CD1A
protein-codingCD1a molecule, the group of CD molecules|C1-set domain containing
Gene summary
This gene encodes a member of the CD1 family of transmembrane glycoproteins, which are structurally related to the major histocompatibility complex (MHC) proteins and form heterodimers with beta-2-microglobulin. The CD1 proteins mediate the presentation of primarily lipid and glycolipid antigens of self or microbial origin to T cells. The human genome contains five CD1 family genes organized in a cluster on chromosome 1. The CD1 family members are thought to differ in their cellular localization and specificity for particular lipid ligands. The protein encoded by this gene localizes to the plasma membrane and to recycling vesicles of the early endocytic system. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]
- CD1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.8 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 CD1A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001763.3. 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 | 1 | 2 | |||
| missense | 50 | 8 | 1 | 59 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 51 | 9 | 1 | 61 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001754.2 | 6 | MANE Select | |
| Ensembl | ENSP00000289429.5 | 6 | MANE Select | |
| RefSeq | NP_001307581.1 | 6 | Standard | |
| Ensembl | ENSP00000564780.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Tight junction - Homo sapiens (human)
- Hematopoietic cell lineage - Homo sapiens (human)
- Immune System
- Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
- Adaptive Immune System
Biological Process
- positive regulation of T cell mediated cytotoxicity
- adaptive immune response
- immune response
- antigen processing and presentation, endogenous lipid antigen via MHC class Ib
- antigen processing and presentation, exogenous lipid antigen via MHC class Ib
Molecular Function
- protein binding
- endogenous lipid antigen binding
- exogenous lipid antigen binding
- lipopeptide binding
Cellular Component
- extracellular space
- plasma membrane
- integral component of plasma membrane
- external side of plasma membrane
- endosome membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000289429
- Coding exons
- 6
- Length
- 4133
- Individuals with no LoFs
- 125522
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 224
- Defined
- 125746
- p
- 0.000891
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.611 | 215 | 191 | 1.12 | 0.0000108 | 2138 |
| Missense (PolyPhen) | 77 | 67.045 | 1.1485 | 767 | ||
| Synonymous | -1.01 | 82 | 71.2 | 1.15 | 0.00000379 | 633 |
| Loss of Function | -2.50 | 29 | 17.7 | 1.64 | 8.38e-7 | 188 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0069 | 0.0069 | notable |
| Latino/Admixed American | 0.0017 | 0.0017 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00033 | 0.00033 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00016 | 0.00016 | rare |
| South Asian | 0.00016 | 0.00016 | rare |
| Other | 0.0038 | 0.0038 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Antigen-presenting protein that binds self and non-self lipid and glycolipid antigens and presents them to T-cell receptors on natural killer T-cells. {ECO:0000269|PubMed:11231314, ECO:0000269|PubMed:16272286, ECO:0000269|PubMed:18178838}.;
Recessive Scores
- pRec
- 0.264
Intolerance Scores
- LoFtool
- 0.933
- RVIS EVS
- 0.11
- RVIS percentile EVS
- 62
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0218
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |