NANOS2
nanos C2HC-type zinc finger 2, the group of Zinc fingers C2HC-type
Basic information
Region (hg38): 19:45913214-45914778
Links
Phenotypes
GenCC
Source:
No genCC data.
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 NANOS2 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 | 12 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 1 | 0 |
Variants in NANOS2
This is a list of pathogenic ClinVar variants found in the NANOS2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-45914283-C-A | not specified | Uncertain significance (Oct 12, 2024) | ||
| 19-45914289-C-A | not specified | Uncertain significance (Apr 14, 2022) | ||
| 19-45914318-G-A | not specified | Uncertain significance (Jan 23, 2024) | ||
| 19-45914363-G-A | not specified | Uncertain significance (Dec 19, 2022) | ||
| 19-45914435-C-T | not specified | Uncertain significance (Oct 21, 2021) | ||
| 19-45914443-G-A | not specified | Uncertain significance (Sep 08, 2024) | ||
| 19-45914443-G-T | not specified | Uncertain significance (Nov 06, 2023) | ||
| 19-45914464-G-C | not specified | Uncertain significance (Jan 09, 2025) | ||
| 19-45914521-C-A | not specified | Uncertain significance (Mar 11, 2025) | ||
| 19-45914534-C-T | not specified | Uncertain significance (Mar 01, 2024) | ||
| 19-45914539-G-A | not specified | Uncertain significance (Jul 14, 2023) | ||
| 19-45914539-G-T | not specified | Uncertain significance (Aug 02, 2021) | ||
| 19-45914542-C-T | not specified | Uncertain significance (Oct 26, 2022) | ||
| 19-45914566-G-T | not specified | Likely benign (May 03, 2023) | ||
| 19-45914569-G-A | not specified | Uncertain significance (Feb 11, 2022) | ||
| 19-45914582-G-A | not specified | Uncertain significance (Feb 04, 2025) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NANOS2 | protein_coding | protein_coding | ENST00000341294 | 1 | 1562 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0517 | 0.710 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.484 | 89 | 103 | 0.866 | 0.00000738 | 887 |
| Missense in Polyphen | 34 | 52.091 | 0.6527 | 421 | ||
| Synonymous | 0.769 | 42 | 48.8 | 0.860 | 0.00000387 | 296 |
| Loss of Function | 0.689 | 2 | 3.36 | 0.595 | 1.44e-7 | 34 |
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) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a key role in the sexual differentiation of germ cells by promoting the male fate but suppressing the female fate. Represses the female fate pathways by suppressing meiosis, which in turn results in the promotion of the male fate. Maintains the suppression of meiosis by preventing STRA8 expression, which is required for premeiotic DNA replication, after CYP26B1 is decreased. Regulates the localization of the CCR4-NOT deadenylation complex to P-bodies and plays a role in recruiting the complex to trigger the degradation of mRNAs involved in meiosis. Required for the maintenance of the spermatogonial stem cell population. Not essential for the assembly of P-bodies but is required for the maintenance of their normal state (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.510
Intolerance Scores
- loftool
- 0.164
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.4
Haploinsufficiency Scores
- pHI
- 0.273
- hipred
- N
- hipred_score
- 0.139
- ghis
- 0.434
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.307
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nanos2
- Phenotype
- cellular phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype;
Gene ontology
- Biological process
- mRNA catabolic process;multicellular organism development;spermatogenesis;negative regulation of translation;cell differentiation;germ-line stem cell population maintenance;negative regulation of meiotic nuclear division;positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
- Cellular component
- P-body;nucleus;cytoplasm;perinuclear region of cytoplasm
- Molecular function
- mRNA binding;protein binding;zinc ion binding