CD58
Basic information
Region (hg38): 1:116514534-116571039
Previous symbols: [ "LFA3" ]
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 CD58 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 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 7 | 3 | 1 |
Variants in CD58
This is a list of pathogenic ClinVar variants found in the CD58 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-116514821-A-C | not specified | Uncertain significance (Aug 22, 2023) | ||
| 1-116519238-T-C | not specified | Uncertain significance (Jan 06, 2023) | ||
| 1-116521932-G-A | not specified | Likely benign (Nov 16, 2021) | ||
| 1-116521970-G-C | not specified | Likely benign (Jun 09, 2022) | ||
| 1-116535967-C-T | not specified | Uncertain significance (Aug 08, 2022) | ||
| 1-116535977-T-C | not specified | Likely benign (Dec 19, 2022) | ||
| 1-116536106-T-C | not specified | Uncertain significance (Aug 02, 2023) | ||
| 1-116536189-T-G | not specified | Uncertain significance (Apr 23, 2024) | ||
| 1-116544347-T-C | not specified | Uncertain significance (Jun 30, 2022) | ||
| 1-116544355-G-A | not specified | Uncertain significance (Nov 02, 2023) | ||
| 1-116544574-T-C | not specified | Uncertain significance (Jan 05, 2022) | ||
| 1-116544604-C-A | not specified | Uncertain significance (Apr 29, 2024) | ||
| 1-116558335-A-G | Benign (Jan 18, 2019) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CD58 | protein_coding | protein_coding | ENST00000369489 | 6 | 56505 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.251 | 0.743 | 119138 | 0 | 1 | 119139 | 0.00000420 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.724 | 105 | 128 | 0.820 | 0.00000589 | 1630 |
| Missense in Polyphen | 15 | 31.673 | 0.47359 | 441 | ||
| Synonymous | 1.01 | 36 | 44.6 | 0.807 | 0.00000202 | 457 |
| Loss of Function | 2.39 | 3 | 11.9 | 0.253 | 5.64e-7 | 159 |
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) | 0.00000939 | 0.00000939 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Ligand of the T-lymphocyte CD2 glycoprotein. This interaction is important in mediating thymocyte interactions with thymic epithelial cells, antigen-independent and -dependent interactions of T-lymphocytes with target cells and antigen- presenting cells and the T-lymphocyte rosetting with erythrocytes. In addition, the LFA-3/CD2 interaction may prime response by both the CD2+ and LFA-3+ cells.;
- Pathway
- Cell adhesion molecules (CAMs) - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Neutrophil degranulation;Innate Immune System;Immune System;Cell surface interactions at the vascular wall;Hemostasis
(Consensus)
Recessive Scores
- pRec
- 0.206
Intolerance Scores
- loftool
- 0.479
- rvis_EVS
- 0.62
- rvis_percentile_EVS
- 83.14
Haploinsufficiency Scores
- pHI
- 0.162
- hipred
- N
- hipred_score
- 0.145
- ghis
- 0.431
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.453
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- heterotypic cell-cell adhesion;neutrophil degranulation;leukocyte migration;cellular response to interferon-gamma;cellular response to tumor necrosis factor;cell-cell adhesion;positive regulation of interleukin-8 secretion
- Cellular component
- plasma membrane;integral component of plasma membrane;cell surface;membrane;secretory granule membrane;extracellular exosome;ficolin-1-rich granule membrane
- Molecular function
- signaling receptor binding;protein binding