ANP32D

Summary

ANP32D (acidic nuclear phosphoprotein 32 family member D, HGNC:16676) is a protein-coding gene on chromosome 12q13.11, encoding Acidic leucine-rich nuclear phosphoprotein 32 family member D (O95626).

Phosphoprotein 32 (PP32) is a tumor suppressor that can inhibit several types of cancers, including prostate and breast cancers. The protein encoded by this gene is one of at least two proteins that are similar in amino acid sequence to PP32 and are part of the same acidic nuclear phosphoprotein gene family. However, unlike PP32, the encoded protein is tumorigenic. The tumor suppressor function of PP32 has been localized to a 25 amino acid region that is absent in the protein encoded by this gene. This gene does not contain introns.

Source: NCBI Gene 23519 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 24 total
• MANE Select transcript: NM_012404

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16676
Approved symbol	ANP32D
Name	acidic nuclear phosphoprotein 32 family member D
Location	12q13.11
Locus type	gene with protein product
Status	Approved
Aliases	PP32R2
Ensembl gene	ENSG00000139223
Ensembl biotype	protein_coding
OMIM	606878
Entrez	23519

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000266594

RefSeq mRNA: 1 — MANE Select: NM_012404 NM_012404

CCDS: CCDS31788

Canonical transcript exons

ENST00000266594 — 1 exons

Exon	Start	End
ENSE00000937139	48472559	48473622

Expression profiles

Bgee: expression breadth broad, 14 present calls, max score 72.18.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	72.18	gold quality
hair follicle	UBERON:0002073	64.99	gold quality
diaphragm	UBERON:0001103	63.92	gold quality
tongue squamous epithelium	UBERON:0006919	63.62	gold quality
gingival epithelium	UBERON:0001949	54.96	gold quality
mucosa of paranasal sinus	UBERON:0005030	54.58	gold quality
kidney epithelium	UBERON:0004819	52.96	gold quality
parotid gland	UBERON:0001831	51.80	gold quality
Brodmann (1909) area 46	UBERON:0006483	51.70	gold quality
quadriceps femoris	UBERON:0001377	51.28	gold quality
vastus lateralis	UBERON:0001379	50.94	gold quality
gingiva	UBERON:0001828	50.63	gold quality
tibialis anterior	UBERON:0001385	50.17	silver quality
metanephric glomerulus	UBERON:0004736	50.11	gold quality
deltoid	UBERON:0001476	50.05	gold quality
bone marrow cell	CL:0002092	49.85	gold quality
epithelial cell of pancreas	CL:0000083	49.55	gold quality
cervix squamous epithelium	UBERON:0006922	49.20	gold quality
myocardium	UBERON:0002349	49.14	gold quality
cardiac muscle of right atrium	UBERON:0003379	49.13	gold quality
olfactory bulb	UBERON:0002264	48.92	gold quality
type B pancreatic cell	CL:0000169	48.83	gold quality
lower lobe of lung	UBERON:0008949	48.55	silver quality
CA1 field of hippocampus	UBERON:0003881	48.50	gold quality
left ventricle myocardium	UBERON:0006566	48.24	gold quality
orbitofrontal cortex	UBERON:0004167	48.20	gold quality
upper arm skin	UBERON:0004263	48.06	gold quality
cervix epithelium	UBERON:0004801	48.04	gold quality
oviduct epithelium	UBERON:0004804	48.00	gold quality
mucosa of urinary bladder	UBERON:0001259	47.80	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.65

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

• results provide independent evidence in support of a role for SENP1 in chronic mountain sickness in individuals of Quechua ancestry and suggest the SENP1 and ANP32D signatures of selection are in tight linkage disequilibrium (LD). (PMID:25225945)
• results highlight that certain malignancies with ANP32C/D overexpression or mutation might be specifically targeted using Hsp90 inhibitors. (PMID:26112988)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	anp32a	ENSDARG00000006487
mus_musculus	Anp32a	ENSMUSG00000032249
rattus_norvegicus	Anp32a	ENSRNOG00000014846
rattus_norvegicus		ENSRNOG00000063773
drosophila_melanogaster	Mapmodulin	FBGN0034282
caenorhabditis_elegans	F33H2.3	WBGENE00009367
caenorhabditis_elegans		WBGENE00020588

Paralogs (3): ANP32B (ENSG00000136938), ANP32A (ENSG00000140350), ANP32E (ENSG00000143401)

Protein

Protein identifiers

Acidic leucine-rich nuclear phosphoprotein 32 family member D — O95626 (reviewed: O95626)

Alternative names: Phosphoprotein 32-related protein 2, Tumorigenic protein pp32r2

All UniProt accessions (1): O95626

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the ANP32 family.

