CD1D

CD1d molecule, the group of CD molecules|C1-set domain containing

Basic information

Region (hg38): 1:158178030-158186427

Links

ENSG00000158473 ∙ NCBI:912 ∙ OMIM:188410 ∙ HGNC:1637 ∙ Uniprot:P15813 ∙ 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 CD1D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD1D 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			17	2	1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	2	1

Variants in CD1D

This is a list of pathogenic ClinVar variants found in the CD1D region.

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

Position	Type	Phenotype	Significance	ClinVar
1-158181133-C-A		not specified	Uncertain significance (Aug 30, 2021)
1-158181138-C-T		not specified	Uncertain significance (Dec 08, 2023)
1-158181458-C-G		not specified	Uncertain significance (Nov 12, 2021)
1-158181464-G-A		not specified	Uncertain significance (Oct 09, 2024)
1-158181538-T-C			Likely benign (Aug 14, 2018)
1-158181578-C-T		not specified	Uncertain significance (Nov 01, 2022)
1-158181583-A-T			Benign (Jun 06, 2017)
1-158181628-C-A		not specified	Uncertain significance (Dec 21, 2023)
1-158181679-A-G		not specified	Uncertain significance (Nov 24, 2024)
1-158181715-T-G		not specified	Uncertain significance (Sep 27, 2021)
1-158182038-T-C		not specified	Uncertain significance (Jan 04, 2024)
1-158182055-G-T		not specified	Uncertain significance (Jul 09, 2021)
1-158182062-G-T		not specified	Uncertain significance (Aug 01, 2024)
1-158182073-C-T		not specified	Uncertain significance (Oct 27, 2023)
1-158182088-A-G		not specified	Uncertain significance (May 20, 2024)
1-158182097-T-C		not specified	Likely benign (Dec 06, 2023)
1-158182145-T-G		not specified	Uncertain significance (Apr 20, 2024)
1-158182218-C-T		not specified	Uncertain significance (Sep 30, 2024)
1-158182247-G-T		not specified	Uncertain significance (Dec 03, 2024)
1-158182257-C-T		not specified	Uncertain significance (Jan 04, 2022)
1-158182274-C-T		not specified	Uncertain significance (Aug 10, 2023)
1-158182293-C-T		not specified	Uncertain significance (Jan 08, 2024)
1-158182902-G-A		not specified	Uncertain significance (Sep 03, 2024)
1-158182962-C-T		not specified	Uncertain significance (Aug 04, 2023)
1-158183045-G-A		not specified	Uncertain significance (Sep 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD1D	protein_coding	protein_coding	ENST00000368171	6	4950

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000188	0.888	125485	1	262	125748	0.00105

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.604	206	183	1.13	0.0000101	2160
Missense in Polyphen		57	49.373	1.1545		647
Synonymous	-0.840	87	77.6	1.12	0.00000424	682
Loss of Function	1.58	12	19.5	0.614	0.00000104	183

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00172	0.00172
Ashkenazi Jewish	0.00	0.00
East Asian	0.0104	0.0104
Finnish	0.00	0.00
European (Non-Finnish)	0.000194	0.000185
Middle Eastern	0.0104	0.0104
South Asian	0.000523	0.000523
Other	0.000986	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Antigen-presenting protein that binds self and non-self glycolipids and presents them to T-cell receptors on natural killer T-cells. {ECO:0000269|PubMed:17475845}.
• Pathway: Tight junction - Homo sapiens (human);Amoebiasis - 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: 0.512

Intolerance Scores

• loftool: 0.756
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.45

Haploinsufficiency Scores

• pHI: 0.0683
• hipred: N
• hipred_score: 0.432
• ghis: 0.490

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.385

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd1d1
• Phenotype: homeostasis/metabolism phenotype; renal/urinary system phenotype; skeleton phenotype; respiratory system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype

Gene ontology

• Biological process: positive regulation of T cell mediated cytotoxicity;immune response;detection of bacterium;heterotypic cell-cell adhesion;positive regulation of T cell proliferation;T cell selection;innate immune response;positive regulation of innate 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;cytoplasm;lysosomal membrane;endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;integral component of plasma membrane;external side of plasma membrane;cell surface;endosome membrane;basolateral plasma membrane
• Molecular function: protein binding;beta-2-microglobulin binding;lipid antigen binding;endogenous lipid antigen binding;exogenous lipid antigen binding;histone binding;cell adhesion molecule binding;lipopeptide binding