NUDCD2

Summary

NUDCD2 (NudC domain containing 2, HGNC:30535) is a protein-coding gene on chromosome 5q34, encoding NudC domain-containing protein 2 (Q8WVJ2). May regulate the LIS1/dynein pathway by stabilizing LIS1 with Hsp90 chaperone.

Predicted to enable unfolded protein binding activity. Predicted to be involved in protein folding. Located in cytosol; intercellular bridge; and mitotic spindle.

Source: NCBI Gene 134492 — RefSeq curated summary.

At a glance

• Gene–disease (curated): multiple congenital anomalies/dysmorphic syndrome (Moderate, GenCC)
• Clinical variants (ClinVar): 1 total — 1 likely-pathogenic
• MANE Select transcript: NM_145266

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30535
Approved symbol	NUDCD2
Name	NudC domain containing 2
Location	5q34
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp686E10109, NudCL2
Ensembl gene	ENSG00000170584
Ensembl biotype	protein_coding
OMIM	620136
Entrez	134492

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 6 protein_coding, 4 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000302764, ENST00000517501, ENST00000519395, ENST00000521797, ENST00000717760, ENST00000717761, ENST00000717762, ENST00000717763, ENST00000717764, ENST00000887706, ENST00000938468, ENST00000969893

RefSeq mRNA: 2 — MANE Select: NM_145266 NM_001329991, NM_145266

CCDS: CCDS4361

Canonical transcript exons

ENST00000302764 — 4 exons

Exon	Start	End
ENSE00001164681	163459862	163460102
ENSE00003471579	163457562	163457610
ENSE00004033373	163446526	163454050
ENSE00004033381	163456929	163457080

Expression profiles

Bgee: expression breadth ubiquitous, 252 present calls, max score 97.67.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 27.8987 / max 144.1649, expressed in 1815 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
64692	26.6083	1812
64691	1.2903	924

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	97.67	gold quality
ventricular zone	UBERON:0003053	96.75	gold quality
secondary oocyte	CL:0000655	94.81	gold quality
ganglionic eminence	UBERON:0004023	94.02	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	93.40	gold quality
upper arm skin	UBERON:0004263	93.02	gold quality
spinal cord	UBERON:0002240	92.99	gold quality
Brodmann (1909) area 46	UBERON:0006483	92.63	gold quality
corpus epididymis	UBERON:0004359	90.79	gold quality
adult organism	UBERON:0007023	90.67	gold quality
parotid gland	UBERON:0001831	90.38	gold quality
penis	UBERON:0000989	90.25	gold quality
medial globus pallidus	UBERON:0002477	89.82	gold quality
substantia nigra	UBERON:0002038	89.79	gold quality
skin of hip	UBERON:0001554	89.71	gold quality
colonic epithelium	UBERON:0000397	89.70	gold quality
decidua	UBERON:0002450	89.64	gold quality
seminal vesicle	UBERON:0000998	89.54	gold quality
cartilage tissue	UBERON:0002418	89.49	gold quality
bronchial epithelial cell	CL:0002328	89.48	gold quality
oral cavity	UBERON:0000167	89.44	gold quality
globus pallidus	UBERON:0001875	89.30	gold quality
bronchus	UBERON:0002185	89.02	gold quality
midbrain	UBERON:0001891	88.82	gold quality
amygdala	UBERON:0001876	88.74	gold quality
thymus	UBERON:0002370	88.48	gold quality
mucosa of sigmoid colon	UBERON:0004993	88.39	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	88.32	gold quality
upper leg skin	UBERON:0004262	88.28	gold quality
biceps brachii	UBERON:0001507	88.22	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.34
E-ENAD-17	no	1631.61
E-MTAB-6058	no	307.36
E-MTAB-2983	no	280.87
E-MTAB-9801	no	2.56

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting NUDCD2, 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-4282	99.99	75.36	6408
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-202-5P	99.78	67.65	991
HSA-MIR-8076	99.78	68.52	1170
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-4677-5P	99.70	70.09	1940
HSA-MIR-4663	99.62	65.33	957
HSA-MIR-885-5P	99.59	68.59	879
HSA-MIR-154-3P	99.50	70.05	831
HSA-MIR-487A-3P	99.50	69.95	840
HSA-MIR-5583-3P	99.06	65.68	1018
HSA-MIR-4686	98.77	66.87	964
HSA-MIR-3149	98.77	67.13	1639
HSA-MIR-1-5P	98.70	68.66	1017
HSA-MIR-3920	97.75	69.02	1168

