/threonine kinase activity	2
regulation of protein serine/threonine kinase activity	1
cyclin-dependent protein kinase regulator activity	1
kinase binding	1
serine/threonine protein kinase complex	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

878 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CNPPD1	SMIM14	Q96QK8	546
CNPPD1	RCC1L	Q96I51	452
CNPPD1	LRRC70	Q7Z2Q7	434
CNPPD1	DTD2	Q96FN9	405
CNPPD1	TPGS2	Q68CL5	397
CNPPD1	CCNJL	Q8IV13	377
CNPPD1	ZNF90	Q03938	370
CNPPD1	TMEM185A	Q8NFB2	370
CNPPD1	SLC23A3	Q6PIS1	368
CNPPD1	CCDC146	Q8IYE0	360
CNPPD1	CCDC186	Q7Z3E2	348
CNPPD1	INO80D	Q53TQ3	320
CNPPD1	LRPAP1	P30533	317
CNPPD1	TESK1	Q15569	313
CNPPD1	DNAJB14	Q8TBM8	313

IntAct

5 interactions, top by confidence:

A	B	Type	Score
CNPPD1	SLC27A2	psi-mi:“MI:0914”(association)	0.530
CNPPD1	TNNC2	psi-mi:“MI:0914”(association)	0.350
RSPH1	CNPPD1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (13): UBB (Affinity Capture-MS), OMA1 (Affinity Capture-MS), SLC27A2 (Affinity Capture-MS), CDK5 (Affinity Capture-MS), PLS1 (Affinity Capture-MS), PLS1 (Affinity Capture-MS), UBB (Affinity Capture-MS), CDK5 (Affinity Capture-MS), OMA1 (Affinity Capture-MS), SLC27A2 (Affinity Capture-MS), TNNC2 (Affinity Capture-MS), CNPPD1 (Affinity Capture-RNA), CNPPD1 (Two-hybrid)

ESM2 similar proteins: D4A929, E1BP92, E1CHH8, O15037, O95238, P29473, P57059, P60924, P97270, Q14154, Q15572, Q2LGB3, Q4JF29, Q4R6Y5, Q562E7, Q58EX7, Q5E9J2, Q5HZE8, Q5JYT7, Q5ND34, Q5R4U5, Q5XIS1, Q5ZJH7, Q62406, Q6P773, Q6P7B2, Q6PDZ2, Q6ZS11, Q7TNI2, Q7TSI1, Q80UF7, Q80UW3, Q8BLR5, Q8BSD4, Q8CFK6, Q8IUC6, Q8K158, Q8K330, Q8NDX1, Q8TB24

Diamond homologs: Q5E9J2, Q5R4U5, Q5ZJH7, Q6P7B2, Q75HV0, Q8K158, Q9BV87

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	69
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2013 predictions. Top by Δscore:

Variant	Effect	Δscore
2:219173126:CAG:C	acceptor_gain	1.0000
2:219173346:TCACC:T	donor_loss	1.0000
2:219173348:A:T	donor_loss	1.0000
2:219173349:C:CA	donor_loss	1.0000
2:219173463:CCACA:C	acceptor_gain	1.0000
2:219173464:CACA:C	acceptor_gain	1.0000
2:219173464:CACAC:C	acceptor_gain	1.0000
2:219173465:ACA:A	acceptor_gain	1.0000
2:219173466:CA:C	acceptor_gain	1.0000
2:219173466:CAC:C	acceptor_gain	1.0000
2:219173468:C:CC	acceptor_gain	1.0000
2:219173468:CTG:C	acceptor_loss	1.0000
2:219173477:G:GC	acceptor_gain	1.0000
2:219174145:CCAG:C	donor_gain	1.0000
2:219175105:CTCC:C	acceptor_gain	1.0000
2:219175106:TCC:T	acceptor_gain	1.0000
2:219175107:CC:C	acceptor_gain	1.0000
2:219175107:CCC:C	acceptor_gain	1.0000
2:219175108:CC:C	acceptor_gain	1.0000
2:219175109:C:CC	acceptor_gain	1.0000
2:219175589:A:AC	donor_gain	1.0000
2:219175590:C:CC	donor_gain	1.0000
2:219175668:AATGT:A	acceptor_gain	1.0000
2:219175669:ATGT:A	acceptor_gain	1.0000
2:219175670:TGT:T	acceptor_gain	1.0000
2:219175670:TGTC:T	acceptor_loss	1.0000
2:219175671:GT:G	acceptor_gain	1.0000
2:219175672:TCTGC:T	acceptor_loss	1.0000
2:219175673:C:CA	acceptor_loss	1.0000
2:219175673:C:CC	acceptor_gain	1.0000

AlphaMissense

2625 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:219174844:C:A	W148C	0.999
2:219174844:C:G	W148C	0.999
2:219174846:A:G	W148R	0.999
2:219174846:A:T	W148R	0.999
2:219174892:C:A	K132N	0.998
2:219174892:C:G	K132N	0.998
2:219174791:A:G	F166S	0.997
2:219174891:A:C	Y133D	0.997
2:219174895:A:C	S131R	0.997
2:219174895:A:T	S131R	0.997
2:219174897:T:G	S131R	0.997
2:219174899:G:T	A130D	0.997
2:219175001:A:G	F123S	0.997
2:219173462:G:T	A193D	0.996
2:219174799:C:A	E163D	0.996
2:219174799:C:G	E163D	0.996
2:219174845:C:G	W148S	0.996
2:219174894:T:C	K132E	0.996
2:219175000:G:C	F123L	0.996
2:219175000:G:T	F123L	0.996
2:219175002:A:G	F123L	0.996
2:219175052:A:G	L106P	0.996
2:219174204:A:G	W172R	0.995
2:219174204:A:T	W172R	0.995
2:219174790:G:C	F166L	0.995
2:219174790:G:T	F166L	0.995
2:219174792:A:G	F166L	0.995
2:219174887:A:G	L134P	0.995
2:219174893:T:A	K132M	0.995
2:219174998:A:G	L124P	0.995

dbSNP variants (sampled 300 via entrez): RS1000271328 (2:219176030 T>C), RS1001437508 (2:219175922 C>A,T), RS1001505823 (2:219174614 C>T), RS1001870314 (2:219176176 C>T), RS1002005708 (2:219172500 G>A), RS1002996102 (2:219174377 C>A,T), RS1003270513 (2:219179255 T>A), RS1003447924 (2:219178090 C>A,G,T), RS1003798270 (2:219173829 C>A), RS1003821548 (2:219177824 C>A), RS1003824102 (2:219177779 A>G), RS1004064772 (2:219177978 A>C,G), RS1004828023 (2:219178529 G>A), RS1005044696 (2:219173633 TTTTATTTATTTTTA>T), RS1005063731 (2:219174010 G>A)

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

3 associations (top):

Study	Trait	p-value
GCST012226_198	Waist circumference adjusted for body mass index	1.000000e-08
GCST90002400_343	Plateletcrit	5.000000e-12
GCST90002402_289	Platelet count	4.000000e-15

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0007789	BMI-adjusted waist circumference
EFO:0007985	platelet crit
EFO:0004309	platelet count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases abundance, increases expression	2
Air Pollutants	increases expression, increases abundance	2
Valproic Acid	affects expression, decreases expression	2
triphenyl phosphate	affects expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
abrine	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Arsenic	increases abundance, increases expression	1
Drugs, Chinese Herbal	increases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	increases expression	1
Cadmium Chloride	increases expression	1
Lactic Acid	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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