RefSeq proteins (1): NP_036536* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001611	Leu-rich_rpt	Repeat
IPR032675	LRR_dom_sf	Homologous_superfamily
IPR045081	AN32	Family

Pfam: PF14580

UniProt features (9 total): repeat 5, sequence conflict 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O95626-F1	95.57	0.94

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 15 (showing top): HP1SITEFACTOR_Q6, FOXJ2_02, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, EVI1_04, ZHOU_INFLAMMATORY_RESPONSE_LIVE_UP, PR_Q2, MEF2_04, HARALAMBIEVA_PBMC_FLUARIX_AGE_50_74YO_CORR_WITH_28D_MEM_B_CELL_RESPONSE_AT_28DY_POSITIVE, TGCCAAR_NF1_Q6, TAAWWATAG_RSRFC4_Q2, ZHOU_INFLAMMATORY_RESPONSE_FIMA_UP, chr12q13, CDX2_Q5, YTATTTTNR_MEF2_02, ZHOU_INFLAMMATORY_RESPONSE_LPS_UP

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

274 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ANP32D	SENP1	Q9P0U3	620
ANP32D	C12orf54	Q6X4T0	480
ANP32D	EGLN1	Q9GZT9	418
ANP32D	OR12D3	Q9UGF7	405
ANP32D	BRINP3	Q76B58	392
ANP32D	GTF3C6	Q969F1	367
ANP32D	NPC1	O15118	353
ANP32D	RAB11FIP2	Q7L804	352
ANP32D	CBX6	O95503	350
ANP32D	APOBEC3H	Q6NTF7	349
ANP32D	RNF7	Q9UBF6	349
ANP32D	PRKAA1	Q13131	348
ANP32D	MDH1B	Q5I0G3	327
ANP32D	ADH7	P40394	325
ANP32D	EPAS1	Q99814	311

IntAct

0 interactions, top by confidence:

BioGRID (2): ANP32A (Cross-Linking-MS (XL-MS)), ANP32B (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A1Z1Q3, B2RXH8, B7ZW38, C9J202, F4K487, O35381, O43423, O43719, O60812, O95626, P0C5K4, P0DME0, P0DMR1, P39687, P49911, P97822, Q01105, Q28XE2, Q3V124, Q4V8G2, Q5F4A3, Q5H9L4, Q5I0J8, Q5RB63, Q5XIE0, Q5Z5Q3, Q5ZMN0, Q63945, Q6A1I3, Q6NKT5, Q6NUW5, Q6P1U7, Q6PAF6, Q6YSF3, Q7ZY40, Q7ZYB4, Q86QS6, Q8AVC1, Q8BGC0, Q8BVM9

Diamond homologs: O01615, O35381, O62220, O95626, P39687, P49911, P51122, P97822, Q28XE2, Q3SZC6, Q5F4A3, Q5XIE0, Q5ZMN0, Q64G17, Q6A1I3, Q6NUW5, Q6P1U7, Q6PAF6, Q6YSF3, Q7ZUP0, Q86QS6, Q8AVC1, Q8HY67, Q8ILI6, Q92688, Q9BTT0, Q9EST5, Q9EST6, Q9SCQ7, Q9V895, O43423, O88984, Q4P5F9, Q5BGW9, Q7Y180, Q7ZY40, Q9UBU9, Q9V4Q8, P34390, Q5Y2C3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	24
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

190 predictions. Top by Δscore:

