ANP32A

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

Basic information

Region (hg38): 15:68778534-68820897

Previous symbols: [ "C15orf1" ]

Links

ENSG00000140350 ∙ NCBI:8125 ∙ OMIM:600832 ∙ HGNC:13233 ∙ Uniprot:P39687 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ANP32A gene.

• not provided (4 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANP32A gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			1			1
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding					1	1
Total	0	0	3	0	2

Variants in ANP32A

This is a list of pathogenic ClinVar variants found in the ANP32A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-68780086-C-T		not specified	Uncertain significance (Jun 05, 2023)
15-68780116-G-GT			Uncertain significance (Aug 01, 2021)
15-68780122-G-T			Benign (Jun 21, 2018)
15-68780127-T-C		not specified	Uncertain significance (Sep 25, 2023)
15-68783027-C-T		not specified	Uncertain significance (Dec 28, 2023)
15-68787920-C-G			Uncertain significance (Jan 10, 2022)
15-68787929-G-C			Benign (Jun 21, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANP32A	protein_coding	protein_coding	ENST00000465139	7	42363

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.990	0.0104	124777	0	1	124778	0.00000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.53	54	137	0.393	0.00000800	1658
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000883	0.00000883
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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}.
• Pathway: 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 (Consensus)

Recessive Scores

• pRec: 0.260

Intolerance Scores

• loftool: 0.455
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.548
• hipred: Y
• hipred_score: 0.677
• ghis: 0.679

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.799

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Anp32a
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: nucleocytoplasmic transport;intracellular signal transduction;regulation of mRNA stability
• Cellular component: nucleus;nucleoplasm;cytoplasm;endoplasmic reticulum;perinuclear region of cytoplasm
• Molecular function: RNA binding;protein binding;histone binding