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.

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.

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						0
missense			30	5	1	36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	30	5	1

Variants in CD1A

This is a list of pathogenic ClinVar variants found in the CD1A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-158255188-C-G		not specified	Uncertain significance (Jul 19, 2022)
1-158255189-A-T		not specified	Uncertain significance (Nov 21, 2024)
1-158255204-A-G		not specified	Uncertain significance (Jun 28, 2022)
1-158255218-G-A		not specified	Likely benign (Jul 14, 2022)
1-158255260-G-A		not specified	Uncertain significance (Sep 01, 2021)
1-158255263-T-C		not specified	Uncertain significance (Sep 06, 2022)
1-158255277-A-T		not specified	Uncertain significance (Apr 22, 2024)
1-158255285-T-C		not specified	Uncertain significance (Nov 08, 2024)
1-158255293-C-T			Benign (Jun 30, 2017)
1-158255302-C-T		not specified	Uncertain significance (Jun 13, 2022)
1-158255320-C-T		not specified	Uncertain significance (Jul 02, 2024)
1-158255329-G-A		not specified	Uncertain significance (Oct 25, 2022)
1-158256097-T-C		not specified	Uncertain significance (Feb 28, 2023)
1-158256099-G-C		not specified	Likely benign (Feb 08, 2023)
1-158256175-A-G		not specified	Uncertain significance (Oct 25, 2022)
1-158256185-G-C		not specified	Uncertain significance (Aug 27, 2024)
1-158256231-C-T		not specified	Uncertain significance (May 09, 2023)
1-158256232-G-A		not specified	Uncertain significance (Oct 22, 2021)
1-158256265-C-A		not specified	Uncertain significance (Aug 26, 2024)
1-158256277-G-A		not specified	Uncertain significance (Dec 19, 2022)
1-158256783-C-T			Benign (Jun 30, 2017)
1-158256857-T-G		not specified	Uncertain significance (May 24, 2024)
1-158256899-G-A		not specified	Uncertain significance (Aug 07, 2024)
1-158256900-G-A			Likely benign (Aug 15, 2018)
1-158256920-A-C		not specified	Uncertain significance (Oct 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD1A	protein_coding	protein_coding	ENST00000289429	6	4133

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.20e-24	0.00000598	125522	0	224	125746	0.000891

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.611	215	191	1.12	0.0000108	2138
Missense in Polyphen		77	67.045	1.1485		767
Synonymous	-1.01	82	71.2	1.15	0.00000379	633
Loss of Function	-2.50	29	17.7	1.64	8.38e-7	188

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00862	0.00865
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000160	0.000158
Middle Eastern	0.000326	0.000326
South Asian	0.000163	0.000163
Other	0.00376	0.00375

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

	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;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