Variant	Effect	Δscore
12:48473124:G:GT	donor_gain	0.7500
12:48473212:CTCAG:C	donor_loss	0.6900
12:48473213:TCAGG:T	donor_loss	0.6900
12:48473214:CAGGT:C	donor_loss	0.6900
12:48473215:AGG:A	donor_loss	0.6900
12:48473216:GG:G	donor_loss	0.6900
12:48473218:T:A	donor_loss	0.6900
12:48473267:GGAC:G	donor_gain	0.6600
12:48473268:G:GT	donor_gain	0.6600
12:48473409:GCC:G	donor_gain	0.6600
12:48473175:G:GT	donor_gain	0.6500
12:48473411:C:CG	donor_gain	0.6500
12:48473271:G:GG	donor_gain	0.6200
12:48473181:GA:G	donor_gain	0.6100
12:48473411:C:G	donor_gain	0.6100
12:48473178:GAGGA:G	donor_gain	0.6000
12:48473187:G:GT	donor_gain	0.5900
12:48473219:A:C	donor_loss	0.5600
12:48473254:A:T	donor_gain	0.5600
12:48473286:G:GT	donor_gain	0.5600
12:48473147:GGGCT:G	donor_gain	0.5500
12:48473331:G:GT	donor_gain	0.5200
12:48473211:GCTCA:G	donor_loss	0.5100
12:48473195:GGA:G	donor_gain	0.4900
12:48473196:GAG:G	donor_gain	0.4900
12:48473265:G:GT	donor_gain	0.4900
12:48473268:GAC:G	donor_gain	0.4900
12:48473198:G:GG	donor_gain	0.4700
12:48473450:T:G	donor_gain	0.4700
12:48473139:G:GT	donor_gain	0.4600

AlphaMissense

863 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:48472942:T:C	L93P	0.940
12:48472804:T:C	L47S	0.936
12:48472933:T:A	L90H	0.922
12:48473017:T:C	L118S	0.915
12:48472861:T:A	L66H	0.912
12:48472948:T:C	L95S	0.906
12:48472870:T:C	L69P	0.903
12:48472933:T:C	L90P	0.901
12:48472785:T:C	F41L	0.899
12:48472787:T:A	F41L	0.899
12:48472787:T:G	F41L	0.899
12:48472942:T:A	L93Q	0.898
12:48472912:T:C	L83S	0.897
12:48472923:T:C	C87R	0.897
12:48472870:T:A	L69H	0.893
12:48472963:T:C	I100T	0.885
12:48473023:T:C	L120P	0.881
12:48472729:T:C	L22P	0.880
12:48473008:T:A	L115H	0.880
12:48473033:C:G	C123W	0.874
12:48472774:T:A	L37H	0.865
12:48472942:T:G	L93R	0.864
12:48473023:T:A	L120H	0.864
12:48473031:T:C	C123R	0.860
12:48472843:T:C	L60S	0.858
12:48473025:T:C	F121L	0.858
12:48473027:C:A	F121L	0.858
12:48473027:C:G	F121L	0.858
12:48472729:T:A	L22H	0.856
12:48472933:T:G	L90R	0.845

dbSNP variants (sampled 300 via entrez): RS1000812574 (12:48472235 C>T), RS1001719432 (12:48473422 A>C,T), RS1003711082 (12:48470632 G>C), RS1004772892 (12:48474036 G>A,T), RS1005573238 (12:48472530 G>A,C,T), RS1008623018 (12:48473764 C>T), RS1009131208 (12:48473562 G>A), RS1009653769 (12:48471840 C>T), RS1010069395 (12:48472564 C>A), RS1012508343 (12:48470980 C>T), RS1012890140 (12:48470691 T>A,G), RS1013482353 (12:48472025 T>C,G), RS1014296069 (12:48471467 T>C), RS1015291780 (12:48471228 TAACATAATA>T), RS1015344204 (12:48471424 A>T)

Disease associations

OMIM: gene MIM:606878 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST008526_72	Coffee consumption	6.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0006781	coffee consumption measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
MT19c compound	increases expression	1
Arsenic Trioxide	increases expression	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	increases methylation	1
Diethylhexyl Phthalate	decreases expression	1
Hydrogen Peroxide	affects expression	1

Clinical trials (associated diseases)

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