NPDC1

Summary

NPDC1 (neural proliferation, differentiation and control 1, HGNC:7899) is a protein-coding gene on chromosome 9q34.3, encoding Neural proliferation differentiation and control protein 1 (Q9NQX5). Suppresses oncogenic transformation in neural and non-neural cells and down-regulates neural cell proliferation.

Predicted to be located in plasma membrane.

Source: NCBI Gene 56654 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 73 total
• MANE Select transcript: NM_015392

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:7899
Approved symbol	NPDC1
Name	neural proliferation, differentiation and control 1
Location	9q34.3
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp586J0523, CAB-, CAB1
Ensembl gene	ENSG00000107281
Ensembl biotype	protein_coding
OMIM	605798
Entrez	56654

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 14 protein_coding, 3 retained_intron

ENST00000371600, ENST00000371601, ENST00000472668, ENST00000485589, ENST00000488145, ENST00000496498, ENST00000872938, ENST00000872939, ENST00000872940, ENST00000872941, ENST00000872942, ENST00000872943, ENST00000872944, ENST00000872945, ENST00000872946, ENST00000952624, ENST00000952625

RefSeq mRNA: 1 — MANE Select: NM_015392 NM_015392

CCDS: CCDS7024

Canonical transcript exons

ENST00000371601 — 9 exons

Exon	Start	End
ENSE00000734120	137040671	137040737
ENSE00001194470	137039971	137040067
ENSE00001194490	137041062	137041187
ENSE00001252466	137040357	137040436
ENSE00001252475	137040514	137040598
ENSE00001252493	137040814	137040984
ENSE00001455629	137045878	137046177
ENSE00003531817	137042927	137043073
ENSE00003847858	137039463	137039864

Expression profiles

Bgee: expression breadth ubiquitous, 137 present calls, max score 99.67.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 78.5972 / max 685.8172, expressed in 1659 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
103295	43.8512	1598
103294	33.9426	1577
103297	0.3980	208
103296	0.3068	137
103291	0.0765	30
103292	0.0221	9

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	99.67	gold quality
cerebellar hemisphere	UBERON:0002245	99.63	gold quality
cerebellum	UBERON:0002037	99.62	gold quality
cerebellar cortex	UBERON:0002129	99.62	gold quality
pituitary gland	UBERON:0000007	99.48	gold quality
adenohypophysis	UBERON:0002196	99.44	gold quality
right frontal lobe	UBERON:0002810	99.15	gold quality
prostate gland	UBERON:0002367	99.13	gold quality
Brodmann (1909) area 9	UBERON:0013540	98.98	gold quality
cerebellar vermis	UBERON:0004720	98.97	gold quality
primary visual cortex	UBERON:0002436	98.94	gold quality
hypothalamus	UBERON:0001898	98.93	gold quality
right uterine tube	UBERON:0001302	98.88	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	98.85	gold quality
left uterine tube	UBERON:0001303	98.83	gold quality
Ammon’s horn	UBERON:0001954	98.83	gold quality
nucleus accumbens	UBERON:0001882	98.82	gold quality
anterior cingulate cortex	UBERON:0009835	98.81	gold quality
temporal lobe	UBERON:0001871	98.77	gold quality
amygdala	UBERON:0001876	98.77	gold quality
superior frontal gyrus	UBERON:0002661	98.77	gold quality
fundus of stomach	UBERON:0001160	98.76	gold quality
apex of heart	UBERON:0002098	98.68	gold quality
endocervix	UBERON:0000458	98.65	gold quality
putamen	UBERON:0001874	98.65	gold quality
caudate nucleus	UBERON:0001873	98.62	gold quality
tibial nerve	UBERON:0001323	98.61	gold quality
substantia nigra	UBERON:0002038	98.61	gold quality
brain	UBERON:0000955	98.59	gold quality
right lung	UBERON:0002167	98.53	gold quality

Single-cell (SCXA)

Detected in 21 experiment(s), a significant marker in 19.

