ANP32D

acidic nuclear phosphoprotein 32 family member D, the group of ANP32 acidic nuclear phosphoproteins

Basic information

Region (hg38): 12:48472558-48473622

Links

ENSG00000139223 ∙ NCBI:23519 ∙ OMIM:606878 ∙ HGNC:16676 ∙ Uniprot:O95626 ∙ 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 ANP32D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANP32D 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						0
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in ANP32D

This is a list of pathogenic ClinVar variants found in the ANP32D region.

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

Position	Type	Phenotype	Significance	ClinVar
12-48472704-A-G		not specified	Uncertain significance (Aug 17, 2022)
12-48472708-C-A		not specified	Uncertain significance (Apr 19, 2023)
12-48472716-G-A		not specified	Uncertain significance (Jun 29, 2023)
12-48472723-A-G		not specified	Uncertain significance (Oct 26, 2022)
12-48472758-G-T		not specified	Uncertain significance (Jul 17, 2023)
12-48472764-T-A		not specified	Uncertain significance (Jun 01, 2022)
12-48472869-C-A		not specified	Uncertain significance (May 09, 2023)
12-48472971-C-T		not specified	Uncertain significance (Jun 29, 2023)
12-48473025-T-A		not specified	Uncertain significance (Mar 28, 2023)
12-48473044-A-T		not specified	Uncertain significance (Feb 28, 2023)
12-48473050-A-G		not specified	Uncertain significance (Jan 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANP32D	protein_coding	protein_coding	ENST00000266594	1	396

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.624	80	65.8	1.22	0.00000325	861
Missense in Polyphen		18	14.902	1.2079		233
Synonymous	-2.43	45	28.5	1.58	0.00000149	247
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.595
• rvis_EVS: 0.7
• rvis_percentile_EVS: 85.42

Haploinsufficiency Scores

• pHI: 0.117
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.159

Gene Damage Prediction

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

Gene ontology

• Biological process: nucleocytoplasmic transport
• Cellular component: nucleus;perinuclear region of cytoplasm
• Molecular function: histone binding