Literature-anchored findings (GeneRIF, showing 5)

• NudCL2, a homolog of Aspergillus NudC, which shares significant homology with human NudC and NudCL was identified. It regulates the LIS1/dynein pathway by stabilizing LIS1 with Hsp90 chaperone. (PMID:20133715)
• NudC-like protein 2 restrains centriole amplification by stabilizing HERC2. (PMID:31427565)
• NudCL2 regulates cell migration by stabilizing both myosin-9 and LIS1 with Hsp90. (PMID:32665550)
• Biallelic variants in NUDCD2 associated with a multiple malformation syndrome with cholestasis and renal failure. (PMID:37272762)
• NudCL2 is required for cytokinesis by stabilizing RCC2 with Hsp90 at the midbody. (PMID:38801297)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	nudcd2	ENSDARG00000078059
mus_musculus	Nudcd2	ENSMUSG00000020328
rattus_norvegicus	Nudcd2	ENSRNOG00000060914

Paralogs (2): NUDCD3 (ENSG00000015676), NUDC (ENSG00000090273)

Protein

Protein identifiers

NudC domain-containing protein 2 — Q8WVJ2 (reviewed: Q8WVJ2)

All UniProt accessions (2): Q8WVJ2, E5RFP0

UniProt curated annotations — full annotation on UniProt →

Function. May regulate the LIS1/dynein pathway by stabilizing LIS1 with Hsp90 chaperone.

Subunit / interactions. Interacts with LIS1.

Subcellular location. Chromosome. Centromere. Kinetochore. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Spindle pole.

RefSeq proteins (2): NP_001316920, NP_660309* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007052	CS_dom	Domain
IPR008978	HSP20-like_chaperone	Homologous_superfamily
IPR037898	NudC_fam	Family
IPR037902	p23_NUDCD2	Domain

Pfam: PF04969

UniProt features (7 total): modified residue 3, initiator methionine 1, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WVJ2-F1	83.68	0.53

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 (3): 2, 142, 145

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 138 (showing top): TGCGCANK_UNKNOWN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOCC_MICROTUBULE_ORGANIZING_CENTER, GTGCCTT_MIR506, GOBP_PROTEIN_MATURATION, YU_MYC_TARGETS_UP, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOCC_CENTROSOME, GOBP_PROTEIN_FOLDING, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, FISCHER_DREAM_TARGETS, ACEVEDO_LIVER_CANCER_UP, BRACHAT_RESPONSE_TO_CAMPTOTHECIN_UP, BERENJENO_TRANSFORMED_BY_RHOA_UP

GO Biological Process (1): protein folding (GO:0006457)

GO Molecular Function (2): obsolete unfolded protein binding (GO:0051082), protein binding (GO:0005515)

GO Cellular Component (11): kinetochore (GO:0000776), spindle pole (GO:0000922), cytoplasm (GO:0005737), centrosome (GO:0005813), cytosol (GO:0005829), microtubule cytoskeleton (GO:0015630), intercellular bridge (GO:0045171), mitotic spindle (GO:0072686), chromosome, centromeric region (GO:0000775), chromosome (GO:0005694), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
intracellular membraneless organelle	3
spindle	2
cellular process	1
protein maturation	1
binding	1
condensed chromosome, centromeric region	1
supramolecular complex	1
intracellular anatomical structure	1
centriole	1
microtubule organizing center	1
cytoplasm	1
cytoskeleton	1
chromosomal region	1

Protein interactions and networks

STRING

2066 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NUDCD2	NUDCD3	Q8IVD9	713
NUDCD2	NUDC	Q9Y266	704
NUDCD2	NUDCD1	Q96RS6	590
NUDCD2	FBXO24	O75426	589
NUDCD2	PAFAH1B1	P43034	540
NUDCD2	MED9	Q9NWA0	486
NUDCD2	KLHL38	Q2WGJ6	463
NUDCD2	LINC02914	Q52M58	447
NUDCD2	ZNF570	Q96NI8	427
NUDCD2	PTGES3	Q15185	402
NUDCD2	NAA50	Q9GZZ1	384
NUDCD2	ZNF716	A6NP11	372
NUDCD2	ZNF627	Q7L945	370
NUDCD2	PLEKHB2	Q96CS7	370
NUDCD2	NDEL1	Q9GZM8	367

