SRXN1
Basic information
Region (hg38): 20:646615-653200
Previous symbols: [ "C20orf139" ]
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 SRXN1 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 | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 0 | 0 |
Variants in SRXN1
This is a list of pathogenic ClinVar variants found in the SRXN1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 20-648826-C-T | not specified | Uncertain significance (Jul 05, 2023) | ||
| 20-648838-C-G | not specified | Uncertain significance (Dec 18, 2023) | ||
| 20-648839-C-T | not specified | Uncertain significance (Dec 10, 2024) | ||
| 20-648862-C-T | not specified | Uncertain significance (Sep 23, 2023) | ||
| 20-653011-G-C | not specified | Uncertain significance (Jul 25, 2023) | ||
| 20-653058-T-C | not specified | Uncertain significance (Jun 23, 2023) | ||
| 20-653095-C-A | not specified | Uncertain significance (Apr 22, 2022) | ||
| 20-653127-T-C | not specified | Uncertain significance (Dec 16, 2023) | ||
| 20-653130-G-T | not specified | Uncertain significance (Nov 15, 2024) | ||
| 20-653140-G-A | not specified | Uncertain significance (Jul 07, 2024) | ||
| 20-653145-G-C | not specified | Uncertain significance (May 31, 2023) | ||
| 20-653145-G-T | not specified | Uncertain significance (Apr 08, 2022) | ||
| 20-653181-C-T | not specified | Uncertain significance (Mar 29, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SRXN1 | protein_coding | protein_coding | ENST00000381962 | 2 | 6756 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0697 | 0.752 | 125585 | 0 | 2 | 125587 | 0.00000796 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.295 | 54 | 60.5 | 0.893 | 0.00000339 | 823 |
| Missense in Polyphen | 30 | 28.676 | 1.0462 | 322 | ||
| Synonymous | 0.368 | 27 | 29.5 | 0.914 | 0.00000175 | 301 |
| Loss of Function | 0.931 | 2 | 4.01 | 0.499 | 2.57e-7 | 39 |
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) | 0.00000881 | 0.00000881 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Contributes to oxidative stress resistance by reducing cysteine-sulfinic acid formed under exposure to oxidants in the peroxiredoxins PRDX1, PRDX2, PRDX3 and PRDX4. Does not act on PRDX5 or PRDX6. May catalyze the reduction in a multi-step process by acting both as a specific phosphotransferase and a thioltransferase. {ECO:0000269|PubMed:15448164, ECO:0000269|PubMed:15590625}.;
- Pathway
- Photodynamic therapy-induced NFE2L2 (NRF2) survival signaling
(Consensus)
Haploinsufficiency Scores
- pHI
- 0.103
- hipred
- Y
- hipred_score
- 0.672
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.982
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Srxn1
- Phenotype
- homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; immune system 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
- response to oxidative stress;cellular response to oxidative stress;oxidation-reduction process;cellular oxidant detoxification
- Cellular component
- cytosol
- Molecular function
- protein binding;ATP binding;oxidoreductase activity, acting on a sulfur group of donors;sulfiredoxin activity