CD38
CD38 molecule, the group of CD molecules
Basic information
Region (hg38): 4:15778275-15853232
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 CD38 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 | 1 | |||||
| missense | 11 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 2 | 1 |
Variants in CD38
This is a list of pathogenic ClinVar variants found in the CD38 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-15778448-G-A | not specified | Uncertain significance (May 30, 2023) | ||
| 4-15778592-C-T | not specified | Uncertain significance (Oct 13, 2023) | ||
| 4-15778624-C-T | Benign (Jun 29, 2018) | |||
| 4-15778640-G-C | not specified | Uncertain significance (Aug 19, 2023) | ||
| 4-15816548-G-A | not specified | Uncertain significance (May 26, 2024) | ||
| 4-15824905-G-C | not specified | Uncertain significance (Apr 01, 2024) | ||
| 4-15824942-T-C | not specified | Uncertain significance (Mar 17, 2023) | ||
| 4-15824975-T-C | not specified | Uncertain significance (Aug 10, 2021) | ||
| 4-15834253-A-G | not specified | Uncertain significance (Mar 20, 2023) | ||
| 4-15834300-A-G | not specified | Uncertain significance (Oct 26, 2022) | ||
| 4-15838131-A-C | not specified | Uncertain significance (Apr 13, 2022) | ||
| 4-15838170-A-G | Benign (Jul 31, 2018) | |||
| 4-15840465-G-C | not specified | Uncertain significance (May 30, 2023) | ||
| 4-15840467-T-G | Likely benign (Apr 24, 2018) | |||
| 4-15840469-C-T | not specified | Uncertain significance (Dec 21, 2022) | ||
| 4-15840490-C-T | not specified | Likely benign (May 11, 2022) | ||
| 4-15848589-C-A | not specified | Uncertain significance (May 20, 2024) | ||
| 4-15848597-A-T | not specified | Uncertain significance (Jun 29, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CD38 | protein_coding | protein_coding | ENST00000226279 | 8 | 74956 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000231 | 0.738 | 125539 | 1 | 208 | 125748 | 0.000831 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.0647 | 167 | 165 | 1.01 | 0.00000800 | 1982 |
| Missense in Polyphen | 49 | 51.685 | 0.94805 | 668 | ||
| Synonymous | 0.961 | 52 | 61.6 | 0.844 | 0.00000306 | 548 |
| Loss of Function | 1.19 | 11 | 16.2 | 0.680 | 6.88e-7 | 180 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00956 | 0.00915 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000110 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000328 | 0.000325 |
| Middle Eastern | 0.000110 | 0.000109 |
| South Asian | 0.0000663 | 0.0000653 |
| Other | 0.00100 | 0.000978 |
dbNSFP
Source:
- Function
- FUNCTION: Synthesizes the second messagers cyclic ADP-ribose and nicotinate-adenine dinucleotide phosphate, the former a second messenger for glucose-induced insulin secretion. Also has cADPr hydrolase activity. Also moonlights as a receptor in cells of the immune system.;
- Pathway
- Oxytocin signaling pathway - Homo sapiens (human);Nicotinate and nicotinamide metabolism - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);Salivary secretion - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);NAD+ metabolism;NAD+ biosynthetic pathways;Cell-type Dependent Selectivity of CCK2R Signaling;Vitamin B3 (nicotinate and nicotinamide) metabolism;Metabolism;Nicotinate Nicotinamide metabolism;Nicotinate metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors;Pentose phosphate pathway
(Consensus)
Recessive Scores
- pRec
- 0.355
Intolerance Scores
- loftool
- 0.890
- rvis_EVS
- -0.6
- rvis_percentile_EVS
- 17.91
Haploinsufficiency Scores
- pHI
- 0.0540
- hipred
- N
- hipred_score
- 0.240
- ghis
- 0.558
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.985
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cd38
- Phenotype
- immune system phenotype; hematopoietic system phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- Biological process
- response to hypoxia;signal transduction;positive regulation of cytosolic calcium ion concentration;female pregnancy;negative regulation of neuron projection development;artery smooth muscle contraction;NAD metabolic process;positive regulation of cell growth;positive regulation of B cell proliferation;positive regulation of insulin secretion;response to estradiol;response to retinoic acid;response to progesterone;response to hydroperoxide;response to drug;negative regulation of apoptotic process;negative regulation of bone resorption;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of vasoconstriction;B cell receptor signaling pathway;long-term synaptic depression;response to interleukin-1;apoptotic signaling pathway
- Cellular component
- nucleus;plasma membrane;cell surface;membrane;integral component of membrane;basolateral plasma membrane;secretory granule membrane;extracellular exosome
- Molecular function
- NAD+ nucleosidase activity;transferase activity;phosphorus-oxygen lyase activity;identical protein binding;NAD(P)+ nucleosidase activity;NAD+ nucleotidase, cyclic ADP-ribose generating