IntAct

94 interactions, top by confidence:

A	B	Type	Score
ATG13	ULK1	psi-mi:“MI:2364”(proximity)	0.940
RPGR	NPHP4	psi-mi:“MI:2364”(proximity)	0.730
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
NEK8	NUDCD2	psi-mi:“MI:0915”(physical association)	0.650
NUDCD2	PAFAH1B1	psi-mi:“MI:0915”(physical association)	0.640
NUDCD2	FBXO24	psi-mi:“MI:0915”(physical association)	0.620
NUDCD2	HSP90AA1	psi-mi:“MI:0915”(physical association)	0.610
NUDCD2	HSP90AA1	psi-mi:“MI:0914”(association)	0.610
PAFAH1B1	HSP90AA1	psi-mi:“MI:0914”(association)	0.610
NUDCD2	DDX3Y	psi-mi:“MI:0915”(physical association)	0.590
NUDCD2	OPTN	psi-mi:“MI:0915”(physical association)	0.560
RCBTB1	ANKRD40	psi-mi:“MI:0914”(association)	0.560
FBXO24	HSP90AB1	psi-mi:“MI:0914”(association)	0.560
RCBTB2	NUDCD2	psi-mi:“MI:0915”(physical association)	0.560
CEP104	CCDC66	psi-mi:“MI:2364”(proximity)	0.540
HERC3	H3-7	psi-mi:“MI:0914”(association)	0.530
NUDCD2	PRMT5	psi-mi:“MI:0915”(physical association)	0.510

BioGRID (450): NUDCD2 (Co-fractionation), NUDCD2 (Affinity Capture-MS), NUDCD2 (Proximity Label-MS), NUDCD2 (Proximity Label-MS), NUDCD2 (Proximity Label-MS), NUDCD2 (Proximity Label-MS), NUDCD2 (Proximity Label-MS), NUDCD2 (Proximity Label-MS), NUDCD2 (Proximity Label-MS), NUDCD2 (Affinity Capture-MS), DDX3Y (Affinity Capture-MS), NUDCD2 (Affinity Capture-MS), NUDCD2 (Proximity Label-MS), NUDCD2 (Affinity Capture-Western), HERC2 (Affinity Capture-Western)

ESM2 similar proteins: A0A3L6DPG1, B0BN85, F8RP11, O35685, O88978, O95757, P27612, P48722, P50503, P54319, Q0IIM3, Q0JL44, Q17QG2, Q2KIK0, Q3T168, Q43468, Q4R4P3, Q5M823, Q5R606, Q5R6Z8, Q5R8R4, Q5RGJ5, Q5XEP2, Q5ZIN1, Q5ZLF0, Q60446, Q61699, Q63525, Q66HA8, Q69YN2, Q6AYK6, Q6N069, Q86X45, Q8CI33, Q8VD33, Q8VZM1, Q8WVJ2, Q92598, Q96EQ0, Q9CQ48

Diamond homologs: Q5M823, Q8WVJ2, Q9CQ48, Q9LV09, Q9VVA6, O35685, O60166, P17624, Q17QG2, Q54M64, Q5ZIN1, Q63525, Q9STN7, Q9Y266, Q503C8

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
NUDCD2	“up-regulates quantity by stabilization”	PAFAH1B1	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 96 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
Anchoring of the basal body to the plasma membrane	5	9.0×	1e-02

GO biological processes:

GO term	Partners	Fold	FDR
telomere maintenance via telomerase	5	41.6×	7e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1879644	GRCh37/hg19 5q33.3-34(chr5:156786013-162945369)x1	Likely pathogenic

SpliceAI

545 predictions. Top by Δscore:

