ANP32A
Basic information
Region (hg38): 15:68778535-68820897
Previous symbols: [ "C15orf1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
missense | 4 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 0 | |||||
non coding | 1 | |||||
Total | 0 | 0 | 5 | 1 | 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) | ||
15-68783001-A-C | not specified | Likely benign (Aug 05, 2024) | ||
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:
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:
- 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