LY75-CD302
protein-codingLY75-CD302 readthrough
Gene summary
This locus represents naturally occurring read-through transcription between the neighboring lymphocyte antigen 75 (LY75) and CD302 molecule (CD302) genes. Alternative splicing results in multiple transcript variants encoding fusion products that share sequence identity with each individual gene product. [provided by RefSeq, Nov 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~132.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to LY75-CD302 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript . Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 2 | 3 | |||
| missense | 5 | 3 | 5 | 13 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 5 | 4 | 8 | 17 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001185688.1 | 39 | Standard | |
| RefSeq | NP_001185689.1 | 38 | Standard | |
| Ensembl | ENSP00000423463.1 | 39 | Standard | |
| Ensembl | ENSP00000421035.1 | 38 | Standard |
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000504764
- Coding exons
- 39
- Length
- 132860
- Individuals with no LoFs
- 125175
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 572
- Defined
- 125748
- p
- 0.00228
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0170 | 963 | 962 | 1.00 | 0.0000483 | 12432 |
| Missense (PolyPhen) | 502 | 518.78 | 0.96765 | 7005 | ||
| Synonymous | 0.980 | 313 | 336 | 0.932 | 0.0000176 | 3239 |
| Loss of Function | 2.20 | 84 | 109 | 0.773 | 0.00000509 | 1342 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0055 | 0.0054 | notable |
| Latino/Admixed American | 0.0018 | 0.0016 | notable |
| Ashkenazi Jewish | 0.0097 | 0.0097 | notable |
| East Asian | 0.0017 | 0.0017 | notable |
| Finnish | 0.0016 | 0.0016 | notable |
| European (Non-Finnish) | 0.0016 | 0.0015 | notable |
| South Asian | 0.0024 | 0.0023 | notable |
| Other | 0.0035 | 0.0034 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Acts as an endocytic receptor to direct captured antigens from the extracellular space to a specialized antigen- processing compartment (By similarity). Causes reduced proliferation of B-lymphocytes. {ECO:0000250}.;
Intolerance Scores
- RVIS EVS
- 4.07
- RVIS percentile EVS
- 99.67
Essentials
- Essential (CRISPR)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114