CD1D
CD1d molecule, the group of CD molecules|C1-set domain containing
Basic information
Region (hg38): 1:158178029-158186427
Links
Phenotypes
GenCC
Source:
No genCC data.
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 CD1D 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 | 17 | 20 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 17 | 2 | 1 |
Variants in CD1D
This is a list of pathogenic ClinVar variants found in the CD1D region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-158181133-C-A | not specified | Uncertain significance (Aug 30, 2021) | ||
| 1-158181138-C-T | not specified | Uncertain significance (Dec 08, 2023) | ||
| 1-158181458-C-G | not specified | Uncertain significance (Nov 12, 2021) | ||
| 1-158181538-T-C | Likely benign (Aug 14, 2018) | |||
| 1-158181578-C-T | not specified | Uncertain significance (Nov 01, 2022) | ||
| 1-158181583-A-T | Benign (Jun 06, 2017) | |||
| 1-158181628-C-A | not specified | Uncertain significance (Dec 21, 2023) | ||
| 1-158181715-T-G | not specified | Uncertain significance (Sep 27, 2021) | ||
| 1-158182038-T-C | not specified | Uncertain significance (Jan 04, 2024) | ||
| 1-158182055-G-T | not specified | Uncertain significance (Jul 09, 2021) | ||
| 1-158182073-C-T | not specified | Uncertain significance (Oct 27, 2023) | ||
| 1-158182088-A-G | not specified | Uncertain significance (May 20, 2024) | ||
| 1-158182097-T-C | not specified | Likely benign (Dec 06, 2023) | ||
| 1-158182145-T-G | not specified | Uncertain significance (Apr 20, 2024) | ||
| 1-158182257-C-T | not specified | Uncertain significance (Jan 04, 2022) | ||
| 1-158182274-C-T | not specified | Uncertain significance (Aug 10, 2023) | ||
| 1-158182293-C-T | not specified | Uncertain significance (Jan 08, 2024) | ||
| 1-158182962-C-T | not specified | Uncertain significance (Aug 04, 2023) | ||
| 1-158183049-C-T | not specified | Uncertain significance (Jun 17, 2024) | ||
| 1-158183995-C-T | not specified | Uncertain significance (Jan 02, 2024) | ||
| 1-158184014-C-T | not specified | Uncertain significance (Sep 14, 2021) | ||
| 1-158184136-C-G | not specified | Uncertain significance (Feb 06, 2024) | ||
| 1-158184142-G-T | not specified | Uncertain significance (Jun 14, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CD1D | protein_coding | protein_coding | ENST00000368171 | 6 | 4950 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000188 | 0.888 | 125485 | 1 | 262 | 125748 | 0.00105 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.604 | 206 | 183 | 1.13 | 0.0000101 | 2160 |
| Missense in Polyphen | 57 | 49.373 | 1.1545 | 647 | ||
| Synonymous | -0.840 | 87 | 77.6 | 1.12 | 0.00000424 | 682 |
| Loss of Function | 1.58 | 12 | 19.5 | 0.614 | 0.00000104 | 183 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00172 | 0.00172 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0104 | 0.0104 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000194 | 0.000185 |
| Middle Eastern | 0.0104 | 0.0104 |
| South Asian | 0.000523 | 0.000523 |
| Other | 0.000986 | 0.000978 |
dbNSFP
Source:
- Function
- FUNCTION: Antigen-presenting protein that binds self and non-self glycolipids and presents them to T-cell receptors on natural killer T-cells. {ECO:0000269|PubMed:17475845}.;
- Pathway
- Tight junction - Homo sapiens (human);Amoebiasis - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System
(Consensus)
Recessive Scores
- pRec
- 0.512
Intolerance Scores
- loftool
- 0.756
- rvis_EVS
- 0.02
- rvis_percentile_EVS
- 55.45
Haploinsufficiency Scores
- pHI
- 0.0683
- hipred
- N
- hipred_score
- 0.432
- ghis
- 0.490
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.385
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cd1d1
- Phenotype
- homeostasis/metabolism phenotype; renal/urinary system phenotype; skeleton phenotype; respiratory system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype;
Gene ontology
- Biological process
- positive regulation of T cell mediated cytotoxicity;immune response;detection of bacterium;heterotypic cell-cell adhesion;positive regulation of T cell proliferation;T cell selection;innate immune response;positive regulation of innate immune response;antigen processing and presentation, endogenous lipid antigen via MHC class Ib;antigen processing and presentation, exogenous lipid antigen via MHC class Ib;regulation of immune response
- Cellular component
- extracellular space;cytoplasm;lysosomal membrane;endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;integral component of plasma membrane;external side of plasma membrane;cell surface;endosome membrane;basolateral plasma membrane
- Molecular function
- protein binding;beta-2-microglobulin binding;lipid antigen binding;endogenous lipid antigen binding;exogenous lipid antigen binding;histone binding;cell adhesion molecule binding;lipopeptide binding