NANOS3
Basic information
Region (hg38): 19:13862063-13880757
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 NANOS3 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 | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 2 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 0 | 2 |
Variants in NANOS3
This is a list of pathogenic ClinVar variants found in the NANOS3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-13877267-T-G | not specified | Uncertain significance (Jun 11, 2021) | ||
| 19-13877279-C-G | not specified | Uncertain significance (Aug 04, 2023) | ||
| 19-13877310-G-A | not specified | Uncertain significance (Nov 21, 2024) | ||
| 19-13877367-T-TGGAGCCGGTGTCAGCGCC | Benign (Dec 31, 2019) | |||
| 19-13877432-G-A | not specified | Uncertain significance (Nov 10, 2024) | ||
| 19-13877440-G-C | not specified | Uncertain significance (Jun 01, 2023) | ||
| 19-13877540-G-A | not specified | Uncertain significance (Sep 27, 2022) | ||
| 19-13877647-G-C | not specified | Uncertain significance (Dec 11, 2024) | ||
| 19-13877708-C-A | not specified | Uncertain significance (Jan 09, 2024) | ||
| 19-13877744-C-CGAG | Benign (Feb 20, 2018) | |||
| 19-13880468-C-G | not specified | Uncertain significance (Mar 07, 2024) | ||
| 19-13880487-C-T | not specified | Uncertain significance (Nov 28, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NANOS3 | protein_coding | protein_coding | ENST00000339133 | 2 | 18695 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0392 | 0.850 | 125071 | 0 | 6 | 125077 | 0.0000240 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.35 | 81 | 123 | 0.657 | 0.00000825 | 1176 |
| Missense in Polyphen | 12 | 46.426 | 0.25848 | 441 | ||
| Synonymous | -1.38 | 69 | 55.8 | 1.24 | 0.00000402 | 427 |
| Loss of Function | 1.29 | 3 | 6.55 | 0.458 | 4.54e-7 | 60 |
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) | 0.0000447 | 0.0000441 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a role in the maintenance of the undifferentiated state of germ cells regulating the spermatogonia cell cycle and inducing a prolonged transit in G1 phase. Affects cell proliferation probably by repressing translation of specific mRNAs. Maintains the germ cell lineage by suppressing both Bax- dependent and -independent apoptotic pathways. Essential in the early stage embryo to protect the migrating primordial germ cells (PGCs) from apoptosis. {ECO:0000269|PubMed:21421998}.;
Recessive Scores
- pRec
- 0.262
Intolerance Scores
- loftool
- 0.470
- rvis_EVS
- 0.04
- rvis_percentile_EVS
- 56.25
Haploinsufficiency Scores
- pHI
- 0.248
- hipred
- N
- hipred_score
- 0.187
- ghis
- 0.669
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.137
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nanos3
- Phenotype
- reproductive system phenotype; endocrine/exocrine gland phenotype;
Zebrafish Information Network
- Gene name
- nanos3
- Affected structure
- primordial germ cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- regulation of translation;multicellular organism development;germ cell development;spermatogenesis;negative regulation of translation;oogenesis;regulation of cell cycle;positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay;negative regulation of apoptotic signaling pathway
- Cellular component
- P-body;nucleus;cytoplasm;cytoplasmic stress granule;perinuclear region of cytoplasm
- Molecular function
- RNA binding;protein binding;zinc ion binding