SPRR2E
Basic information
Region (hg38): 1:153093135-153106184
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 SPRR2E 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 0 | 0 |
Variants in SPRR2E
This is a list of pathogenic ClinVar variants found in the SPRR2E region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-153093544-T-C | not specified | Uncertain significance (Jan 17, 2024) | ||
| 1-153093559-G-T | not specified | Uncertain significance (Sep 25, 2024) | ||
| 1-153093582-A-T | not specified | Uncertain significance (Jun 10, 2024) | ||
| 1-153093604-A-G | not specified | Uncertain significance (Jul 29, 2023) | ||
| 1-153093658-A-C | not specified | Uncertain significance (Feb 26, 2024) | ||
| 1-153093663-G-A | not specified | Uncertain significance (Mar 08, 2024) | ||
| 1-153093669-G-T | not specified | Uncertain significance (Jan 30, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SPRR2E | protein_coding | protein_coding | ENST00000368751 | 1 | 13050 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0601 | 0.512 | 124834 | 0 | 5 | 124839 | 0.0000200 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.319 | 43 | 37.5 | 1.15 | 0.00000169 | 452 |
| Missense in Polyphen | ||||||
| Synonymous | -0.0171 | 15 | 14.9 | 1.01 | 7.91e-7 | 135 |
| Loss of Function | -1.47 | 1 | 0.234 | 4.27 | 9.82e-9 | 3 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000116 | 0.000116 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000886 | 0.00000886 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Cross-linked envelope protein of keratinocytes. It is a keratinocyte protein that first appears in the cell cytosol, but ultimately becomes cross-linked to membrane proteins by transglutaminase. All that results in the formation of an insoluble envelope beneath the plasma membrane.;
- Pathway
- Keratinization;Developmental Biology;Formation of the cornified envelope
(Consensus)
Intolerance Scores
- loftool
- 0.775
- rvis_EVS
- 0.24
- rvis_percentile_EVS
- 68.72
Haploinsufficiency Scores
- pHI
- 0.0879
- hipred
- N
- hipred_score
- 0.112
- ghis
- 0.405
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.000347
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- epidermis development;peptide cross-linking;keratinocyte differentiation;cornification
- Cellular component
- cornified envelope;cytoplasm;cytosol
- Molecular function
- structural molecule activity;protein binding;structural constituent of epidermis