Experiment	Marker?	Max mean expression
E-HCAD-11	yes	787.93
E-HCAD-38	yes	449.26
E-MTAB-10287	yes	81.04
E-HCAD-4	yes	62.72
E-MTAB-10553	yes	57.89
E-HCAD-1	yes	55.13
E-GEOD-135922	yes	46.45
E-HCAD-6	yes	43.38
E-GEOD-134144	yes	39.03
E-MTAB-6701	yes	37.34
E-MTAB-8410	yes	35.22
E-CURD-46	yes	34.45
E-GEOD-125970	yes	31.48
E-GEOD-81547	yes	22.87
E-HCAD-9	yes	18.95

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): GLI1

miRNA regulators (miRDB)

13 targeting NPDC1, 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-3119	99.92	71.34	2390
HSA-MIR-3140-3P	99.88	68.47	2069
HSA-MIR-221-5P	99.86	65.45	1052
HSA-MIR-8073	99.86	65.21	1118
HSA-MIR-6751-5P	99.56	64.99	1145
HSA-MIR-6809-5P	99.13	68.45	1223
HSA-MIR-7113-3P	98.75	65.71	1120
HSA-MIR-6818-3P	98.56	68.23	1307
HSA-MIR-517-5P	97.13	68.43	781
HSA-MIR-6872-3P	97.08	66.99	750
HSA-MIR-5009-5P	94.82	63.89	775
HSA-MIR-8058	94.76	63.41	632
HSA-MIR-6889-5P	90.26	64.13	291

Literature-anchored findings (GeneRIF, showing 2)

• NPDC-1 has a role in regulating neuronal proliferation and is degraded by the ubiquitin/proteasome system through a PEST degradation motif (PMID:15229225)
• Human gene mapped to chromosome 9q34.3. (PMID:15563841)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	npdc1b	ENSDARG00000056156
danio_rerio	npdc1a	ENSDARG00000074697
mus_musculus	Npdc1	ENSMUSG00000015094
rattus_norvegicus		ENSRNOG00000090761
drosophila_melanogaster	CG44247	FBGN0265182
caenorhabditis_elegans		WBGENE00000277

Protein

Protein identifiers

Neural proliferation differentiation and control protein 1 — Q9NQX5 (reviewed: Q9NQX5)

All UniProt accessions (3): Q9NQX5, A0A087WYK7, Q5SPY9

UniProt curated annotations — full annotation on UniProt →

Function. Suppresses oncogenic transformation in neural and non-neural cells and down-regulates neural cell proliferation. Might be involved in transcriptional regulation.

Subcellular location. Membrane.

Tissue specificity. Strongly expressed in adult brain; especially in hippocampus, frontal lobe and temporal lobe.

Similarity. Belongs to the NPDC1/cab-1 family.

RefSeq proteins (1): NP_056207* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009635	NPDC1	Family

Pfam: PF06809

UniProt features (12 total): sequence conflict 5, region of interest 2, signal peptide 1, chain 1, transmembrane region 1, compositionally biased region 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NQX5-F1	69.30	0.19

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): 229

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell

MSigDB gene sets: 137 (showing top): REACTOME_ADAPTIVE_IMMUNE_SYSTEM, YORDY_RECIPROCAL_REGULATION_BY_ETS1_AND_SP100_UP, CCANNAGRKGGC_UNKNOWN, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM2, GGARNTKYCCA_UNKNOWN, SANSOM_APC_TARGETS_DN, PTF1BETA_Q6, RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_UP, CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_16, VALK_AML_CLUSTER_10, HAMAI_APOPTOSIS_VIA_TRAIL_UP, SWEET_LUNG_CANCER_KRAS_UP, CHEN_METABOLIC_SYNDROM_NETWORK, MODULE_49

GO Biological Process (0):

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

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Adaptive Immune System	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

572 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NPDC1	CCDC183	Q5T5S1	523
NPDC1	PIANP	Q8IYJ0	519
NPDC1	MAMDC4	Q6UXC1	483
NPDC1	LCN12	Q6JVE5	470
NPDC1	CARNS1	A5YM72	454
NPDC1	PPP1R18	Q6NYC8	445
NPDC1	CACNB3	P54284	391
NPDC1	COLEC12	Q5KU26	378
NPDC1	SLC2A1	P11166	376
NPDC1	APLP1	P51693	375
NPDC1	GTF2F2	P13984	346
NPDC1	RETREG3	Q86VR2	339
NPDC1	SULT4A1	Q9BR01	333
NPDC1	SORCS1	Q8WY21	330
NPDC1	LINS1	Q8NG48	329

