CD38

CD38 molecule, the group of CD molecules

Basic information

Region (hg38): 4:15778274-15853232

Links

ENSG00000004468 ∙ NCBI:952 ∙ OMIM:107270 ∙ HGNC:1667 ∙ Uniprot:P28907 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CD38 gene.

• Inborn genetic diseases (11 variants)
• not provided (3 variants)

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	1
missense			10	2		12
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	10	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)
4-15824942-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)
4-15848597-A-T		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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