NXT2
Basic information
Region (hg38): X:109535780-109544698
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 NXT2 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 | 3 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 2 | 1 | 0 |
Variants in NXT2
This is a list of pathogenic ClinVar variants found in the NXT2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| X-109535925-G-C | Likely benign (Nov 01, 2022) | |||
| X-109535940-A-T | not specified | Uncertain significance (Sep 01, 2021) | ||
| X-109536945-A-C | not specified | Uncertain significance (Dec 01, 2022) | ||
| X-109541475-G-T | Male infertility | Uncertain significance (May 07, 2024) | ||
| X-109541554-A-AT | Male infertility | Likely pathogenic (May 07, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NXT2 | protein_coding | protein_coding | ENST00000218004 | 5 | 8910 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.834 | 0.163 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.12 | 41 | 66.8 | 0.614 | 0.00000456 | 1300 |
| Missense in Polyphen | 3 | 21.548 | 0.13923 | 437 | ||
| Synonymous | 0.135 | 23 | 23.8 | 0.965 | 0.00000153 | 362 |
| Loss of Function | 2.26 | 0 | 5.92 | 0.00 | 3.74e-7 | 120 |
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: Regulator of protein export for NES-containing proteins. Also plays a role in mRNA nuclear export.;
- Pathway
- Influenza A - Homo sapiens (human);Ribosome biogenesis in eukaryotes - Homo sapiens (human);mRNA surveillance pathway - Homo sapiens (human);RNA transport - Homo sapiens (human)
(Consensus)
Recessive Scores
- pRec
- 0.0289
Intolerance Scores
- loftool
- rvis_EVS
- 0.01
- rvis_percentile_EVS
- 54.63
Haploinsufficiency Scores
- pHI
- 0.00230
- hipred
- N
- hipred_score
- 0.427
- ghis
- 0.555
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.612
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Nxt2
- Phenotype
Zebrafish Information Network
- Gene name
- nxt2
- Affected structure
- heart
- Phenotype tag
- abnormal
- Phenotype quality
- quality
Gene ontology
- Biological process
- protein import into nucleus;nucleocytoplasmic transport;mRNA transport
- Cellular component
- nucleoplasm;cytosol;nuclear pore central transport channel;perinuclear region of cytoplasm
- Molecular function
- protein binding;protein transporter activity