IntAct

123 interactions, top by confidence:

A	B	Type	Score
MDFI	NPDC1	psi-mi:“MI:0915”(physical association)	0.800
NPDC1	MDFI	psi-mi:“MI:0915”(physical association)	0.800
KRTAP5-9	NPDC1	psi-mi:“MI:0915”(physical association)	0.720
NPDC1	KRTAP10-7	psi-mi:“MI:0915”(physical association)	0.720
KRTAP10-9	NPDC1	psi-mi:“MI:0915”(physical association)	0.720
NPDC1	KHDRBS2	psi-mi:“MI:0915”(physical association)	0.720
NPDC1	KRTAP10-9	psi-mi:“MI:0915”(physical association)	0.720
KHDRBS2	NPDC1	psi-mi:“MI:0915”(physical association)	0.720
KRTAP10-7	NPDC1	psi-mi:“MI:0915”(physical association)	0.720
PILRA	NPDC1	psi-mi:“MI:0915”(physical association)	0.670
NPDC1	PILRA	psi-mi:“MI:0407”(direct interaction)	0.670
	NPDC1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (93): NPDC1 (Two-hybrid), NPDC1 (Two-hybrid), KHDRBS2 (Two-hybrid), KRTAP10-7 (Two-hybrid), KRTAP10-9 (Two-hybrid), KRTAP10-1 (Two-hybrid), KRTAP10-5 (Two-hybrid), KRTAP10-3 (Two-hybrid), NOTCH2NL (Two-hybrid), HIST1H1T (Affinity Capture-MS), PTER (Affinity Capture-MS), POMGNT2 (Affinity Capture-MS), ATP11A (Affinity Capture-MS), CCDC94 (Affinity Capture-MS), FAM115C (Affinity Capture-MS)

ESM2 similar proteins: A0A0U1RQ45, A0A0U1RQS6, A0A2R8YCJ5, A2A699, A2AEV7, A6NGB7, A6NJG2, A6NKF7, A6NKL6, A6NL88, A8MVW0, A9JSM3, B2RU40, B8ZZ34, C9JH25, D4A9R4, J3QNX5, P0CG09, P98077, Q0VD38, Q14761, Q17QH7, Q29RK8, Q2KJ18, Q2M3V2, Q3SX20, Q5BJT1, Q5HZJ5, Q5RKR3, Q5T442, Q64697, Q69YZ2, Q6PB97, Q6PCT2, Q6UXK2, Q6ZMQ8, Q6ZVH7, Q6ZW31, Q80XF7, Q8BLS7

Diamond homologs: Q64322, Q93249, Q9NQX5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 37 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Keratinization	14	31.2×	5e-17

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	56
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1461 predictions. Top by Δscore:

Variant	Effect	Δscore
9:137040349:CCACT:C	donor_loss	1.0000
9:137040350:CACTC:C	donor_loss	1.0000
9:137040351:ACTCA:A	donor_loss	1.0000
9:137040352:CTCA:C	donor_loss	1.0000
9:137040353:TCACC:T	donor_loss	1.0000
9:137040354:CACC:C	donor_loss	1.0000
9:137040355:A:AC	donor_gain	1.0000
9:137040355:A:C	donor_loss	1.0000
9:137040355:AC:A	donor_gain	1.0000
9:137040355:ACCG:A	donor_gain	1.0000
9:137040356:C:CA	donor_gain	1.0000
9:137040356:CC:C	donor_gain	1.0000
9:137040356:CCG:C	donor_gain	1.0000
9:137040356:CCGC:C	donor_gain	1.0000
9:137040356:CCGCT:C	donor_gain	1.0000
9:137040432:CCAGG:C	acceptor_gain	1.0000
9:137040433:CAGG:C	acceptor_gain	1.0000
9:137040433:CAGGC:C	acceptor_gain	1.0000
9:137040434:AGG:A	acceptor_gain	1.0000
9:137040435:GG:G	acceptor_gain	1.0000
9:137040436:GC:G	acceptor_loss	1.0000
9:137040437:C:CC	acceptor_gain	1.0000
9:137040437:CT:C	acceptor_loss	1.0000
9:137041056:TCTCA:T	donor_loss	1.0000
9:137041057:CTCA:C	donor_loss	1.0000
9:137041058:TCAC:T	donor_loss	1.0000
9:137041059:CACCA:C	donor_loss	1.0000
9:137041060:A:AC	donor_gain	1.0000
9:137041061:C:CC	donor_gain	1.0000
9:137041061:C:CG	donor_loss	1.0000

