GeneBe

CD1A

CD1a molecule, the group of CD molecules|C1-set domain containing

Basic information

Region (hg38): 1:158254424-158258269

Previous symbols: [ "CD1" ]

Links

ENSG00000158477 ∙ NCBI:909 ∙ OMIM:188370 ∙ HGNC:1634 ∙ Uniprot:P06126 ∙ 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 CD1A gene.

  • not_specified (49 variants)
  • not_provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD1A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001763.3. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
 1
missense
42
clinvar
7
clinvar
1
clinvar
 50
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 42 8 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CD1Aprotein_codingprotein_codingENST00000289429 64133
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
4.20e-240.0000059812552202241257460.000891
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.6112151911.120.00001082138
Missense in Polyphen7767.0451.1485767
Synonymous-1.018271.21.150.00000379633
Loss of Function-2.502917.71.648.38e-7188

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.008620.00865
Ashkenazi Jewish0.000.00
East Asian0.0003260.000326
Finnish0.000.00
European (Non-Finnish)0.0001600.000158
Middle Eastern0.0003260.000326
South Asian0.0001630.000163
Other0.003760.00375

dbNSFP

Source: dbNSFP

Function
FUNCTION: Antigen-presenting protein that binds self and non-self lipid and glycolipid antigens and presents them to T-cell receptors on natural killer T-cells. {ECO:0000269|PubMed:11231314, ECO:0000269|PubMed:16272286, ECO:0000269|PubMed:18178838}.;
Pathway
Tight junction - 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
0.264

Intolerance Scores

loftool
0.933
rvis_EVS
0.11
rvis_percentile_EVS
62

Haploinsufficiency Scores

pHI
0.0771
hipred
N
hipred_score
0.112
ghis
0.502

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.0218

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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;regulation of immune response
Cellular component
extracellular space;plasma membrane;integral component of plasma membrane;external side of plasma membrane;endosome membrane;membrane raft
Molecular function
protein binding;endogenous lipid antigen binding;exogenous lipid antigen binding;lipopeptide binding