CD1E

CD1e molecule, the group of CD molecules|C1-set domain containing

Basic information

Region (hg38): 1:158353695-158357553

Links

ENSG00000158488 ∙ NCBI:913 ∙ OMIM:188411 ∙ HGNC:1638 ∙ Uniprot:P15812 ∙ 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 CD1E gene.

• Inborn genetic diseases (16 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD1E 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			15	1	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	2

Variants in CD1E

This is a list of pathogenic ClinVar variants found in the CD1E region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-158354383-A-G		not specified	Uncertain significance (Sep 13, 2023)
1-158354431-G-A		not specified	Uncertain significance (Sep 27, 2021)
1-158354472-C-T		not specified	Uncertain significance (Apr 06, 2022)
1-158354541-C-T		not specified	Uncertain significance (Sep 26, 2022)
1-158354623-A-G			Benign (Apr 10, 2018)
1-158354647-C-T		not specified	Uncertain significance (Aug 16, 2021)
1-158355323-G-A		not specified	Uncertain significance (Dec 01, 2022)
1-158355372-A-G		not specified	Uncertain significance (Dec 20, 2021)
1-158355434-C-T		not specified	Uncertain significance (Oct 12, 2021)
1-158355528-C-T		not specified	Uncertain significance (Jul 19, 2023)
1-158355534-T-C		not specified	Uncertain significance (Aug 08, 2022)
1-158355959-G-T		not specified	Uncertain significance (Jan 23, 2024)
1-158355970-G-C		not specified	Uncertain significance (Nov 30, 2022)
1-158355976-G-A		not specified	Likely benign (Oct 22, 2021)
1-158355993-C-T			Benign (Apr 10, 2018)
1-158356750-C-T		not specified	Uncertain significance (Sep 23, 2023)
1-158356759-C-T		not specified	Uncertain significance (Jul 17, 2023)
1-158356768-G-C		not specified	Uncertain significance (Sep 29, 2022)
1-158356774-C-T		not specified	Uncertain significance (Dec 19, 2023)
1-158356871-A-G		not specified	Uncertain significance (Mar 06, 2023)
1-158356876-C-T		not specified	Uncertain significance (Jul 25, 2023)
1-158356877-G-A		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD1E	protein_coding	protein_coding	ENST00000368167	6	4090

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.26e-18	0.000667	125677	0	71	125748	0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.110	224	219	1.02	0.0000121	2509
Missense in Polyphen		48	43.944	1.0923		555
Synonymous	-1.02	93	81.3	1.14	0.00000390	776
Loss of Function	-1.00	24	19.3	1.25	0.00000106	185

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000561	0.000549
Ashkenazi Jewish	0.00	0.00
East Asian	0.000831	0.000816
Finnish	0.00	0.00
European (Non-Finnish)	0.000240	0.000237
Middle Eastern	0.000831	0.000816
South Asian	0.000491	0.000490
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: T-cell surface glycoprotein CD1e, soluble binds diacetylated lipids, including phosphatidyl inositides and diacylated sulfoglycolipids, and is required for the presentation of glycolipid antigens on the cell surface. The membrane- associated form is not active. {ECO:0000269|PubMed:10948205, ECO:0000269|PubMed:16311334, ECO:0000269|PubMed:21788486}.
• Pathway: Tight junction - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0974

Intolerance Scores

• loftool: 0.994
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.57

Haploinsufficiency Scores

• pHI: 0.172
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00276

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• 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
• Cellular component: Golgi membrane;extracellular space;early endosome;late endosome;plasma membrane;integral component of plasma membrane;external side of plasma membrane;lysosomal lumen
• Molecular function: endogenous lipid antigen binding;exogenous lipid antigen binding;lipopeptide binding