AlphaMissense

2031 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:137039988:A:G	C290R	0.996
9:137039841:G:C	N303K	0.995
9:137039841:G:T	N303K	0.995
9:137039832:G:C	F306L	0.994
9:137039832:G:T	F306L	0.994
9:137039834:A:G	F306L	0.994
9:137039986:G:C	C290W	0.993
9:137040001:G:C	F285L	0.993
9:137040001:G:T	F285L	0.993
9:137040003:A:G	F285L	0.993
9:137039978:A:G	L293P	0.992
9:137039994:A:C	Y288D	0.990
9:137039994:A:G	Y288H	0.989
9:137042953:C:G	C78S	0.988
9:137042954:A:T	C78S	0.988
9:137039833:A:C	F306C	0.987
9:137039987:C:G	C290S	0.987
9:137039988:A:T	C290S	0.987
9:137039989:C:A	E289D	0.987
9:137039989:C:G	E289D	0.987
9:137039994:A:T	Y288N	0.987
9:137043043:C:G	C48S	0.987
9:137043044:A:T	C48S	0.987
9:137039978:A:T	L293Q	0.986
9:137039987:C:T	C290Y	0.986
9:137039982:C:G	G292R	0.985
9:137039993:T:C	Y288C	0.985
9:137043019:C:G	C56S	0.985
9:137043020:A:T	C56S	0.985
9:137039996:A:T	V287E	0.984

dbSNP variants (sampled 300 via entrez): RS1000009815 (9:137046748 A>G,T), RS1000379835 (9:137041870 G>A), RS1000530182 (9:137047280 G>A), RS1001179467 (9:137046382 G>C), RS1001193803 (9:137044870 A>T), RS1001646469 (9:137045115 C>T), RS1001662912 (9:137044601 C>G,T), RS1001978154 (9:137041215 G>A,C,T), RS1002397967 (9:137041420 G>C), RS1002600204 (9:137046187 G>A,C,T), RS1002702988 (9:137039302 C>T), RS1002752432 (9:137041598 G>A,C), RS1002908961 (9:137043887 C>T), RS1003186564 (9:137044194 T>C), RS1003238927 (9:137043892 C>T)

Disease associations

OMIM: gene MIM:605798 | 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
GCST004609_11	Monocyte percentage of white cells	1.000000e-10
GCST004610_107	White blood cell count	4.000000e-10
GCST004627_5	Lymphocyte count	1.000000e-20
GCST90002394_336	Monocyte percentage of white cells	2.000000e-24
GCST90002407_85	White blood cell count	7.000000e-16

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007989	monocyte percentage of leukocytes
EFO:0004587	lymphocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, affects expression, increases methylation, affects cotreatment	3
sodium arsenite	decreases expression, increases expression	2
Tobacco Smoke Pollution	affects expression, decreases expression	2
FR900359	decreases phosphorylation	1
azoxystrobin	decreases expression	1
deguelin	decreases expression	1
K 7174	increases expression	1
bisphenol S	increases methylation	1
picoxystrobin	decreases expression	1
(+)-JQ1 compound	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Temozolomide	increases expression	1
Vorinostat	decreases expression	1
Atrazine	decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Cadmium	increases expression	1
Doxorubicin	decreases expression	1
Estradiol	affects cotreatment, decreases expression	1
Hydralazine	affects cotreatment, increases expression	1
Piroxicam	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Smoke	decreases expression	1
Cyclosporine	decreases expression	1
Copper Sulfate	affects expression	1
Acrylamide	decreases expression	1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_E2ED	HAP1 NPDC1 (-) 1	Cancer cell line	Male
CVCL_E2EE	HAP1 NPDC1 (-) 2	Cancer cell line	Male
CVCL_E2EF	HAP1 NPDC1 (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

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