Variant	Effect	Δscore
5:163456925:TTACT:T	donor_loss	1.0000
5:163456926:TACTT:T	donor_loss	1.0000
5:163456927:A:AC	donor_gain	1.0000
5:163456927:A:C	donor_loss	1.0000
5:163456927:ACTT:A	donor_gain	1.0000
5:163456928:C:CC	donor_gain	1.0000
5:163456928:CTT:C	donor_gain	1.0000
5:163456928:CTTC:C	donor_gain	1.0000
5:163456928:CTTCT:C	donor_gain	1.0000
5:163456930:T:TA	donor_gain	1.0000
5:163457081:C:CC	acceptor_gain	1.0000
5:163459857:GCTAC:G	donor_loss	1.0000
5:163459858:CTACC:C	donor_loss	1.0000
5:163459859:TACCT:T	donor_loss	1.0000
5:163459860:ACCTT:A	donor_loss	1.0000
5:163453869:A:C	donor_gain	0.9900
5:163453912:T:C	donor_gain	0.9900
5:163456922:GACTT:G	donor_loss	0.9900
5:163457079:CT:C	acceptor_gain	0.9900
5:163457080:TC:T	acceptor_loss	0.9900
5:163457081:C:CA	acceptor_loss	0.9900
5:163457556:CCTTA:C	donor_loss	0.9900
5:163457557:CTTAC:C	donor_loss	0.9900
5:163457558:TTA:T	donor_loss	0.9900
5:163457559:T:TG	donor_loss	0.9900
5:163457560:A:AT	donor_loss	0.9900
5:163457561:CCC:C	donor_loss	0.9900
5:163453892:T:TA	donor_gain	0.9800
5:163454049:TT:T	acceptor_gain	0.9800
5:163454051:C:CC	acceptor_gain	0.9800

AlphaMissense

1021 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:163454033:G:C	F136L	0.999
5:163454033:G:T	F136L	0.999
5:163454035:A:G	F136L	0.999
5:163457021:A:G	W100R	0.999
5:163457021:A:T	W100R	0.999
5:163457046:C:A	K91N	0.999
5:163457046:C:G	K91N	0.999
5:163457571:A:G	W77R	0.999
5:163457571:A:T	W77R	0.999
5:163454034:A:G	F136S	0.998
5:163456939:A:G	F127S	0.998
5:163456954:A:G	L122P	0.998
5:163457019:C:A	W100C	0.998
5:163457019:C:G	W100C	0.998
5:163457048:T:C	K91E	0.998
5:163459990:A:G	W21R	0.998
5:163459990:A:T	W21R	0.998
5:163454013:C:T	G143E	0.997
5:163454039:A:C	F134L	0.997
5:163454039:A:T	F134L	0.997
5:163454041:A:G	F134L	0.997
5:163457053:A:G	L89P	0.997
5:163457065:A:T	V85D	0.997
5:163456938:G:C	F127L	0.996
5:163456938:G:T	F127L	0.996
5:163456940:A:G	F127L	0.996
5:163457020:C:G	W100S	0.996
5:163457059:A:T	I87N	0.996
5:163454034:A:C	F136C	0.995
5:163454040:A:G	F134S	0.995

dbSNP variants (sampled 300 via entrez): RS1000057593 (5:163449622 A>G), RS1000128828 (5:163450799 C>T), RS1000146521 (5:163450789 C>A,T), RS1000162278 (5:163457244 G>A), RS1000278532 (5:163456773 T>A,C), RS1000408692 (5:163449282 A>G), RS1000518526 (5:163451124 G>C), RS1001041779 (5:163452266 A>G), RS1001318065 (5:163450157 A>G), RS1001347958 (5:163455226 T>C), RS1001375651 (5:163456668 G>A), RS1001417543 (5:163455594 T>G), RS1001557998 (5:163452007 C>T), RS1001749553 (5:163449977 G>A,T), RS1001818062 (5:163461244 G>A)

Disease associations

OMIM: gene MIM:620136 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
multiple congenital anomalies/dysmorphic syndrome	Moderate	Autosomal recessive

Mondo (1): multiple congenital anomalies/dysmorphic syndrome (MONDO:0019042)

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, affects cotreatment, increases expression	2
sodium arsenite	decreases expression	2
dicrotophos	decreases expression	1
monomethylarsonous acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
ICG 001	decreases expression	1
LDN 193189	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Temozolomide	increases expression	1
Sunitinib	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Dexamethasone	affects cotreatment, increases expression	1
Formaldehyde	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Ivermectin	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Quercetin	decreases expression	1
Rotenone	increases expression	1
Thiram	decreases expression	1
Valproic Acid	affects expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Cyclosporine	decreases expression	1
Copper Sulfate	decreases expression	1
Lactic Acid	decreases expression	1
Vitamin K 3	affects expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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