ANP32A

protein-coding

acidic nuclear phosphoprotein 32 family member A, the group of INHAT complex|MicroRNA protein coding host genes|ANP32 acidic nuclear phosphoproteins|SET complex

Gene summary

Enables RNA binding activity. Involved in nucleocytoplasmic transport. Located in several cellular components, including endoplasmic reticulum; nucleoplasm; and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C15orf1

MANE transcript

NM_006305.4

Inheritance

—

ClinVar variants

U:11B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr15:68,778,535-68,820,897

External References & Databases

Ensembl (ENSG00000140350)

Transcript & Mutation Effects

hg38 • Region Span ~42.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ANP32A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 7

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006305.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			8 clinvar	1 clinvar		9
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	11	1	1	13

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 72 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006305.4	RefSeq	NP_006296.1	7	MANE Select
ENST00000465139.6	Ensembl	ENSP00000417864.2	7	MANE Select
ENST00000409628.6	Ensembl	ENSP00000386496.2	3	Standard
ENST00000560303.1	Ensembl	ENSP00000453838.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

granzyme a mediated apoptosis pathway
Metabolism of RNA
HuR (ELAVL1) binds and stabilizes mRNA
Regulation of mRNA stability by proteins that bind AU-rich elements
Validated nuclear estrogen receptor alpha network

Biological Process

nucleocytoplasmic transport
intracellular signal transduction
regulation of mRNA stability

Molecular Function

RNA binding
protein binding
histone binding

Cellular Component

nucleus
nucleoplasm
cytoplasm
endoplasmic reticulum
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000465139
Coding exons: 7
Length: 42363
Individuals with no LoFs: 124777
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 124778
p: 0.00000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.53	54	137	0.393	0.00000800	1658
Missense (PolyPhen)		4	30.705	0.13027		452
Synonymous	0.0385	60	60.4	0.994	0.00000451	426
Loss of Function	3.43	0	13.7	0.00	6.67e-7	180

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Implicated in a number of cellular processes, including proliferation, differentiation, caspase-dependent and caspase- independent apoptosis, suppression of transformation (tumor suppressor), inhibition of protein phosphatase 2A, regulation of mRNA trafficking and stability in association with ELAVL1, and inhibition of acetyltransferases as part of the INHAT (inhibitor of histone acetyltransferases) complex. Plays a role in E4F1- mediated transcriptional repression. {ECO:0000269|PubMed:10400610, ECO:0000269|PubMed:11360199, ECO:0000269|PubMed:15642345, ECO:0000269|PubMed:17557114}.;

Recessive Scores

pRec: 0.260

Intolerance Scores

LoFtool: 0.455
RVIS EVS: -0.08
RVIS percentile EVS: 47.79

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.799

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Low	Medium
Primary Immunodeficiency	Medium	Low	Medium
Cancer	Medium	Medium	Medium