CD1C

CD1c molecule, the group of CD molecules|C1-set domain containing

Basic information

Region (hg38): 1:158289923-158294774

Previous symbols: [ "CD1" ]

Links

ENSG00000158481 ∙ NCBI:911 ∙ OMIM:188340 ∙ HGNC:1636 ∙ Uniprot:P29017 ∙ 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 CD1C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD1C 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	2	3
missense			26	6	1	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	26	7	3

Variants in CD1C

This is a list of pathogenic ClinVar variants found in the CD1C region.

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

Position	Type	Phenotype	Significance	ClinVar
1-158290080-T-C		not specified	Likely benign (May 17, 2023)
1-158291137-C-T		not specified	Uncertain significance (Mar 20, 2023)
1-158291141-G-A			Benign (Jun 25, 2018)
1-158291200-G-A		not specified	Likely benign (Dec 04, 2024)
1-158291247-G-C		not specified	Uncertain significance (Jul 20, 2021)
1-158291284-G-T		not specified	Uncertain significance (Jul 14, 2024)
1-158291392-A-T		not specified	Uncertain significance (May 04, 2022)
1-158291395-C-T		not specified	Uncertain significance (Sep 27, 2021)
1-158292108-C-T		not specified	Uncertain significance (Aug 13, 2021)
1-158292133-G-T		not specified	Uncertain significance (Aug 16, 2021)
1-158292177-T-C		not specified	Uncertain significance (Dec 17, 2023)
1-158292206-C-T		not specified	Uncertain significance (Dec 21, 2023)
1-158292210-C-T		not specified	Uncertain significance (Jan 23, 2024)
1-158292233-C-G		not specified	Uncertain significance (Jan 03, 2022)
1-158292246-A-G		not specified	Uncertain significance (Jul 06, 2022)
1-158292315-G-A		not specified	Uncertain significance (Mar 05, 2025)
1-158292322-C-T			Likely benign (Nov 01, 2024)
1-158292344-A-G		not specified	Uncertain significance (Jan 20, 2023)
1-158292357-A-G		not specified	Uncertain significance (Dec 12, 2023)
1-158292661-C-T		not specified	Uncertain significance (Aug 04, 2024)
1-158292670-G-A		not specified	Uncertain significance (Oct 18, 2021)
1-158292684-G-T		not specified	Uncertain significance (Sep 27, 2024)
1-158292686-C-T		not specified	Uncertain significance (Oct 12, 2021)
1-158292748-C-T		not specified	Uncertain significance (Sep 23, 2023)
1-158292785-T-C		not specified	Likely benign (Dec 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD1C	protein_coding	protein_coding	ENST00000368170	6	3845

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.60e-8	0.396	125708	0	30	125738	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.232	186	177	1.05	0.00000907	2169
Missense in Polyphen		36	34.436	1.0454		441
Synonymous	-0.919	79	69.3	1.14	0.00000346	653
Loss of Function	0.826	14	17.8	0.788	9.16e-7	184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000300	0.000300
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000475	0.0000462
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.00	0.00
South Asian	0.000164	0.000163
Other	0.00	0.00

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:10786796, ECO:0000269|PubMed:10890914, ECO:0000269|PubMed:10899914, ECO:0000269|PubMed:21167756}.
• 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: 0.196

Intolerance Scores

• loftool: 0.865
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.92

Haploinsufficiency Scores

• pHI: 0.0466
• hipred: N
• hipred_score: 0.112
• ghis: 0.465

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.126

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;T cell activation involved in 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;lysosome;plasma membrane;integral component of plasma membrane;external side of plasma membrane;endosome membrane
• Molecular function: endogenous lipid antigen binding;exogenous lipid antigen binding;glycolipid binding;lipopeptide binding