CD1B

CD1b molecule, the group of CD molecules|C1-set domain containing

Basic information

Region (hg38): 1:158327951-158331531

Previous symbols: [ "CD1" ]

Links

ENSG00000158485 ∙ NCBI:910 ∙ OMIM:188360 ∙ HGNC:1635 ∙ Uniprot:P29016 ∙ 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 CD1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD1B 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			29	2	2	33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	2	3

Variants in CD1B

This is a list of pathogenic ClinVar variants found in the CD1B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-158328249-T-C		not specified	Uncertain significance (Sep 22, 2021)
1-158328250-G-C		not specified	Uncertain significance (Dec 18, 2023)
1-158328922-G-A		not specified	Likely benign (Dec 20, 2023)
1-158328948-C-T		not specified	Uncertain significance (Nov 25, 2024)
1-158328953-C-G		not specified	Uncertain significance (Sep 02, 2024)
1-158328990-A-G		not specified	Uncertain significance (Jan 03, 2024)
1-158329003-A-G		not specified	Uncertain significance (Apr 07, 2022)
1-158329417-C-T		not specified	Uncertain significance (Nov 08, 2024)
1-158329418-G-A		not specified	Uncertain significance (Nov 18, 2023)
1-158329465-C-T		not specified	Uncertain significance (Aug 05, 2024)
1-158329471-T-C		not specified	Uncertain significance (Dec 27, 2023)
1-158329517-C-T			Benign (Jan 11, 2018)
1-158329537-C-T		not specified	Likely benign (Jan 10, 2023)
1-158329600-C-G		not specified	Uncertain significance (Feb 08, 2023)
1-158329600-C-T		not specified	Uncertain significance (Aug 16, 2021)
1-158329621-C-A		not specified	Uncertain significance (Dec 13, 2023)
1-158329643-G-A		not specified	Uncertain significance (Dec 06, 2022)
1-158329880-A-T		not specified	Uncertain significance (Jul 11, 2023)
1-158329924-G-A		not specified	Uncertain significance (Apr 24, 2024)
1-158330028-A-G		not specified	Uncertain significance (Aug 04, 2024)
1-158330031-C-A		not specified	Uncertain significance (Apr 09, 2024)
1-158330062-T-A		not specified	Uncertain significance (Jul 14, 2022)
1-158330106-G-C		not specified	Uncertain significance (Oct 07, 2024)
1-158330109-A-C		not specified	Uncertain significance (May 31, 2023)
1-158330814-C-T			Benign (Jan 11, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD1B	protein_coding	protein_coding	ENST00000368168	6	3581

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.36e-11	0.115	125373	1	373	125747	0.00149

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.927	215	180	1.19	0.00000952	2144
Missense in Polyphen		44	43.089	1.0212		539
Synonymous	-1.68	88	70.1	1.25	0.00000376	670
Loss of Function	0.435	17	19.0	0.892	0.00000116	183

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00237	0.00237
Ashkenazi Jewish	0.00228	0.00228
East Asian	0.000167	0.000163
Finnish	0.000185	0.000185
European (Non-Finnish)	0.00209	0.00209
Middle Eastern	0.000167	0.000163
South Asian	0.000622	0.000621
Other	0.00228	0.00228

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:10981968, ECO:0000269|PubMed:14716313}.
• 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: 0.167

Intolerance Scores

• loftool: 0.853
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.6

Haploinsufficiency Scores

• pHI: 0.0592
• 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: 0.282

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;lysosomal membrane;plasma membrane;external side of plasma membrane;cell surface;endosome membrane;integral component of membrane
• Molecular function: protein binding;endogenous lipid antigen binding;exogenous lipid antigen binding;lipopeptide binding