CD1E

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

Basic information

Region (hg38): 1:158353696-158357553

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.

• not_specified (45 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. These statistics are base on transcript: NM_000030893.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1		1	2
missense			49	3	1	53
nonsense			2			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	52	3	2

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